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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

MOFLUX Intensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: Modeling Archive

This Modeling Archive is in support the publication “Intensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: A Mechanistic Modeling Analysis” (Liang et al., 2021). Here we provide model code, inputs, outputs and evaluation datasets for the Microbial ENzyme Decomposition (MEND) model for the Missouri Ozarks AmeriFlux eddy covariance measurement site (MOFLUX) near Ashland, Missouri USA. The MEND model was developed with explicit representation of microbial and enzyme pools to mechanistically simulate the role of microbial organisms and extracellular enzymes in soil organic carbon (SOC) decomposition. Long-term SOC dynamics under intensified moisture extremes are studied using the MEND model that is parameterized with 11 years of measurements from the MOFLUX forest. The model explicitly represents microbial dormancy and resuscitation, different types of SOC-degrading enzymes, and how they vary with changes in soil moisture (Wang et al. 2015, 2019). A combination of two levels of frequency and severity of soil moisture, as well as a control with normal interannual variability, are used to simulate a range of moisture scenarios over 100 years. The code of Microbial-ENzyme Decomposition (MEND) as well as the input and output data are included in the archive. A user’s manual (MEND_Readme.pdf) is included with instructions for compiling and running the model to simulate soil organic carbon decomposition under various moisture scenarios. This dataset contains the modelling archive contained within a compressed (*.zip) file, a file-level metadata file in comma separate (*.csv) format, and two instructional files in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Polyunsaturated Fatty Acids Mend Macrophage Transcriptome, Glycome, and Phenotype in the Patients with Neurodegenerative Diseases, Including Alzheimer’s Disease

Macrophages of healthy subjects have a pro-resolution phenotype, upload amyloid-β (Aβ) into endosomes, and degrade Aβ, whereas macrophages of patients with Alzheimer’s disease (AD) generally have a pro-inflammatory phenotype and lack energy for brain clearance of Aβ. To clarify the pathogenesis of sporadic AD and therapeutic effects of polyunsaturated fatty acids (PUFA) with vitamins B and D and antioxidants on monocyte/macrophage (MM) migration in the AD brain, MM transcripts in energy and Aβ degradation, MM glycome, and macrophage clearance of Aβ. We followed for 31.3 months (mean) ten PUFA-supplemented neurodegenerative patients: 3 with subjective cognitive impairment (SCI), 2 with mild cognitive impairment (MCI), 3 MCI/vascular cognitive impairment, 2 with dementia with Lewy bodies, and 7 non-supplemented caregivers. We examined: monocyte migration in the brain and a blood-brain barrier model by immunochemistry and electron microscopy; macrophage transcriptome by RNAseq; macrophage glycome by N-glycan profiling and LTQ-Orbitrap mass spectrometry; and macrophage phenotype and phagocytosis by immunofluorescence. MM invade Aβ plaques, upload but do not degrade Aβ, and release Aβ into vessels, which develop cerebrovascular amyloid angiopathy (CAA); PUFA upregulate energy and Aβ degradation enzyme transcripts in macrophages; PUFA enhance sialylated N-glycans in macrophages; PUFA reduce oxidative stress and increase pro-resolution MM phenotype, mitochondrial membrane potential, and Aβ phagocytosis (p < 0.001). Macrophages of SCI, MCI, and AD patients have interrelated defects in the transcriptome, glycome, Aβ phagocytosis, and Aβ degradation. PUFA mend macrophage transcriptome, enrich glycome, enhance Aβ clearance, and benefit the cognition of early-stage AD patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Concentration‐Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering

Abstract Enzyme‐based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis ( Is PETase) is capable of PET hydrolysis under mild conditions but suffers from concentration‐dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET‐degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable Is PETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.

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

Arabidopsis Dehiscence Zone Polygalacturonase 1 (ADPG1) releases latent defense signals in stems with reduced lignin content

There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene Arabidopsis Dehiscence Zone Polygalacturonase 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Structural modification of polysaccharides: A biochemical-genetic approach

Polysaccharides have a wide range of industrial and biomedical applications. An industry trend is underway towards the increased use of bacteria to produce polysaccharides. Long term goals of this work are the adaptation and enhancement of saccharide properties for electronic and optic applications. In this report we illustrate the application of enzyme-bearing bacteriophage on strains of the enteric bacterium Klebsiella pneumoniae, which produces a polysaccharide with the relatively rare rheological property of drag-reduction. This has resulted in the production of new polysaccharides with enhanced rheological properties. Our laboratory is developing techniques for processing and structurally modifying bacterial polysaccharides and oligosaccharides which comprise their basic polymeric repeat units. Our research has focused on bacteriophage which produce specific polysaccharide degrading enzymes. This has lead to the development of enzymes generated by bacteriophage as tools for polysaccharide modification and purification. These enzymes were used to efficiently convert the native material to uniform-sized high molecular weight polymers, or alternatively into high-purity oligosaccharides. Enzyme-bearing bacteriophage also serve as genetic selection tools for bacteria that produce new families of polysaccharides with modified structures.

Kern, Roger G.↗
DOE OSTI2021

Integrated multi-wavelength microscope combining TIRFM and IRM modalities for imaging cellulases and other processive enzymes

We describe a multimodal microscope for visualizing processive enzymes moving on immobilized substrates. The instrument combines interference reflection microscopy (IRM) with multi-wavelength total internal reflectance fluorescence microscopy (TIRFM). The microscope can localize quantum dots with a precision of 2.8 nm at 100 frames/s, and was used to image the dynamics of the cellulase, Cel7a interacting with surface-immobilized cellulose. The instrument, which was built with off-the-shelf components and is controlled by custom software, is suitable for tracking other degradative enzymes such as collagenases, as well as motor proteins moving along immobilized tracks.

09 BIOMASS FUELS↗
DOE OSTI2020

PHOTO‐SENSITIVE LEAF ROLLING 1 encodes a polygalacturonase that modifies cell wall structure and drought tolerance in rice

Summary The biosynthesis and modification of cell wall composition and structure are controlled by hundreds of enzymes and have a direct consequence on plant growth and development. However, the majority of these enzymes has not been functionally characterised. Rice mutants with leaf‐rolling phenotypes were screened in a field. Phenotypic analysis under controlled conditions was performed for the selected mutant and the relevant gene was identified by map‐based cloning. Cell wall composition was analysed by glycome profiling assay. We identified a photo‐sensitive leaf rolling 1 ( psl1 ) mutant with ‘napping’ (midday depression of photosynthesis) phenotype and reduced growth. The PSL1 gene encodes a cell wall‐localised polygalacturonase (PG), a pectin‐degrading enzyme. psl1 with a 260‐bp deletion in its gene displayed leaf rolling in response to high light intensity and/or low humidity. Biochemical assays revealed PG activity of recombinant PSL1 protein. Significant modifications to cell wall composition in the psl1 mutant compared with the wild‐type plants were identified. Such modifications enhanced drought tolerance of the mutant plants by reducing water loss under osmotic stress and drought conditions. Taken together, PSL1 functions as a PG that modifies cell wall biosynthesis, plant development and drought tolerance in rice.

Zhang, Guangheng↗
DOE OSTI2025

Multi‐Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi

Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time‐, substrate‐ and species‐specific responses at multi‐omics levels for the tested fungi, highlighting species‐specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value‐added bioproducts.

CAZy↗
DOE OSTI2021

Production of Biofuels from Biomass by Fungi

The use of abundantly available lignocellulosic biomass as a feedstock for biofuels has emerged as a sustainable alternative to fossil fuels. Industries across the world have shifted their focus to enhancing bioconversion through fungi, efficient and tractable organisms capable of producing valuable cost-effective enzymes. The many capabilities of fungal species offer opportunities for the tailored production of valuable compounds from a variety of substrates. This review details a high level examination of how fungal enzymes degrade plant polysaccharides to simple sugars through the sensitive coordination of transcription factors. Scientists have used a variety of tools like genetically engineering fungi, combining various species, and altering industrial/process conditions to enhance biomass deconstruction and fermentation while solving obstacles like inhibitory compounds. While ethanol and biodiesel are highlighted, additional biofuels are mentioned. These advances have uncovered themes like synergism and biocatalysis, led to the discovery of new fungal species, and revealed unique enzymatic mechanisms. Notably, this research highlights the complexity of metabolic systems within and between fungi. Fungi have been indispensable to the biofuel industry and future research will be crucial for energy sustainability.

Ottum, Eva MN↗
DOE OSTI2020

Expression of the Trichoderma reesei expansin-like protein, swollenin, in poplar results in biomass with improved sugar release by enzymatic hydrolysis

Ethanol production from lignocellulosic biomass has been considered an alternative to corn-based ethanol and fossil fuel. However, the secondary cell wall structure prevents efficient degradation of cellulose. Expression of cell wall degrading enzymes has been suggested as one solution to generate suitable feedstocks for lignocellulosic ethanol production. Swollenin (SWO), originating from Trichoderma reesei, disrupts cellulose structure with low-level hydrolytic activity to the glucan chain. Previously, characterization of T. reesei SWO has been carried out in multiple microorganisms and tobacco. This study heterologously overexpressed T. reesei SWO in hybrid poplar (Populus tremula × alba), a promising feedstock for biofuel production, under the control of either the constitutive Cauliflower Mosaic Virus 35S (CaMV 35S) promoter or the putative vascular tissue specific Subterranean Clover Stunt Virus S7 (SCSV) promoter. Transgenic poplar lines with high or moderate SWO expression level showed abnormal growth and reduced biomass production, along with increased glucose and reduced lignin contents. Increased cellulose crystallinity was observed in two transgenic events. This study also investigated the effect of in planta SWO expression on cellulose saccharification efficiency and found that transgenic events improved glucan conversion rates compared to wild type poplar. The results suggest SWO-overexpressing transgenic poplar lines could be a potential feedstock for ethanol production.

09 BIOMASS FUELS↗
DOE OSTI2022

Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria

Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, in this work, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.

42 ENGINEERING↗
DOE OSTI2023

Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment

It has been proposed that competition between ectomycorrhizal (ECM) fungi and free-living saprotrophs for resources like nitrogen (N) slows decomposition and increases the soil carbon storage in ECM ecosystems compared to arbuscular (AM) ecosystems. However, empirical evidence for the generality of such ECM effects is equivocal, and confounding mechanisms have been proposed that affect the magnitude and direction of ECM effects on soil carbon. Here, for this work, we conduct a theoretical modeling experiment, where we explicitly incorporate mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model. We use the model to explore the conditions under which ECM N acquisition processes can induce stronger saprotrophic N limitation and result in slower decomposition rates and greater soil organic carbon accumulation compared to AM processes. We found that the ECM fungi more strongly inhibited decomposition when litter inputs were N-depleted and relatively recalcitrant and when ECM fungi possessed a strong capacity to mine N from both recalcitrant soil organic matter and microbial necromass. Climate and seasonality also played a role as the ECM competition effect was strongest at low mean annual temperatures and when litterfall peaked seasonally. Priming effects driven by high root exudation rates in ECM-dominated systems could overwhelm the competition effect and reduce soil carbon under some circumstances. The ECM effect on decomposition in our simulations was highly context dependent. Based on our model results, we expect to see a strong ECM competition effect in temperate deciduous and boreal forests with relatively recalcitrant litter inputs, and with ECM fungi that produce oxidases and necromass-degrading enzymes. However, even a relatively strong ECM competition effect on decomposition only increased soil organic carbon accumulation by ~10%.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Xylem-dwelling pathogen unaffected by local xylem vessel network properties in grapevines ( Vitis spp.)

Abstract Background and aims Xylella fastidiosa (Xf) is the xylem-dwelling bacterium associated with Pierce’s disease (PD), which causes mortality in agriculturally important species, such as grapevine (Vitis vinifera). The development of PD symptoms in grapevines depends on the ability of Xf to produce cell-wall-degrading enzymes to break up intervessel pit membranes and systematically spread through the xylem vessel network. Our objective here was to investigate whether PD resistance could be mechanistically linked to xylem vessel network local connectivity. Methods We used high-resolution X-ray micro-computed tomography (microCT) imaging to identify and describe the type, area and spatial distribution of intervessel connections for six different grapevine genotypes from three genetic backgrounds, with varying resistance to PD (four PD resistant and two PD susceptible). Key results Our results suggest that PD resistance is unlikely to derive from local xylem network connectivity. The intervessel pit area (Ai) varied from 0.07 ± 0.01 mm2 mm−3 in Lenoir to 0.17 ± 0.03 mm2 mm−3 in Blanc do Bois, both PD resistant. Intervessel contact fraction (Cp) was not statically significant, but the two PD-susceptible genotypes, Syrah (0.056 ± 0.015) and Chardonnay (0.041 ± 0.013), were among the most highly connected vessel networks. Neither Ai nor Cp explained differences in PD resistance among the six genotypes. Bayesian re-analysis of our data shows moderate evidence against the effects of the traits analysed: Ai (BF01 = 4.88), mean vessel density (4.86), relay diameter (4.30), relay density (3.31) and solitary vessel proportion (3.19). Conclusions Our results show that radial and tangential xylem network connectivity is highly conserved within the six different Vitis genotypes we sampled. The way that Xf traverses the vessel network may limit the importance of local network properties to its spread and may confer greater importance on host biochemical responses.

Plant Sciences↗
DOE OSTI2023

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Mason, Cayla N. (ORCID:0000000345983824)↗