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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Morpho-physiological and transcriptomic responses of field pennycress to waterlogging

Field pennycress (Thlaspi arvense) is a new biofuel winter annual crop with extreme cold hardiness and a short life cycle, enabling off-season integration into corn and soybean rotations across the U.S. Midwest. Pennycress fields are susceptible to winter snow melt and spring rainfall, leading to waterlogged soils. The objective of this research was to determine the extent to which waterlogging during the reproductive stage affected gene expression, morphology, physiology, recovery, and yield between two pennycress lines (SP32-10 and MN106). In a controlled environment, total pod number, shoot/root dry weight, and total seed count/weight were significantly reduced in SP32-10 in response to waterlogging, whereas primary branch number, shoot dry weight, and single seed weight were significantly reduced in MN106. This indicated waterlogging had a greater negative impact on seed yield in SP32-10 than MN106. We compared the transcriptomic response of SP32-10 and MN106 to determine the gene expression patterns underlying these different responses to seven days of waterlogging. The number of differentially expressed genes (DEGs) between waterlogged and control roots were doubled in MN106 (3,424) compared to SP32-10 (1,767). Functional enrichment analysis of upregulated DEGs revealed Gene Ontology (GO) terms associated with hypoxia and decreased oxygen, with genes in these categories encoding proteins involved in alcoholic fermentation and glycolysis. Additionally, downregulated DEGs revealed GO terms associated with cell wall biogenesis and suberin biosynthesis, indicating suppressed growth and energy conservation. Interestingly, MN106 waterlogged roots exhibited significant stronger regulation of these genes than SP32-10, displaying a more robust transcriptomic response overall. Together, these results reveal the reconfiguration of cellular and metabolic processes in response to the severe energy crisis invoked by waterlogging in pennycress.

ERF-VII↗
DOE OSTI2020

Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature

Drought is the leading cause of agricultural yield loss among all abiotic stresses, and the link between water deficit and phloem protein contents is relatively unexplored. Here we collected phloem exudates from Solanum lycopersicum leaves during periods of drought stress and recovery. Our analysis identified 2558 proteins, the most abundant of which were previously localized to the phloem. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggests that the protein content of phloem sap is complex, and includes proteins that function in chaperone systems, branched-chain amino acid synthesis, trehalose metabolism, and RNA silencing. We observed 169 proteins whose abundance changed significantly within the phloem sap, either during drought or recovery. Proteins that became significantly more abundant during drought include members of lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are decreased during drought. Our experiment has achieved an in-depth profiling of phloem sap protein contents during drought stress and recovery that supports previous findings and provides new evidence that multiple biological processes are involved in drought adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Machine Learning-Based Classification of Lignocellulosic Biomass from Pyrolysis-Molecular Beam Mass Spectrometry Data

High-throughput analysis of biomass is necessary to ensure consistent and uniform feedstocks for agricultural and bioenergy applications and is needed to inform genomics and systems biology models. Pyrolysis followed by mass spectrometry such as molecular beam mass spectrometry (py-MBMS) analyses are becoming increasingly popular for the rapid analysis of biomass cell wall composition and typically require the use of different data analysis tools depending on the need and application. Here, the authors report the py-MBMS analysis of several types of lignocellulosic biomass to gain an understanding of spectral patterns and variation with associated biomass composition and use machine learning approaches to classify, differentiate, and predict biomass types on the basis of py-MBMS spectra. Py-MBMS spectra were also corrected for instrumental variance using generalized linear modeling (GLM) based on the use of select ions relative abundances as spike-in controls. Machine learning classification algorithms e.g., random forest, k-nearest neighbor, decision tree, Gaussian Naïve Bayes, gradient boosting, and multilayer perceptron classifiers were used. The k-nearest neighbors (k-NN) classifier generally performed the best for classifications using raw spectral data, and the decision tree classifier performed the worst. After normalization of spectra to account for instrumental variance, all the classifiers had comparable and generally acceptable performance for predicting the biomass types, although the k-NN and decision tree classifiers were not as accurate for prediction of specific sample types. Gaussian Naïve Bayes (GNB) and extreme gradient boosting (XGB) classifiers performed better than the k-NN and the decision tree classifiers for the prediction of biomass mixtures. The data analysis workflow reported here could be applied and extended for comparison of biomass samples of varying types, species, phenotypes, and/or genotypes or subjected to different treatments, environments, etc. to further elucidate the sources of spectral variance, patterns, and to infer compositional information based on spectral analysis, particularly for analysis of data without a priori knowledge of the feedstock composition or identity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms

Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk–benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production: A Process Model for Lipid-Producing Energy Crops

Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 and 180 °C for 10 min) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.

09 BIOMASS FUELS↗
DOE OSTI2020

Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass

Lignocellulosic materials are plant-derived feedstocks, such as crop residues (e.g., corn stover, rice straw, and sugar cane bagasse) and purpose-grown energy crops (e.g., miscanthus, and switchgrass) that are available in large quantities to produce biofuels, biochemicals, and animal feed. Plant polysaccharides (i.e., cellulose, hemicellulose, and pectin) embedded within cell walls are highly recalcitrant towards conversion into useful products. Ammonia fiber expansion (AFEX) is a thermochemical pretreatment that increases accessibility of polysaccharides to enzymes for hydrolysis into fermentable sugars. These released sugars can be converted into fuels and chemicals in a biorefinery. Here, we describe a laboratory-scale batch AFEX process to produce pretreated biomass on the gram-scale without any ammonia recycling. The laboratory-scale process can be used to identify optimal pretreatment conditions (e.g., ammonia loading, water loading, biomass loading, temperature, pressure, residence time, etc.) and generates sufficient quantities of pretreated samples for detailed physicochemical characterization and enzymatic/microbial analysis. The yield of fermentable sugars from enzymatic hydrolysis of corn stover pretreated using the laboratory-scale AFEX process is comparable to pilot-scale AFEX process under similar pretreatment conditions. This paper is intended to provide a detailed standard operating procedure for the safe and consistent operation of laboratory-scale reactors for performing AFEX pretreatment of lignocellulosic biomass.

09 BIOMASS FUELS↗
NASA NTRS1964

Flexible honeycomb structure can bend to fit compound curves

For flexibility in forming a curved surface, a honeycomb configuration using multiple pleats has proved superior to the usual core structures. The partial pleats formed in individual cell walls permit movements to and from the central axis without tearing.

Carmody, R. J.↗
NASA NTRS1973

Zeta potential control for electrophoresis cells

Zeta potential arises from fact that ions tend to be adsorbed on surface of cell walls. This potential interfaces with electric field sensed by migrating particles and degrades resolution of separation. By regulating sign and magnitude of applied potential induced charge can be used to increase or decrease effective wall zeta potential.

Fogal, G. L.↗
NASA NTRS1974

Methods for improved resolution of flow electrophoresis cells

First method involves remote adjusting of zeta potential. Second approach sandwiches two conducting metal plates between opposite cell walls and thin insulating layer. Third method forces buffer to flow in direction opposite particle streams.

Mccreight, L. R.↗
NASA NTRS1975

L-phase variants of Agromyces ramosus

Earlier results suggested that Agromyces ramosus possibly might exist naturally in soil as a cell-wall-defective form. The purpose of the present study was to test this hypothesis by determining whether the laboratory-adapted strains of A. ramosus could be artificially induced into the L-phase and, if so, to examine some parameters affecting induction and the stability of the L-forms. The hypothesis was also tested by attempting to revert the laboratory L-phase strains by subjecting them to the technique originally used for isolation of the bacterial form from soil. It is shown that A. ramosus is easily induced into the L-phase by growing it on an agar media containing low levels of penicillin or glycine. The L-forms are found to be stable after initial contact with the inducing agent and to be unable to be reverted to the bacterial form. However, this lack of reversion does not completely negate the hypothesis that L-forms might occur in nature, because it is possible that L-forms existing in the natural state are less stable than those found in the laboratory where there is little selective pressure toward reversion.

Horwitz, A. H.↗
NASA NTRS1976

Study of metabolism and energetics in hypogravity: Degenerative effects of prolonged hypogravity

The role of gravity in the formation of rigid, lignified plant cell walls hence to the development of the erect land plant body is examined. An experiment was proposed with a general hypothesis that a chosen plant, a dwarf marigold, would display degenerative changes in mechanical supportive systems under hypogravity because normal lignin-cellulose wall structure fails to develop. Observational and experimental results are given.

Siegel, S. M.↗
NASA NTRS1976

Higher plant metabolism and energetics in hypogravity: Amino acid metabolism in higher plants

Laboratory's investigation into the amino acid metabolism of dwarf marigolds exposed to an environment of simulated hypogravity is summarized. Using both in vivo, and/or in vitro studies, the following effects of hypogravitational stress have been shown: (1) increased proline incorporation into cell wall protein, (2) inhibition of amino acid decarboxylation, (3) decrease in glutamic acid decarboxylase activity; and (4) decrease in the relative amount of a number of soluble amino acids present in deproteinized extracts of marigold leaves. It is concluded from these data there are several rapid, major alterations in amino acid metabolism associated with hypogravitational stress in marigolds. The mechanism(s) and generality of these effects with regard to other species is still unknown.

Mazelis, M.↗
NASA NTRS1977

Power deposition in He from the volumetric He-3/n,p/H-3 reaction

Calculations are presented in this paper which show the amount of power that can be expected to be deposited in He-3 for typical direct nuclear-pumped lasers presently in use. The calculations were performed taking into consideration the cylindrical geometry of the system, the depletion of the thermal flux across the tube cross section, and the energy loss of the protons to the cell walls. If a laser efficiency of 1% is assumed, the results indicate a steady-state laser output of 12.5 kW from a volume of 152.6 cu cm or 82 W/cu cm can be achieved.

De Young, R. J.↗
NASA NTRS1978

Power deposition in volumetric /U-235/F6-He fission-pumped nuclear lasers

The power deposition in (U-235)F6-He fission-pumped nuclear lasers is studied. Specifically, means to maximize the energy density in the He gas are assessed. Primary loss mechanisms are identified as the fission-fragment transport to the laser-cell wall and UF6 gas excitation. The losses are thus strongly dependent on UF6 concentration. It is found that maximum power will be deposited in a laser tube when the tube radius is as large as the range of fission fragments. Experimental results indicate that when the tube radius equals the fission-fragment range, the ratio of a UF6 partial pressure to total pressure is 0.15, and the UF6-He mixing ratio is 1:6, maximum power will be deposited.

Wilson, J. W.↗
NASA NTRS1980

Lipids as a principle for the identification of Archaebacteria

The 'Archaebacteria' consist of several distinct subgroups including methanogens, extreme halophiles and specific thermoacidophiles. These bacteria are distinct from other bacteria with respect to their characteristic RNA compositions, the absence of muramic acid in the cell walls and the predominance of nonsaponifable lipids. The lipid composition of the Archaebacteria consists of isoprenoid and hydroisoprenoid hydrocarbons and isopranyl glycerol ether lipids. The pathways for the biosynthesis of the lipid components are those shared by most microorganisms and demonstrate a close relationship; however, an independent line of descent is indicated by the formation of the isopranyl glycerol ether lipids. This discontinuity formulates a point for delineating the early stages of biological evolution and for dividing bacteria into two subgroups.

Tornabene, T. G.↗
NASA NTRS1980

Design optimization of sinusoidal glass honeycomb for flat plate solar collectors

The design of honeycomb made of sinusoidally corrugated glass strips was optimized for use in water-cooled, single-glazed flat plate solar collectors with non-selective black absorbers. Cell diameter (d), cell height (L), and pitch/diameter ratio (P/d) maximizing solar collector performance and cost effectiveness for given cell wall thickness (t sub w) and optical properties of glass were determined from radiative and convective honeycomb characteristics and collector performance all calculated with experimentally validated algorithms. Relative lifetime values were estimated from present materials costs and postulated production methods for corrugated glass honeycomb cover assemblies. A honeycomb with P/d = 1.05, d = 17.4 mm, L = 146 mm and t sub w = 0.15 mm would provide near-optimal performance over the range delta T sub C greater than or equal to 0 C and less than or equal to 80 C and be superior in performance and cost effectiveness to a non-honeycomb collector with a 0.92/0.12 selective black absorber.

Mcmurrin, J. C.↗
NASA NTRS1982

Paradigm transition in cosmic plasma physics

New discoveries in cosmic plasma physics are described, and their applications to solar, interstellar, galactic, and cosmological problems are discussed. The new discoveries include the existence of double layers in magnetized plasmas and in the low magnetosphere, and energy transfer by electric current in the auroral circuit. It is argued that solar flares and the solar wind-magnetosphere interaction should not be interpreted in terms of magnetic merging theories, and that electric current needs to be explicitly taken account of in understanding these phenomena. The filamentary structure of cosmic plasmas may be caused by electric currents in space, and the pinch effect may have a central role to play in the evolutionary history of interstellar clouds, stars, and solar systems. Space may have a cellular structure, with the cell walls formed by thin electric current layers. Annihilation may be the source of energy for quasars and the Hubble expansion, and the big bang cosmology may well be wrong.

Alfven, H.↗