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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a field grown transgenic poplar engineered with a monolignol 4-O-methyltransferase (MOMT4). The poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR experiments. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (hsqcetgpsisp2.2) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. The NMR spectra provides structural characteristics information about lignin in field grown transgenic MOMT4 poplar. Additional meta data is embedded in the raw spectra figures.

Lignin structure, HSQC, poplar, field trial, MOMT4↗
DOE OSTI2024

Carbon-13 NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of 13C nuclear magnetic resonance (NMR) spectra of lignin isolated from transgenic monolignol 4-O-methyltransferase (MOMT4) engineered poplar. The transgenic poplar was collected from a 3-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h. The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR characterization. 13C experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (zgpg) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following conditions: spectra width 229 ppm, 64k data points, 1s pulse delay, and 6k scans. All the data was processed using the Bruker’s TopSpin 3.6 software. Additional meta data is embedded in the raw spectra files.

13C NMR, lignin, poplar, field trial, MOMT4, CBI↗
DOE OSTI2024

Cellulose crystallinity index (CrI) of switchgrass measured by solid-state NMR

Here we present a curated dataset of switchgrass cellulose crystallinity index (CrI) measured using solid state nuclear magnetic resonance (NMR) spectroscopy. Seventy-two topline switchgrass lines grown in greenhouse were collected and ground to -20/+80 mesh. The switchgrass was then Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extractives-free switchgrass was holopulped by using peracetic acid at 5 g loading per g biomass and the solution consistency was adjusted to 5% with DI water. Holopulping was conducted at room temperature for 24 h with stirring. The obtained holocellulose was washed excessively with DI water and air-dried at room temperature for 24 h. The dried holocellulose was treated with hydrochloric acid (2.5 M) for 2 h to remove hemicellulose. The isolated cellulose was collected by filtration, rinsed with DI water, and used to analyze cellulose crystallinity by solid-state NMR. The NMR samples were prepared by packing the moisturized cellulose into 4-mm cylindrical Zirconia MAS rotors. Cross polarization/magic angle spinning (CP/MAS) NMR analysis of cellulose was carried out on a Bruker Avance III 400-MHz spectrometer operating at 100.59 MHz for 13C in a Bruker double-resonance MAS probe head at spinning speeds of 8 kHz. The CP/MAS experiments utilized a 5 ms (90°) proton pulse, 1.5 ms contact pulse, 4 s recycle delay and 4000 scans. The cellulose crystallinity index was determined from the areas of the cellulose crystalline C4 signal (δ 86-92 ppm) over the entire C4 regions (δ 79-92 ppm) in the NMR spectra.

Cellulose, crystallinity index, switchgrass, solid↗
DOE OSTI2024

Proton NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of 1H nuclear magnetic resonance (NMR) spectra of lignin isolated from transgenic monolignol 4-O-methyltransferase (MOMT4) engineered poplar. The transgenic poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. Two replicates were collected for each transgenic poplar for the 1H NMR analysis. The poplar samples were Soxhlet-extracted with toluene/ethanol to remove the extractives and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h. The ball-milled materials were subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide and transferred into a 5 mm NMR tube. 1H NMR experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (zg) on a Prodigy platform cryoprobe. The NMR spectra were acquired with 16 ppm spectra width, 32k data points, 3s pulse delay, and 16 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. Additional meta data is embedded in the raw spectra files.

1H NMR, lignin, poplar, field trial, MOMT4, CBI↗
DOE OSTI2024

Heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from switchgrass residues after fermentation with milling

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a herbaceous energy crop (Panicum virgatum L.). The lowland variant “Timber” switchgrass from Ernst seeds was used. The switchgrass was knife milled and passed through a 2 mm sieve prior to consolidated bioprocessing (CBP) process. Switchgrass was suspended in Milli-Q water and autoclaved for 90 min on liquid cycles. The residues after autoclaving were then subjected to CBP using coculture of Clostridium thermocellum (C. thermocellum DSM 1313 (LL1004)) and Thermoanaerobacterium thermosaccarolyticum ( T. thermosaccharolyticum HG-8 ATCC 31960 (LL1244)). Once-fermented and twice-fermented (FF) switchgrass were subjected to ball and disc milling in bioreactors at 55 °C and 60, 48 grams/L solids loadings for primary and secondary fermentation respectively. When fermentations were completed, the residual solids were rinsed with milli-Q water. Lignin was isolated from the pretreated residues after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 600 rpm for 2 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and characterized using 13C–1H HSQC in a Bruker Avance III HD 500-MHz NMR spectrometer. A standard Bruker pulse sequence (hsqcetgpsisp.2) was used on a Prodigy platform cryoprobe. The spectra were acquired with the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, with a C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software.

Lignin, HSQC, Switchgrass, CBP , Ball mill, Disc m↗
DOE OSTI2024

HSQC spectra of lignin isolated from poplar stems

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from stems of genetically engineered poplar through auxin signaling gene modification. The plants were grown in greenhouse with temperatures between 21 and 23 °C. Plants were harvested and the aboveground stems were cut off an approximately five-inch-long segment from the bottom end of the plant stem, debarked and air-dried for three weeks. The dried stem samples were Wiley milled (mesh size 20), Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted biomass was ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was freeze-dried to recover the lignin. The dry stem lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software. Additional meta data is embedded in the raw spectra figures.

HSQC, lignin, poplar, stems, CBI↗
DOE OSTI2024

HSQC spectra of lignin isolated from poplar roots

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from roots of a greenhouse grown natural population of an energy crop poplar (Populus trichocarpa). Dormant cuttings of field-grown poplar were grown in 6-liter pots in a peat-based media containing bark, perlite, vermiculite, dolomite lime and a wetting agent in an environmentally controlled greenhouse. Temperatures were between 21 and 23 °C, with supplemental lighting to support a 16-h day length using 1000-watt high-pressure sodium lights in greenhouse. Once established, all plants were cut-back, allowed to regrow and harvested at the same time following an eight-month long growth period. Plants were harvested and the belowground roots were washed off soils, blotted, dried in an oven at 70 °C for 3 days, and Wiley milled (mesh size 20). The roots were Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted roots were ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96% (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin software. Additional meta data is embedded in the raw spectra figures.

HSQC, lignin, poplar, roots, CBI↗
DOE OSTI2024

University of Maryland Eastern Shore Common Garden

Located at the University of Maryland Eastern Shore, an HBCU (Historically Black Colleges and Universities), this data set is composed of the geographic coordinates of four transgenic Populus tremula x alba INRA 717-IB4 lines (CHX20, XBAT35, EXO70, DIR18) as well as a wild type (WT), and Empty vector (EV)). Our site is monitored by an ATOMS 41 weather station, which collects solar radiation, air temperature, vapor and atmospheric pressure, precipitation, and other weather variables. We will assess a suite of variables reflecting growth and performance, focusing on root allocation and soil carbon sequestration.

CBI, Populus, common garden, transgenic↗
DOE OSTI2024

Elemental profiling and genomewide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

Samples were collected from a population of 1,089 black cottonwood genotypes (P. trichocarpa) assembled from native stands to encompass the central portion of the natural range of the species, stretching from 38.8° to 54.3° N Q13 latitude from California, USA, to British Columbia, Canada. Establishment of the common garden, growth conditions, and site maintenance have been described by Muchero et al (2015). In this study, leaf samples for ionomic profiling were collected from 4-year-old trees, during the growing season, in July 2012, from a field located in Clatskanie, Oregon, USA (46°6′11″N 123°12′13″W). The field site was located in a protected alluvial floodplain containing a uniform Wauna-Locoda silt loam soil area characterized by an acidic pH, in Columbia County, Oregon. A subset of 584 out of the 1,089 P. trichocarpa genotypes were represented in this sampling. These genotypes were randomly selected to represent the geographical distribution of the population. A single fully mature (LPI 7-9) leaf on the south side of the tree exposed to full sunlight conditions was removed from the tree within a 6-hour window centering on solar noon and immediately frozen under dry ice before processing. Leaf samples of 584 P. trichocarpa genotypes were finely ground to 40 mm particle size using a mortar and pestle, and ionomic composition was analyzed using ICP-MS. In total, 20 elements were profiled, including aluminum (Al27), arsenic (As75), boron (B11), cadmium (Cd111), calcium (Ca43), cobalt (Co), copper (Cu), iron (Fe57), magnesium (Mg25), manganese (Mn55), molybdenum (Mo), nickel (Ni60), phosphorus (P31), potassium (K39), rubidium (Rb85), selenium (Se82), sodium (Na23), strontium (Sr88), sulfur (S34), and zinc (Zn66), following a protocol established by Ziegler et al. (2013). For each sample, 75mg of powder was digested overnight in 2.5 mL HNO3 containing 20 parts per billion (ppb) indium as an internal standard, following the protocol described in Ziegler et al. (2013). Following a dilution, concentration of the 20 elements was measured using an Elan 6000 DRC-e mass spectrometer (Perkin-Elmer SCIEX) connected to a PFA microflow nebulizer (Elemental Scientific) and Apex HF desolvator (Elemental Scientific). One measurement per sample per genotype was done. For subsequent analyses, the quantifications were converted to total element concentration.

CBI ionomics, GWAS, plasma-mass spectrometry, neut↗
DOE OSTI2026

2020_Experiment_1

An early APPL experiment. Many of the RGB's are blank due to Color Segmentation issues. Partial metadata exists in the level0 directory

APPL↗
DOE OSTI2026

2020_Experiment_2

First successful experimental run of APPL from 2020. Demonstrates a raw RGB image, metadata, and a successful mask. A Poplar tree

APPL↗
DOE OSTI2026

3D-RGB

An early attempt at using 3D point clouds to scan plants grown in the APPL facility.

3D RGB↗
DOE OSTI2026

3_Drought_Experiment_1

This is an early experiment in the APPL facility at ORNL looking at the effect of drought on various Populus genotypes. Nisqually-1, WV-94, BESC-394, BESC-198, BESC-24, BESC-375

APPL↗
DOE OSTI2026

Early_Commisioning_Data

This is very early commissioning data (2019) from the newly established APPL facility at ORNL. Instruments, and technologies are in active development at this stage.

APPL↗
DOE OSTI2026

PSI_Testing

Testing data for PSI Instrumentation from 2019 - 2022

appl↗
DOE OSTI2025

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗
DOE OSTI2025

Genetic_and_epigenetic_signatures_of_Populus_Trichocarpa_in_response_to_abiotic_stress

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. Approximately 5% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

CBI↗
DOE OSTI2026

Genome_shuffling_enables_quantitative_trait_locus_mapping_in_Bacillus_subtilis

Genetic mapping is a powerful tool for eukaryotic genetics that has only been applied to bacteria in limited circumstances. Quantitative trait locus (QTL) mapping generally relies on sexual recombination to break linkages between genes, yet bacteria rarely undergo sufficient homologous recombination to generate suitable mapping populations. In this work, we used iterative biparental genome shuffling by protoplast fusion inBacillus subtilisto generate a population of bacteria with substantial random recombination throughout their genomes. Individual shuffled progeny were arrayed in well plates, resequenced, and characterized for a range of complex phenotypes including spore germination and swarming motility. Genetic mapping of the resulting phenotypes identified high-confidence QTLs of moderate size (∼10 kb), and these associations were validated through targeted genetic swaps. ThisB. subtilisQTL population can easily be used to map additional phenotypes, and the general approach for QTL mapping is applicable in a wide range of bacteria.

Bacillus subtilis↗