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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Visual Orbits of Spectroscopic Binaries with the CHARA Array. I. HD 224355

We present the visual orbit of the double-lined spectroscopic binary HD 224355 from interferometric observations with the CHARA Array, as well as an updated spectroscopic analysis using echelle spectra from the Apache Point Observatory 3.5 m telescope. By combining the visual and spectroscopic orbital solutions, we find the binary components to have masses of M 1 = 1.626 ± 0.005M ⊙ and M 2 = 1.608 ± 0.005M ⊙ , and a distance of d = 63.98 ± 0.26 pc. Using the distance and the component angular diameters found by fitting spectrophotometry from the literature to spectral energy distribution models, we estimate the stellar radii to be R 1 = 2.65 ± 0.21R ⊙ and R 2 = 2.47 ± 0.23R ⊙ . We then compare these observed fundamental parameters to the predictions of stellar evolution models, finding that both components are evolved toward the end of the main sequence with an estimated age of 1.9 Gyr.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Lignin is nature’s largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter , Aminobacter , Bacillus , Burkholderia , Lysinibacillus , Microvirga , Mycobacterium , Ochrobactrum , Paenibacillus , Pseudomonas , Pseudoxanthomonas , Rhizobiales and Sphingobium . These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Development of a Technology Roadmap for Online Monitoring of Nuclear Power Plants

The nuclear power industry has recently recognized the potential cost saving that can be achieved from migrating the current manual and labor dependent surveillance and preventive maintenance activities to data-driven online monitoring methods. Since then, several efforts have been launched with various degrees of momentum to tackle specific surveillance or preventive maintenance activities. The light water reactor sustainability program (LWRS) program has anticipated this need and launched an effort that aimed to develop a technology roadmap for the nuclear power industry. Because the roadmap has to be focused towards the user or application’s value, and because nuclear power plants have different process efficiencies and deficiencies, the technology roadmap has to be plant independent. Achieving this objective required optimizing the extent of details described by a technology roadmap. The approach followed is for the roadmap to describe the sequence of activities needed to automate a process or equipment activity, but not describe the sequence of processes or equipment to target. For example, the steps required to migrate the inspection of a pump are plant independent. However, defining that the migration of feed water pumps inspections to online monitoring should be performed before inspections of feed water valves is dependent on multiple plant factors such as the plant requirements, labor work capacity, and process or equipment conditions. The technology roadmap was broken down into six elements, four of which have a sequential path of advancement, while the other two are supporting elements to the sequential elements. The sequential part of the roadmap analyzes data collection, analytics, visualization, and management. For these elements of the technology roadmap, the migration of an activity is defined in three states. The base state is defined as the most primitive, manual, and labor dependent process used by some nuclear power plants. The modern state is defined as the state that can be achieved if the activities are augmented or replaced by current technologies that are commercially available or are soon to be available. The state of the art is defined as using technologies of the future, i.e. concept and technologies that are being researched. The data collection part of the technology roadmap defines three states of every process performed in a nuclear power plant. However, the data analytics part is described based on equipment, because automating an activity performed on one equipment required considering multiple data sources. The visualization and data management elements are process or equipment independent. Visualization describes the means to use human factor science and technologies advancement in presenting the data collected and the data analytics results. The data management targets storage, communication, and computational power need, in addition to data integration and sharing. Since storage, communication, and computational power technologies and path for deployment are known to any information technology organization, this effort targeted the cost of data management. This has a direct impact on the feasibility of the automation effort. The supporting elements analyzes the value of automating the activity and the change challenges to tackle. For the support elements, the roadmap targeted describing activities that need to be performed as part of the roadmap development. The value element of the roadmap describes how to analyze the cost saving and the associated risk. The change management identifies multiple factors to consider such as regulation, cybersecurity, resource availability, supporting infrastructure availability, feasibility (power, fitness, environment tolerance, facilities), and cultural change.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Nitrogen Metabolism in Pseudomonas putida : Functional Analysis Using Random Barcode Transposon Sequencing

Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. So we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Wallula Basalt Pilot Demonstration Project: Post-injection Results and Conclusions

Deep underground geologic formations are emerging as a reasonable option for long-term storage of CO 2 , including large continental flood basalt formations. At the GHGT-11 and GHGT-12 conferences, progress was reported on the initial phases for Wallula Basalt Pilot demonstration test (located in Eastern Washington state), where nearly 1,000 metric tons of CO 2 were injected over a 3-week period during July/August 2013. The target CO 2 injection intervals were two permeable basalt interflow reservoir zones with a combined thickness of ~20 m that occur within a layered basalt sequence between a depth of 830-890 m below ground surface. During the two-year post-injection period, downhole fluid samples were periodically collected during this post-injection monitoring phase, coupled with limited wireline borehole logging surveys that provided indirect evidence of on-going chemical geochemical reactions/alterations and CO 2 disposition. A final detailed post-closure field characterization program that included downhole fluid sampling, and performance of hydrologic tests and wireline geophysical surveys. Included as part of the final wireline characterization activities was the retrieval of side-wall cores from within the targeted injection zones. These cores were examined for evidence of in-situ mineral carbonization. Visual observations of the core material identified small globular nodules, translucent to yellow in color, residing within vugs and small cavities of the recovered basalt side-wall cores, which were not evident in pre-injection side-wall cores obtained from the native basalt formation. Characterization by x-ray diffraction identified these nodular precipitates as ankerite, a commonly occurring iron and calcium rich carbonate. Isotopic characterization (δ 13 C, δ 18 O) conducted on the ankerite nodules indicate a distinct isotopic signature that is closely aligned with that of the injected CO 2 . Both the secondary mineral nodules and injected CO 2 are measurably different from the isotopic content of basalt, injection zone groundwater and for naturally occurring calcite. Final post-injection wireline geophysical logging results also indicate the presence of free-phase CO 2 at the top of the two injection interflow zones, with no vertical migration of CO 2 above the injection horizons. Furthermore, these findings are significant and demonstrate the feasibility of sequestering CO 2 in a basalt formation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Novel Super-Resolution Approach to Time-Resolved Volumetric 4-Dimensional Magnetic Resonance Imaging With High Spatiotemporal Resolution for Multi-Breathing Cycle Motion Assessment

Purpose: To develop and evaluate a super-resolution approach to reconstruct time-resolved 4-dimensional magnetic resonance imaging (TR-4DMRI) with a high spatiotemporal resolution for multi-breathing cycle motion assessment. Methods and Materials: A super-resolution approach was developed to combine fast 3-dimensional (3D) cine MRI with low resolution during free breathing (FB) and high-resolution 3D static MRI during breath hold (BH) using deformable image registration. A T1-weighted, turbo field echo sequence, coronal 3D cine acquisition, partial Fourier approximation, and SENSitivity Encoding parallel acceleration were used. The same MRI pulse sequence, field of view, and acceleration techniques were applied in both FB and BH acquisitions; the intensity-based Demons deformable image registration method was used. Under an institutional review board–approved protocol, 7 volunteers were studied with 3D cine FB scan (voxel size: 5 × 5 × 5 mm{sup 3}) at 2 Hz for 40 seconds and a 3D static BH scan (2 × 2 × 2 mm{sup 3}). To examine the image fidelity of 3D cine and super-resolution TR-4DMRI, a mobile gel phantom with multi-internal targets was scanned at 3 speeds and compared with the 3D static image. Image similarity among 3D cine, 4DMRI, and 3D static was evaluated visually using difference image and quantitatively using voxel intensity correlation and Dice index (phantom only). Multi-breathing-cycle waveforms were extracted and compared in both phantom and volunteer images using the 3D cine as the references. Results: Mild imaging artifacts were found in the 3D cine and TR-4DMRI of the mobile gel phantom with a Dice index of >0.95. Among 7 volunteers, the super-resolution TR-4DMRI yielded high voxel-intensity correlation (0.92 ± 0.05) and low voxel-intensity difference (<0.05). The detected motion differences between TR-4DMRI and 3D cine were −0.2 ± 0.5 mm (phantom) and −0.2 ± 1.9 mm (diaphragms). Conclusion: Super-resolution TR-4DMRI has been reconstructed with adequate temporal (2 Hz) and spatial (2 × 2 × 2 mm{sup 3}) resolutions. Further TR-4DMRI characterization and improvement are necessary before clinical applications. Multi-breathing cycles can be examined, providing patient-specific breathing irregularities and motion statistics for future 4D radiation therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

A post-merger enhancement only in star-forming Type 2 Seyfert galaxies: the deep learning view

ABSTRACT Supermassive black holes require a reservoir of cold gas at the centre of their host galaxy in order to accrete and shine as active galactic nuclei (AGN). Major mergers have the ability to drive gas rapidly inwards, but observations trying to link mergers with AGN have found mixed results due to the difficulty of consistently identifying galaxy mergers in surveys. This study applies deep learning to this problem, using convolutional neural networks trained to identify simulated post-merger galaxies from survey-realistic imaging. This provides a fast and repeatable alternative to human visual inspection. Using this tool, we examine a sample of ∼8500 Seyfert 2 galaxies ($L[\mathrm{O\, {\small III}}] \sim 10^{38.5 - 42}$ erg s−1) at z < 0.3 in the Sloan Digital Sky Survey and find a merger fraction of $2.19_{-0.17}^{+0.21}$ per cent compared with inactive control galaxies, in which we find a merger fraction of $2.96_{-0.20}^{+0.26}$ per cent, indicating an overall lack of mergers among AGN hosts compared with controls. However, matching the controls to the AGN hosts in stellar mass and star formation rate reveals that AGN hosts in the star-forming blue cloud exhibit a ∼2 × merger enhancement over controls, while those in the quiescent red sequence have significantly lower relative merger fractions, leading to the observed overall deficit due to the differing M*–SFR distributions. We conclude that while mergers are not the dominant trigger of all low-luminosity, obscured AGN activity in the nearby Universe, they are more important to AGN fuelling in galaxies with higher cold gas mass fractions as traced through star formation.

Avirett-Mackenzie, M. S.↗
DOE OSTI2016

SU-G-JeP2-04: Comparison Between Fricke-Type 3D Radiochromic Dosimeters for Real-Time Dose Distribution Measurements in MR-Guided Radiation Therapy

Purpose: To assess MR signal contrast for different ferrous ion compounds used in Fricke-type gel dosimeters for real-time dose measurements for MR-guided radiation therapy applications. Methods: Fricke-type gel dosimeters were prepared in 4% w/w gelatin prior to irradiation in an integrated 1.5 T MRI and 7 MV linear accelerator system (MR-Linac). 4 different ferrous ion (Fe2?) compounds (referred to as A, B, C, and D) were investigated for this study. Dosimeter D consisted of ferrous ammonium sulfate (FAS), which is conventionally used for Fricke dosimeters. Approximately half of each cylindrical dosimeter (45 mm diameter, 80 mm length) was irradiated to ∼17 Gy. MR imaging during irradiation was performed with the MR-Linac using a balanced-FFE sequence of TR/TE = 5/2.4 ms. An approximate uncertainty of 5% in our dose delivery was anticipated since the MR-Linac had not yet been fully commissioned. Results: The signal intensities (SI) increased between the un-irradiated and irradiated regions by approximately 8.6%, 4.4%, 3.2%, and 4.3% after delivery of ∼2.8 Gy for dosimeters A, B, C, and D, respectively. After delivery of ∼17 Gy, the SI had increased by 24.4%, 21.0%, 3.1%, and 22.2% compared to the un-irradiated regions. The increase in SI with respect to dose was linear for dosimeters A, B, and D with slopes of 0.0164, 0.0251, and 0.0236 Gy{sup −1} (R{sup 2} = 0.92, 0.97, and 0.96), respectively. Visually, dosimeter A had the greatest optical contrast from yellow to purple in the irradiated region. Conclusion: This study demonstrated the feasibility of using Fricke-type dosimeters for real-time dose measurements with the greatest optical and MR contrast for dosimeter A. We also demonstrated the need to investigate Fe{sup 2+} compounds beyond the conventionally utilized FAS compound in order to improve the MR signal contrast in 3D dosimeters used for MR-guided radiation therapy. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. LH- 102SPS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Genomes OnLine Database (GOLD) v.10: new features and updates

The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The eROSITA Final Equatorial-Depth Survey (eFEDS)

Aims. The eROSITA Final Equatorial-Depth Survey (eFEDS), executed during the performance verification phase of the Spectrum-Roentgen-Gamma (SRG)/eROSITA telescope, was completed in November 2019. One of the science goals of this survey is to demonstrate the ability of eROSITA to detect samples of clusters and groups at the final depth of the eROSITA all-sky survey. Methods. Because of the sizeable (≈26" HEW FOV average) point-spread function of eROSITA, high-redshift clusters of galaxies or compact nearby groups hosting bright active galactic nuclei (AGN) can be misclassified as point sources by the source detection algorithms. A total of 346 galaxy clusters and groups in the redshift range of 0.1 < z < 1.3 were identified based on their red sequenc in the eFEDS point source catalog. Results. We examine the multiwavelength properties of these clusters and groups to understand the potential biases in our selection process and the completeness of the extent-selected sample. We find that the majority of the clusters and groups in the point source sample are indeed underluminous and compact compared to the extent-selected sample. Their faint X-ray emission, well below the flux limit of the extent-selected eFEDS clusters, and their compact X-ray emission are likely to be the main reason for this misclassification. In the sample, we confirm that 10% of the sources host AGN in their brightest cluster galaxies (BCGs) through optical spectroscopy and visual inspection. By studying their X-ray, optical, infrared, and radio properties, we establish a method for identifying clusters and groups that host AGN in their BCGs. We successfully test this method on the current point source catalog through the Sloan Digital Sky Survey optical spectroscopy and find eight low-mass clusters and groups with active radio-loud AGN that are particularly bright in the infrared. They include eFEDS J091437.8+024558, eFEDS J083520.1+012516, and eFEDS J092227.1+043339 at redshifts 0.3-0.4. Conclusions. This study helps us to characterize and understand our selection process and assess the completeness of the eROSITA extent-selected samples. The method we developed will be used to identify high-redshift clusters, AGN-dominated groups, and low-mass clusters that are misclassified in the future eROSITA all-sky survey point source catalogs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Evaluation of an active magnetic resonance tracking system for interstitial brachytherapy

Purpose: In gynecologic cancers, magnetic resonance (MR) imaging is the modality of choice for visualizing tumors and their surroundings because of superior soft-tissue contrast. Real-time MR guidance of catheter placement in interstitial brachytherapy facilitates target coverage, and would be further improved by providing intraprocedural estimates of dosimetric coverage. A major obstacle to intraprocedural dosimetry is the time needed for catheter trajectory reconstruction. Herein the authors evaluate an active MR tracking (MRTR) system which provides rapid catheter tip localization and trajectory reconstruction. The authors assess the reliability and spatial accuracy of the MRTR system in comparison to standard catheter digitization using magnetic resonance imaging (MRI) and CT. Methods: The MRTR system includes a stylet with microcoils mounted on its shaft, which can be inserted into brachytherapy catheters and tracked by a dedicated MRTR sequence. Catheter tip localization errors of the MRTR system and their dependence on catheter locations and orientation inside the MR scanner were quantified with a water phantom. The distances between the tracked tip positions of the MRTR stylet and the predefined ground-truth tip positions were calculated for measurements performed at seven locations and with nine orientations. To evaluate catheter trajectory reconstruction, fifteen brachytherapy catheters were placed into a gel phantom with an embedded catheter fixation framework, with parallel or crossed paths. The MRTR stylet was then inserted sequentially into each catheter. During the removal of the MRTR stylet from within each catheter, a MRTR measurement was performed at 40 Hz to acquire the instantaneous stylet tip position, resulting in a series of three-dimensional (3D) positions along the catheter’s trajectory. A 3D polynomial curve was fit to the tracked positions for each catheter, and equally spaced dwell points were then generated along the curve. High-resolution 3D MRI of the phantom was performed followed by catheter digitization based on the catheter’s imaging artifacts. The catheter trajectory error was characterized in terms of the mean distance between corresponding dwell points in MRTR-generated catheter trajectory and MRI-based catheter digitization. The MRTR-based catheter trajectory reconstruction process was also performed on three gynecologic cancer patients, and then compared with catheter digitization based on MRI and CT. Results: The catheter tip localization error increased as the MRTR stylet moved further off-center and as the stylet’s orientation deviated from the main magnetic field direction. Fifteen catheters’ trajectories were reconstructed by MRTR. Compared with MRI-based digitization, the mean 3D error of MRTR-generated trajectories was 1.5 ± 0.5 mm with an in-plane error of 0.7 ± 0.2 mm and a tip error of 1.7 ± 0.5 mm. MRTR resolved ambiguity in catheter assignment due to crossed catheter paths, which is a common problem in image-based catheter digitization. In the patient studies, the MRTR-generated catheter trajectory was consistent with digitization based on both MRI and CT. Conclusions: The MRTR system provides accurate catheter tip localization and trajectory reconstruction in the MR environment. Relative to the image-based methods, it improves the speed, safety, and reliability of the catheter trajectory reconstruction in interstitial brachytherapy. MRTR may enable in-procedural dosimetric evaluation of implant target coverage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A General Framework for Progressive Data Compression and Retrieval

In scientific simulations, observations, and experiments, the transfer of data to and from disk and across networks has become a major bottleneck for data analysis and visualization. Compression techniques have been employed to tackle this challenge, but traditional lossy methods often demand conservative error tolerances to meet the numerical accuracy requirements of both anticipated and unknown data analysis tasks. Progressive data compression and retrieval has emerged as a promising solution, where each analysis task dictates its own accuracy needs. However, few analysis algorithms inherently support progressive data processing, and adapting compression techniques, file formats, client/server frameworks, and APIs to support progressivity can be challenging. Here, this paper presents a framework that enables progressive-precision data queries for any data compressor or numerical representation. Our strategy hinges on a multi-component representation that successively reduces the error between the original and compressed field, allowing each field in the progressive sequence to be expressed as a partial sum of components. We have implemented this approach with four established scientific data compressors and assessed its effectiveness using real-world data sets from the SDRBench collection. The results show that our framework competes in accuracy with the standalone compressors it is based upon. Additionally, (de)compression time is proportional to the number of components requested by the user. Finally, our framework allows for fully lossless compression using lossy compressors when a sufficient number of components are employed.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Full Karyotype Interphase Cell Analysis

Aneuploidy seems to play not only a decisive role in embryonal development but also in tumorigenesis where chromosomal and genomic instability reflect a universal feature of malignant tumors. The cost of whole genome sequencing has fallen significantly, but it is still prohibitive for many institutions and clinical settings. No applied, cost-effective, and efficient technique has been introduced yet aiming at research to assess the ploidy status of all 24 different human chromosomes in interphases simultaneously, especially in single cells. Here, we present the selection of human probe DNA and a technique using multistep fluorescence in situ hybridization (FISH) employing four sets of six labeled FISH probes able to delineate all 24 human chromosomes in interphase cells. This full karyotype analysis approach will provide additional diagnostic potential for single cell analysis. The use of spectral imaging (SIm) has enabled the use of up to eight different fluorochrome labels simultaneously. Thus, scoring can be easily assessed by visual inspection, because SIm permits computer-assigned and distinguishable pseudo-colors to each probe during image processing. This enables full karyotype analysis by FISH of single-cell interphase nuclei.

Baumgartner, Adi↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2016

DEEP NEAR-IR OBSERVATIONS OF THE GLOBULAR CLUSTER M4: HUNTING FOR BROWN DWARFS

We present an analysis of deep Hubble Space Telescope (HST)/Wide Field Camera 3 near-IR (NIR) imaging data of the globular cluster (GC) M4. The best-photometry NIR color–magnitude diagram (CMD) clearly shows the main sequence extending toward the expected end of the hydrogen-burning limit and going beyond this point toward fainter sources. The white dwarf (WD) sequence can be identified. As such, this is the deepest NIR CMD of a GC to date. Archival HST optical data were used for proper-motion cleaning of the CMD and for distinguishing the WDs from brown dwarf (BD) candidates. Detection limits in the NIR are around F110W ≈ 26.5 mag and F160W ≈ 27 mag, and in the optical around F775W ≈ 28 mag. Comparing our observed CMDs with theoretical models, we conclude that we have reached beyond the H-burning limit in our NIR CMD and are probably just above or around this limit in our optical–NIR CMDs. Thus, any faint NIR sources that have no optical counterpart are potential BD candidates, since the optical data are not deep enough to detect them. We visually inspected the positions of NIR sources that are fainter than the H-burning limit in F110W and for which the optical photometry did not return a counterpart. We found in total five sources for which we did not get an optical measurement. For four of these five sources, a faint optical counterpart could be visually identified, and an upper optical magnitude was estimated. Based on these upper optical magnitude limits, we conclude that one source is likely a WD, one source could be either a WD or BD candidate, and the remaining two sources agree with being BD candidates. No optical counterpart could be detected for just one source, which makes this source a good BD candidate. We conclude that we found in total four good BD candidates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes

Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F 2 mapping populations were developed by crossing two different F 1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp.

Abstract The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.

Irving, Thomas B. (ORCID:0000000330404543)↗
DOE OSTI2021

Plant single-cell solutions for energy and the environment

Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species’ cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.

59 BASIC BIOLOGICAL SCIENCES↗