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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio , RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

Han, Biao↗
NASA NTRSDate not supplied

SHERLOC: Results of the first 350 sols of operations

On February 18th 2021, the Perseverance rover landed in Jezero crater, Mars. This site was chosen because orbiter data analysis provides evidence that the crater hosted a stream-fed lake during the Martian Noachian period. The Octavia Butler landing site is located ~1.9 km east of the remnants of a river delta. Deltaic and lacustrine sediments can preserve biosignatures, making Jezero crater a prime target for Mars sample return science. One of the seven instruments on Perseverance’s science payload is SHERLOC –Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals. SHERLOC combines fluorescence and Raman spectroscopy with microscopic imaging to analyze surface material to better understand the history of the aqueous environments recorded in the rocks of Jezero crater and to search for potential biosignatures. SHERLOC imaging obtains high spatial resolution images of geological targets to identify grain-scale structure and texture. SHERLOC spectroscopy enables high-sensitivity detection, characterization, and spatially resolved correlation of trace organic materials. Native fluorescence emissions from aromatic organic species allow for detection and classification of aromatic organic molecules, whereas Raman scattered photons from molecules allow identification of functional groups of organics, chemicals, and minerals. In the first 300 sols, SHERLOC has analyzed 3 natural surfaces, and 5 abraded rock patches created during the Crater Floor Campaign within Jezero crater. SHERLOC has been able to identify phosphates, amorphous/microcrystalline silicate (AMS), olivine, sulfates, and carbonates in abraded patches in the green zone campaign within Jezero Crater Máaz and Séítah formations. Within these detections we have begun to tell the story of what this crater was like when it was full of liquid water over 3 billion years ago. In each of these samples we have identified fluorescence features that are likely aromatic organics native to the rock interiors. We have identified multiple unique fluorescence signatures, within each of the abraded patches. The organic signatures have either been widely distributed over an extended area, which is probably due to planetary wide dust, or have spatially resolved locations that are collocated with different mineral signatures. Note: Additional information available on attachment.

L. W. Beegle↗
DOE OSTI2023

Annotated genome sequence of a fast-growing diploid clone of red alder ( Alnus rubra Bong.)

Abstract Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Isothermal Oxidation of High-Purity Aluminum at High Temperature

The isothermal oxidation in air of high purity aluminum sheet was studied as a function of temperature using Thermogravimetric Analysis simultaneously with Differential Scanning Calorimetry (TGA/DSC). The rates and extents of oxidation were found to be non-linear functions of the temperature, in agreement with the literature. Between 650 °C and 750 °C very little oxidation took place; at 850 °C oxidation occurred after an induction period, while at 950 °C oxidation occurred without an induction period. At oxidation temperatures between 1050 °C and 1150 °C rapid passivation of the surface of the aluminum occurred, while at 1250 °C and above, an initial rapid mass increase was observed, followed by a more gradual increase in mass. The initial rapid increase in mass was accompanied by a significant exotherm, which was quantified by DSC. At temperatures of 1050 °C and above the specimen coalesced into a spheroidal particle, whereas at lower temperatures the original morphology was retained due to the cohesive strength of the native oxide layer. Cross-sections of oxidized specimens were characterized by scanning electron microscopy (SEM); the observed alumina skin thicknesses correlated qualitatively with the observed mass increases. Interrogation of the surface of an oxidized spheroidal particle by SEM showed a fractured alumina shell around a partially hollow core of aluminum which appeared to have grain boundaries.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

The Future of Oaks in the Santa Monica Mountains: A Case Study in Using Remote Sensing Data for Species Distributions Models

The Woolsey Fire began on November 8, 2018, and lasted for almost two weeks, during which it burned almost 100,000 acres of valuable landscape and habitat, including a vast area of woodland. The persistence of key woodland species provides aesthetic, monetary, and ecological value to the landscape through carbon sequestration, air temperature moderation, and erosion mitigation, among other ecosystem services. This study investigated the impact of the Woolsey Fire on native woodland species distributions and identified areas suitable for restoration within the Santa Monica Mountains National Recreation Area. The team partnered with the Resource Conservation District of the Santa Monica Mountains; National Park Service, Santa Monica Mountains National Recreation Area; California Department of Parks and Recreation, Los Angeles County Division; County of Los Angeles Fire Department, Prevention Services Bureau, Forestry Division; County of Los Angeles Department of Regional Planning; and the University of Montana. The Earth observations used include data from Landsat 8 Operational Land Imager, NASA ER-2 Jet Airborne Visible InfraRed Imaging Spectrometer, Shuttle Radar Topography Mission, and RapidEye. The team produced maps of burn severity from the Woolsey Fire, its impact on plant species distributions, and habitat suitability projections for 2050 and 2099 to assist partners in prioritizing areas for restoration. A plant community classification was successfully created using Multiple Endmember Spectral Mixture Analysis (MESMA). Overall accuracy was assessed at 90.54% by comparing the classification to validation pixels derived from ground truth information provided by our partners.

Roger Ly↗
DOE OSTI2024

Exciton and biexciton transient absorption spectra of CdSe quantum dots with varying diameters

Transient absorption (TA) spectroscopy of semiconductor nanocrystals (NCs) is often used for excited state population analysis, but recent results suggest that TA bleach signals associated with multiexcitons in NCs do not scale linearly with exciton multiplicity. In this manuscript, we probe the factors that determine the intensities and spectral positions of exciton and biexciton components in the TA spectra of CdSe quantum dots (QDs) of five diameters. We find that, in all cases, the peak intensity of the biexciton TA spectrum is less than 1.5 times that of the single exciton TA spectrum, in stark contrast to a commonly made assumption that this ratio is 2. The relative intensities of the biexciton and exciton TA signals at each wavelength are determined by at least two factors: the TA spectral intensity and the spectral offset between the two signals. We do not observe correlations between either of these factors and the particle diameter, but we find that both are strongly impacted by replacing the native organic surface-capping ligands with a hole-trapping ligand. These results suggest that surface trapping plays an important role in determining the absolute intensities of TA features for CdSe QDs and not just their decay kinetics. Our work highlights the role of spectral offsets and the importance of surface trapping in governing absolute TA intensities. It also conclusively demonstrates that the biexciton TA spectra of CdSe QDs at the band gap energy are less than twice as intense as those of the exciton.

Chemistry↗
DOE OSTI2025

A simple and highly efficient protocol for 13 C-labeling of plant cell wall for structural and quantitative analyses via solid-state nuclear magnetic resonance

Plant cell walls are made of a complex network of interacting polymers that play a critical role in plant development and responses to environmental changes. Thus, improving plant biomass and fitness requires the elucidation of the structural organization of plant cell walls in their native environment. The 13 C-based multi-dimensional solid-state nuclear magnetic resonance (ssNMR) has been instrumental in revealing the structural information of plant cell walls through 2D and 3D correlation spectral analyses. However, the requirement of enriching plants with 13 C limits the applicability of this method. To our knowledge, there is only a very limited set of methods currently available that achieve high levels of 13 C-labeling of plant materials using 13 CO 2 , and most of them require large amounts of 13 CO 2 in larger growth chambers. In this study, a simplified protocol for 13C-labeling of plant materials is introduced that allows ca 60% labeling of the cell walls, as quantified by comparison with commercially labeled samples. This level of 13 C-enrichment is sufficient for all conventional 2D and 3D correlation ssNMR experiments for detailed analysis of plant cell wall structure. The protocol is based on a convenient and easy setup to supply both 13 C-labeled glucose and 13 CO 2 using a vacuum-desiccator. The protocol does not require large amounts of 13 CO 2 . This study shows that our 13 C-labeling of plant materials can make the accessibility to ssNMR technique easy and affordable. The derived high-resolution 2D and 3D correlation spectra are used to extract structural information of plant cell walls. This helps to better understand the influence of polysaccharide-polysaccharide interaction on plant performance and allows for a more precise parametrization of plant cell wall models.

09 BIOMASS FUELS↗
DOE OSTI2024

Excitation energy transfer in proteoliposomes reconstituted with LH2 and RC-LH1 complexes from Rhodobacter sphaeroides

Abstract Light-harvesting 2 (LH2) and reaction-centre light-harvesting 1 (RC-LH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were reconstituted into proteoliposomes either separately, or together at three different LH2:RC-LH1 ratios, for excitation energy transfer studies. Atomic force microscopy (AFM) was used to investigate the distribution and association of the complexes within the proteoliposome membranes. Absorption and fluorescence emission spectra were similar for LH2 complexes in detergent and liposomes, indicating that reconstitution retains the structural and optical properties of the LH2 complexes. Analysis of fluorescence emission shows that when LH2 forms an extensive series of contacts with other such complexes, fluorescence is quenched by 52.6 ± 1.4%. In mixed proteoliposomes, specific excitation of carotenoids in LH2 donor complexes resulted in emission of fluorescence from acceptor RC-LH1 complexes engineered to assemble with no carotenoids. Extents of energy transfer were measured by fluorescence lifetime microscopy; the 0.72 ± 0.08 ns lifetime in LH2-only membranes decreases to 0.43 ± 0.04 ns with a ratio of 2:1 LH2 to RC-LH1, and to 0.35 ± 0.05 ns for a 1:1 ratio, corresponding to energy transfer efficiencies of 40 ± 14% and 51 ± 18%, respectively. No further improvement is seen with a 0.5:1 LH2 to RC-LH1 ratio. Thus, LH2 and RC-LH1 complexes perform their light harvesting and energy transfer roles when reconstituted into proteoliposomes, providing a way to integrate native, non-native, engineered and de novo designed light-harvesting complexes into functional photosynthetic systems.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2007

Decontamination of Genesis Array Materials by UV Ozone Cleaning

Shortly after the NASA Genesis Mission sample return capsule returned to earth on September 8, 2004, the science team discovered that all nine ultra-pure semiconductor materials were contaminated with a thin molecular organic film approximately 0 to 100 angstroms thick. The organic contaminate layer, possibly a silicone, situated on the surface of the materials is speculated to have formed by condensation of organic matter from spacecraft off-gassing at the Lagrange 1 halo orbit during times of solar exposure. While the valuable solar wind atoms are safely secured directly below this organic contamination and/or native oxide layer in approximately the first 1000 angstroms of the ultra-pure material substrate, some analytical techniques that precisely measure solar wind elemental abundances require the removal of this organic contaminate. In 2005, Genesis science team laboratories began to develop various methods for removing the organic thin film without removing the precious material substrate that contained the solar wind atoms. Stephen Sestak and colleagues at Open University first experimented with ultraviolet radiation ozone (UV/O3) cleaning of several non-flight and flown Genesis silicon wafer fragments under a pure flowing oxygen environment. The UV/O3 technique was able to successfully remove organic contamination without etching into the bulk material substrate. At NASA Johnson Space Center Genesis Curation Laboratory, we have installed an UV/O3 cleaning devise in an ambient air environment to further experimentally test the removal of the organic contamination on Genesis wafer materials. Preliminary results from XPS analysis show that the UV/O3 cleaning instrument is a good non-destructive method for removing carbon contamination from flown Genesis array samples. However, spectroscopic ellipsometry results show little change in the thickness of the surface film. All experiments to date have shown UV/O3 cleaning method to be the best non-destructive method for removing organic contamination from the surface of the Genesis materials. The UV/O3 cleaning process can also clean carbon contamination to levels below non-flight standards. This can be seen by comparing sample 60260's carbon 10667 cps with non-flight Si carbon 21675 cps. Therefore, surface carbon contamination should not hinder the analysis of solar wind.

Calaway, Michael J.↗
DOE OSTI2022

A consolidated bioprocess design to produce multiple high-value platform chemicals from lignocellulosic biomass and its technoeconomic feasibility

5-Hydroxymethyl furfural (HMF) and furfurals are DOE-listed platform chemicals that can be derived from the renewable carbon in the lignocellulosic biomasses and have the potential to replace petroleum-derived alter- natives. High substrate cost and use of expensive solvents limit the economic feasibility of bio-based HMF production on an industrially relevant scale. The study presents an experimental optimized condition that maximizes the chemical-free production of HMF and furfurals without lowering the yield of total fermentable sugars from Saccharum bagasse. Hydrothermal pretreatment at 210 °C for 15 min yielded approximately 10%, 12%, and 46% of HMF, furfurals, and fermentable sugars per gram of dry biomass, respectively. Additionally, the study proposes a consolidated bioprocess model to produce and recover four high-value bioproducts i.e., HMF, furfurals, ethanol, and acetic acid based on the experimental results and evaluates its technoeconomic feasibility considering HMF as the main product. The minimum selling price (MSP) of HMF was estimated to be 930.6 USD/ t which is competitive with its petroleum-derived precursor alternative p-xylene (1,113 USD/t). The sensitivity analysis performed for the process parameters suggests that pretreatment cost and revenues from coproducts immensely influence the MSP of HMF. The preliminary technoeconomic analysis performed on the consolidated bioprocess design indicates that additional revenue streams from diversified coproducts in biorefineries aid in lowering the MSP of high-value bioproducts.

09 BIOMASS FUELS↗
NASA NTRS2024

Hawai’i Climate: Utilizing NASA Earth Observations to Assess Thermal Stress Impacts on Coastal Hawaiian Fishponds

Hawaiian fishponds (loko i’a), ancient aquaculture systems created over 1500 years ago, historically served to harvest prized native fish species. Colonization-induced changes in land management have reduced active loko i’a from over 500 to ~20, destabilizing nearshore ecosystems and diminishing native Hawaiian cultural traditions. In recent decades, efforts to restore loko i’a have intensified as part of a broader emphasis on preserving Hawaiian cultural identity. Anthropogenic-induced climate change threatens these systems, particularly through the increase in frequency and magnitude of marine heatwaves. Though largely unexplored, these events are effectively studied utilizing remote sensing via Earth observations. Leveraging this technique enables autonomous extraction of water quality parameters to inform fishpond management. This study examined seven loko i’a across the main Hawaiian Islands (Hawai’i Island, Moloka’i, Maui, O’ahu, Kaua’i). Sea surface temperature and normalized difference chlorophyll index measurements were derived in fishponds utilizing Landsat 8 Thermal Infrared Sensor Thermal Infrared Sensor and Sentinel-2 MultiSpectral Instrument between 2013 to 2023, while regional patterns in temperature and chlorophyll-a were observed via Aqua’s Moderate Resolution Imaging Spectroradiometer (2002-2021). Employing these sensors, we focused analysis around the 2015 and 2019 marine heatwaves in the Pacific. We observed a heat stress gradient across the archipelago, creating thermally sheltered and unsheltered fishponds, yet identified no notable localized relationships between temperature and chlorophyll-a. Additionally, we applied pre-determined thermal maxima for culturally significant fish species (Striped Mullet: Mugil cephalus; Milkfish: Chanos Chanos) to assess historical habitat suitability within fishponds. While the direct impacts of marine heatwaves on loko i’a ecology are unknown, temperature patterns observed in this study are cause for concern.

Raz Wachtel↗
NASA NTRS1998

Analysis of proteins involved in biodegradation of crop biomass

The biodegradation of crop biomass for re-use in crop production is part of the bioregenerative life support concept proposed by the National Aeronautics and Space Administration (NASA) for long duration, manned space exploration. The current research was conducted in the laboratory to evaluate the use of electrophoretic analysis as a means of rapidly assaying for constitutive and induced proteins associated with the bacterial degradation of crop residue. The proteins involved in crop biomass biodegradation are either constitutive or induced. As a result, effluent and cultures were examined to investigate the potential of using electrophoretic techniques as a means of monitoring the biodegradation process. Protein concentration for optimum banding patterns was determined using the Bio-Rad Protein Assay kit. Four bacterial soil isolates were obtained from the G.W. Carver research Farm at Tuskegee University and used in the decomposition of components of plant biomass. The culture, WDSt3A was inoculated into 500 mL of either Tryptic Soy Broth or Nutrient Broth. Incubation, with shaking of each flask was for 96 hours at 30 C. The cultures consistently gave unique banding patterns under denaturing protein electrophoresis conditions, The associated extracellular enzymes also yielded characteristic banding patterns over a 14-day period, when native electrophoresis techniques were used to examine effluent from batch culture bioreactors. The current study evaluated sample preparation and staining protocols to determine the ease of use, reproducibility and reliability, as well as the potential for automation.

Crawford, Kamau↗
DOE OSTI2021

Rational design and testing of abiotic stress‐inducible synthetic promoters from poplar cis ‐regulatory elements

Summary Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic‐related and salt stress‐inducible synthetic promoters for use in hybrid poplar. De novo motif‐detecting algorithms yielded 30 water‐deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water‐deficit stress motifs (SD18, SD13 and SD9) found in 16 co‐expressed gene promoters, and we discovered a well‐conserved motif for salt response (SS16). We characterized several native poplar stress‐inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five‐to‐eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18‐1, SD9‐2, SS16‐1, SS16‐2 and SS16‐3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18‐1 and SD9‐2 were induced by water‐deficit stress, whereas SS16‐1, SS16‐2 and SS16‐3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.

09 BIOMASS FUELS↗
DOE OSTI2023

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

An Autonomous MCP Bridge to Rucio: Enhancing Data Management Accessibility for High Energy Physics

The Rucio Data Management System [1] is an important tool used by High Energy Physics experiments, including those at Fermi National Accelerator Laboratory, to store and manage exabyte-scale scientific datasets. Despite its central role in coordinating data across globally distributed storage sites, Rucio's command line interface (CLI) presents a steep learning curve, and makes it difficult for scientists to navigate through. To solve this issue, a containerized Model Context Protocol (MCP) [2] server was built that connects Large Language Models directly to Rucio, allowing AI agents to handle data tasks by using simple, natural language rather than memorized terminal commands. The core engineering focus of this project was moving the server away from slow terminal commands that require text parsing and replacing them with a native Python Client API toolset and a planned REST API framework. Moving to the Python API handles data operations directly in memory, which helps clear up formatting errors, provides the AI with clean, structured JSON data and speeds up tool execution. To prove that the system actually works, a benchmarking pipeline was also built with various questions to test the AI across four different model configurations. The questions included finding data scopes, tracking down specific datasets, and checking replication rules. Through benchmarking, early runs showed that with raw terminal text, the model would get confused and stuck, whereas switching to the Python API to feed the AI clean, structured data yielded massive improvement. By creating an intelligent and autonomous bridge to a storage network, this project shows how AI can be implemented in scientific data management, which ultimately helps scientists at Fermilab spend less time sorting through data and more time focusing on their experiments and analysis.

Akella, Kashyap [William Rainey Harper Coll.]↗
NASA NTRS2017

Hypervolatiles in a Jupiter-Family Comet: Observations of 45P/Honda-Mrkos-Pajdusakova Using iSHELL at the NASA-IRTF

We used the new high spectral resolution cross-dispersed facility spectrograph, iSHELL, at the NASA Infrared Telescope Facility on Maunakea, HI, to observe Jupiter-family comet (JFC) 45P/Honda-Mrkos-Pajdusakova. We report water production rates, as well as production rates and abundance ratios relative to H2O, for eight trace parent molecules (native ices), CO, CH4, H2CO, CH3OH, HCN, NH3, C2H2, and C2H6, on 2 days spanning UT 2017 January 6/7 and 7/8, shortly following perihelion. Trace species were measured simultaneously with H2O and/or OH prompt emission, a proxy for H2O production, thereby providing a robust and consistent means of establishing the native ice composition of 45P. Its favorable geocentric radial velocity (approximately minus 35 kilometers per second) permitted sensitive measures of the "hypervolatiles" CO and CH4, which are substantially undercharacterized in JFCs. Our results represent the most precise ground-based measures of CO and CH4 to date in a JFC, providing a foundation for building meaningful statistics regarding their abundances. The abundance ratio for CH4 in 45P (0.79 percent plus or minus 0.06 percent relative to H2O) was consistent with its median value as measured among Oort Cloud comets, whereas CO (0.60 percent plus or minus 0.04 percent) was strongly depleted. Compared with all measured comets, HCN (0.049 percent plus or minus 0.012 percent) was strongly depleted, CH3OH (3.6 percent plus or minus 0.3 percent) was enriched, and the remaining species were consistent with their respective median abundances. The volatile composition measured for 45P could indicate processing of ices prior to their incorporation into its nucleus. Spatial analysis of emissions suggests enhanced release of more volatile species into the sunward-facing hemisphere of the coma.

DiSanti, Michael A.↗
DOE OSTI2020

Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters

Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Yet Another Discriminant Analysis (YADA): A Probabilistic Model for Machine Learning Applications

This paper presents a probabilistic model for various machine learning (ML) applications. While deep learning (DL) has produced state-of-the-art results in many domains, DL models are complex and over-parameterized, which leads to high uncertainty about what the model has learned, as well as its decision process. Further, DL models are not probabilistic, making reasoning about their output challenging. In contrast, the proposed model, referred to as Yet Another Discriminate Analysis(YADA), is less complex than other methods, is based on a mathematically rigorous foundation, and can be utilized for a wide variety of ML tasks including classification, explainability, and uncertainty quantification. YADA is thus competitive in most cases with many state-of-the-art DL models. Ideally, a probabilistic model would represent the full joint probability distribution of its features, but doing so is often computationally expensive and intractable. Hence, many probabilistic models assume that the features are either normally distributed, mutually independent, or both, which can severely limit their performance. YADA is an intermediate model that (1) captures the marginal distributions of each variable and the pairwise correlations between variables and (2) explicitly maps features to the space of multivariate Gaussian variables. Numerous mathematical properties of the YADA model can be derived, thereby improving the theoretic underpinnings of ML. Validation of the model can be statistically verified on new or held-out data using native properties of YADA. However, there are some engineering and practical challenges that we enumerate to make YADA more useful.

97 MATHEMATICS AND COMPUTING↗