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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

Plant Sciences↗
DOE OSTI2026

Analytic rate theory of polariton relaxation that explains long polariton lifetime

Hybridization of a molecular exciton with a quantized photon creates a polariton. Despite extensive experimental investigations, the apparent lifetime of the exciton–polariton is not well-understood. For this work, we examined the steady-state population dynamics for a Holstein–Tavis–Cumming Hamiltonian to illuminate the long-term polaritonic dynamics and lifetime of the exciton–polariton in an optical cavity. For a realistic description of polariton relaxation, cavity loss and various exciton decay channels are included in the model. We found that in the presence of weak but finite exciton loss, the apparent lifetime of the lower polariton coincides with the out-of-cavity exciton lifetime and is independent of cavity-matter detuning. This is a simple explanation for the experimentally observed lifetimes for exciton polaritons and theoretically justifies the dark state reservoir hypothesis. Furthermore, if the upper polariton is initially populated, the system reaches the steady state very quickly, leading to single-exponential polariton relaxation. Starting from the lower polariton leads to a longer pre-steady-state time period, leading to double-exponential relaxation. Finally, we considered the effect of site orientational disorders and the exciton frequency disorderers. Under the collective limit, the effects of this disorder can be included in Fermi’s golden rule population dynamics without explicit sampling. For the exciton energy disorders, numerical calculations are needed. Our theoretical framework is applicable to interpret exciton–polariton experiments, especially related to the measured apparent lifetime of polaritons.

Chemical dynamics↗
DOE OSTI2021

Remarkably coherent population structure for a dominant Antarctic Chlorobium species

Background: In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. Results: A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 10 8 cells ml –1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. Conclusion: The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Robust and optimal alignment of high-dimensional data using maximum likelihood estimation through a random sample consensus framework

Abstract Correcting spatial orientations of groups of high-dimensional data sets such that they are all in a consistent coordinate system is often a time-consuming and error-prone process. Automation of this process can be accomplished by using Generalized Procrustes Analysis to estimate the relative orientations among a population of high-dimensional data sets. A least squares Procrustes solution is applied through a maximum likelihood estimation and random sample consensus framework for robustness. The likelihood model is comprised of a mixture distribution where inliers are modeled using t -distribution and outliers from a uniform distribution. Applications will focus on a synthetic data set that emulates triaxial acceleration data and also real shock data from a population of triaxial accelerometers. Outliers represent either non-rigid body responses, environmental noise, and/or sensor and data acquisition issues. The intended application for the methodology is to robustly automate the rotation of populations of experimentally collected triaxial accelerometer data sets to a single global coordinate system.

LOSAC↗
DOE OSTI2024

Controlling Factors of Chorus Spectral Gaps

Abstract The present study compares a single‐band chorus wave against a banded chorus wave observed by Van Allen Probes at adjacent times, and demonstrates that the single‐band chorus wave is associated with an anisotropic electron population over a broad energy range, while the banded chorus wave is accompanied by an electron phase space density plateau and an electron anisotropy reduction around Landau resonant energies. We further compare banded chorus waves with different spectral gap widths, and show that a wider spectral gap is associated with electron isotropization extending to higher energies with respect to the equatorial Landau resonant energy. We suggest that early generated chorus waves isotropize electrons via Landau resonant acceleration, and the waves that propagate to higher latitudes isotropize electrons at higher energies. The isotropization extending to higher energies leads to a larger spectral gap of new chorus waves after electrons bounce back to the equator.

Li, Jinxing↗
DOE OSTI2021

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Here, using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Residential Solar-Adopter Income and Demographic Trends: 2022 Update

The report describes income, demographic, and other socio-economic trends among U.S. residential rooftop solar adopters. The report is based on data for roughly 1.9 million residential rooftop solar systems installed through 2019, representing 82% of all U.S. systems. With its unique size, geographic scope, and level of detail, this report is intended to serve as a foundational reference document for policy-makers, industry stakeholders, and researchers. Key findings include the following: -Solar adopters generally skew towards higher incomes, though that trend continues to diminish over time. -Solar adopter incomes vary considerably and encompass many low-to-moderate income (LMI) households. -Solar-adopter incomes are consistently higher for systems paired with battery storage, for host-owned systems, and for systems installed on single-family homes. -Solar adopters differ from the broader U.S. population in terms of a variety of other demographic and socioeconomic measures. -State-level comparisons indicate that solar-adopters tend to live in neighborhoods with relatively high non-Hispanic White and Asian populations, and with relatively low Hispanic and Black populations.

14 SOLAR ENERGY↗
DOE OSTI2022

Residential Solar-Adopter Income and Demographic Trends: 2021 Update [Slides]

The report describes income, demographic, and other socio-economic trends among U.S. residential rooftop solar adopters. The report is based on data for roughly 1.9 million residential rooftop solar systems installed through 2019, representing 82% of all U.S. systems. With its unique size, geographic scope, and level of detail, this report is intended to serve as a foundational reference document for policy-makers, industry stakeholders, and researchers. Key findings include the following: Solar adopters generally skew towards higher incomes, though that trend continues to diminish over time. Solar adopter incomes vary considerably and encompass many low-to-moderate income (LMI) households. Solar-adopter incomes are consistently higher for systems paired with battery storage, for host-owned systems, and for systems installed on single-family homes. Solar adopters differ from the broader U.S. population in terms of a variety of other demographic and socioeconomic measures. State-level comparisons indicate that solar-adopters tend to live in neighborhoods with relatively high non-Hispanic White and Asian populations, and with relatively low Hispanic and Black populations. In conjunction with the report, Berkeley Lab has published an updated accompanying set of online data visualizations that allow users to further explore the underlying data. Berkeley Lab is also offering related analytical support to states, local agencies, and other organizations on issues related to solar adoption among low-to-moderate income households.

14 SOLAR ENERGY↗
DOE OSTI2023

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F 6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Exploring the stellar populations of backsplash galaxies

Backsplash galaxies are those that traverse and overshoot cluster cores as they fall into these structures. They are affected by environment, and should stand out in contrast to the infalling population. We target galaxies in the vicinity of clusters (R≳R 200 ) and select a sample in projected phase space (PPS), from the compilation of Sampaio et al. based on SDSS data. We present a statistical analysis, comparing two regions in PPS, with the same projected distance to the cluster but different velocity. The analysis relies on the presence of variations in the stellar population content of backsplash galaxies. We find a lower limit in the fractional contribution of ∼5 per cent with respect to the general sample of infalling galaxies at similar group-centric distance when using single line strength analysis, or ∼15-30 per cent when adopting bivariate distributions. The stellar populations show a subtle but significant difference towards older ages, and a higher fraction of quiescent galaxies. We also compare this set with a general field sample, where a substantially larger difference in galaxy properties is found, with the field sample being consistently younger, metal poorer and with a lower fraction of quiescent galaxies. Noting that our ‘cluster’ sample is located outside of the virial radius, we expect this difference to be caused by pre-processing of the infalling galaxies in the overall higher density regions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A multifunctional copper single-atom electrocatalyst aerogel for smart sensing and producing ammonia from nitrate

Despite modern chemistry’s success in providing affordable fertilizers for feeding the population and supporting the ammonia industry, ineffective nitrogen management has led to pollution of water resources and air, contributing to climate change. Here, we report a multifunctional copper single-atom electrocatalyst-based aerogel (Cu SAA) that integrates the multiscale structure of coordinated single-atomic sites and 3D channel frameworks. The Cu SAA demonstrates an impressive faradaic efficiency of 87% for NH 3 synthesis, as well as remarkable sensing performance with detection limits of 0.15 ppm for NO 3 − and 1.19 ppm for NH 4 + . These multifunctional features enable precise control and conversion of nitrate to ammonia in the catalytic process, facilitating accurate regulation of the ammonium and nitrate ratios in fertilizers. We thus designed the Cu SAA into a smart and sustainable fertilizing system (SSFS), a prototype device for on-site automatic recycling of nutrients with precisely controlled nitrate/ammonium concentrations. The SSFS represents a forward step toward sustainable nutrient/waste recycling, thus permitting efficient nitrogen utilization of crops and mitigating pollutant emissions. This contribution exemplifies how electrocatalysis and nanotechnology can be potentially leveraged to enable sustainable agriculture.

Science & Technology - Other Topics↗
DOE OSTI2022

Columnar Localization and Laminar Origin of Cortical Surface Electrical Potentials

Electrocorticography (ECoG) methodologically bridges basic neuroscience and understanding of human brains in health and disease. However, the localization of ECoG signals across the surface of the brain and the spatial distribution of their generating neuronal sources are poorly understood. To address this gap, we recorded from rat auditory cortex using customized μECoG, and simulated cortical surface electrical potentials with a full-scale, biophysically detailed cortical column model. Experimentally, μECoG-derived auditory representations were tonotopically organized and signals were anisotropically localized to less than or equal to ±200 μm, that is, a single cortical column. Biophysical simulations reproduce experimental findings and indicate that neurons in cortical layers V and VI contribute ∼85% of evoked high-gamma signal recorded at the surface. Cell number and synchrony were the primary biophysical properties determining laminar contributions to evoked μECoG signals, whereas distance was only a minimal factor. Thus, evoked μECoG signals primarily originate from neurons in the infragranular layers of a single cortical column. SIGNIFICANCE STATEMENT ECoG methodologically bridges basic neuroscience and understanding of human brains in health and disease. However, the localization of ECoG signals across the surface of the brain and the spatial distribution of their generating neuronal sources are poorly understood. We investigated the localization and origins of sensory-evoked ECoG responses. We experimentally found that ECoG responses were anisotropically localized to a cortical column. Biophysically detailed simulations revealed that neurons in layers V and VI were the primary sources of evoked ECoG responses. These results indicate that evoked ECoG high-gamma responses are primarily generated by the population spike rate of pyramidal neurons in layers V and VI of single cortical columns and highlight the possibility of understanding how microscopic sources produce mesoscale signals.

Baratham, Vyassa L.↗
DOE OSTI2020

A unified catalog of 204,938 reference genomes from the human gut microbiome

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cannibals in the thick disk II. Radial-velocity monitoring of the young α -rich stars

Determining ages of stars for reconstructing the history of the Milky Way remains one of the most difficult tasks in astrophysics. This involves knowing when it is possible to relate the stellar mass with its age and when it is not. The young α-rich (YAR) stars present such a case in which we are still not sure about their ages because they are relatively massive, implying young ages, but their abundances are α-enhanced, which implies old ages. We report the results from new observations from a long-term radial-velocity-monitoring campaign complemented with high-resolution spectroscopy, as well as new astrometry and seismology of a sample of 41 red giants from the third version of APOKASC, which includes YAR stars. The aim is to better characterize the YAR stars in terms of binarity, mass, abundance trends, and kinematic properties. The radial velocities of HERMES, APOGEE, and Gaia were combined to determine the binary fraction among YAR stars. In combination with their mass estimate, evolutionary status, chemical composition, and kinematic properties, it allowed us to better constrain the nature of these objects. We found that stars with M < 1 M ⊙ were all single, whereas stars with M > 1 M ⊙ could be either single or binary. This is in agreement with theoretical predictions of population synthesis models. Studying their [C/N], [C/Fe], and [N/Fe], trends with mass, it became clear that many YAR stars do not follow the APOKASC stars, favoring the scenario that most of them are the product of mass transfer. Our sample further includes two likely undermassive stars, that is to say of such as low mass that they cannot have reached the red clump within the age of the Universe, unless their low mass is the signature of mass loss in previous evolutionary phases. These stars do not show signatures of currently being binaries. Both YAR and undermassive stars might show some anomalous APOGEE abundances for the elements N, Na, P, K, and Cr; although, higher-resolution optical spectroscopy might be needed to confirm these findings. Considering the significant fraction of stars that are formed in pairs and the variety of ways that makes mass transfer possible, the diversity in properties in terms of binarity, and chemistry of the YAR and undermassive stars studied here implies that most of these objects are likely not young.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

MIDAS2: Metagenomic Intra-species Diversity Analysis System

The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

YbH + formation in an ytterbium ion trap

The trapped 171 Yb + ion is a promising candidate for portable atomic clock applications. However, with buffer-gas cooled ytterbium ions, the ions can be pumped into a low-lying 2 F 7 / 2 state or form YbH + molecules. These dark states reduce the fluorescence signal from the ions and can degrade the clock stability. In this work, we study the dynamics of the populations of the 2 F 7 / 2 state and YbH + molecules under different operating conditions of our 171 Yb + ion system. Our study indicates that 2 F 7 / 2 -state ions can form YbH + molecules through interactions with hydrogen gas. As observed previously, dissociation of YbH + is observed at wavelengths around 369 nm. We also demonstrate YbH+ dissociation using 405 nm light. Moreover, we show that the population in the dark states can be limited by using a single repump laser at 935 nm. Our study provides insights into the molecular formation in a trapped ion system.

74 ATOMIC AND MOLECULAR PHYSICS↗