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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone

ABSTRACT The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming under realistic field conditions in closed and open canopy treatments in Minnesota, USA. Our results show that warming and canopy disturbance shifted bacterial and fungal community structure as dominant bacterial and fungal groups differed in the direction and intensity of their responses. Ectomycorrhizal and saprotrophic fungal communities with greater connectivity (higher prevalence of strongly interconnected taxa based on pairwise co-occurrence relationships) were more resistant to compositional change. Warming effects on soil enzymes involved in the hydrolytic and oxidative liberation of carbon from plant cell walls and nutrients from organic matter were most strongly linked to fungal community responses, although community structure–function relationships differed between fungal guilds. Collectively, these findings indicate that warming and disturbance will influence the composition and function of microbial communities in the temperate-boreal ecotone, and fungal responses are particularly important to understand for predicting future ecosystem functioning.

Microbiology↗
DOE OSTI2020

Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters

ABSTRACT Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3− + CO32−) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. “Cyanobacteria” are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond “Cyanobacteria”. Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among “Cyanobacteria”, but also among members of “Proteobacteria” and “Actinobacteria”.

Scott, Kathleen M.↗
DOE OSTI2021

Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Regional epithelial cell diversity in the small intestine of pigs

Abstract Understanding regional distribution and specialization of small intestinal epithelial cells is crucial for developing methods to control appetite, stress, and nutrient uptake in swine. To establish a better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. EE cells were divided into two subsets based on the level of expression of the EE lineage commitment gene, NEUROD1. NEUROD1hi EE cells had minimal expression of hormone-encoding genes and were dissimilar to EE cells in humans and mice, indicating a subset of EE cells unique to pigs. Recently discovered BEST4 enterocytes were detected in both crypts and villi throughout the small intestine via in situ staining, unlike in humans, where BEST4 enterocytes are found only in small intestinal villi. Proximal-to-distal gradients of expression were noted for hormone-encoding genes in EE cells and nutrient transport genes in enterocytes via scRNA-seq, demonstrating regional specialization. Regional gene expression in EE cells and enterocytes was validated via quantitative PCR (qPCR) analysis of RNA isolated from epithelial cells of different small intestinal locations. Though many genes had similar patterns of regional expression when assessed by qPCR of total epithelial cells, some regional expression was only detected via scRNA-seq, highlighting advantages of scRNA-seq to deconvolute cell type-specific regional gene expression when compared to analysis of bulk samples. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.

Agriculture↗
DOE OSTI2024

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. Furthermore, these findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. Furthermore, this provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

Arabidopsis↗
DOE OSTI2020

Supernovae and their host galaxies – VII. The diversity of Type Ia supernova progenitors

ABSTRACT We present an analysis of the light curve (LC) decline rates (Δm15) of 407 normal and peculiar supernovae (SNe) Ia and global parameters of their host galaxies. As previously known, there is a significant correlation between the Δm15 of normal SNe Ia and global ages (morphologies, colours, and masses) of their hosts. On average, those normal SNe Ia that are in galaxies from the Red Sequence (early-type, massive, old hosts) have faster declining LCs in comparison with those from the Blue Cloud (late-type, less massive, younger hosts) of the colour–mass diagram. The observed correlations between the Δm15 of normal SNe Ia and hosts’ parameters appear to be due to the superposition of at least two distinct populations of faster and slower declining normal SNe Ia from older and younger stellar components. We show, for the first time, that the Δm15 of 91bg- and 91T-like SNe is independent of host morphology and colour. The distribution of hosts on the colour–mass diagram confirms the known tendency for 91bg-like SNe to occur in globally red/old galaxies, while 91T-like events prefer blue/younger hosts. On average, the youngest global ages of 02cx-like SNe hosts and their positions in the colour–mass diagram hint that these events likely originate from young population, but they differ from 91T-like events in the LC decline rate. Finally, we discuss the possible explosion channels and present our favoured SN Ia models that have the potential to explain the observed SN–host relations.

Hakobyan, A. A.↗
DOE OSTI2022

The density distribution and physical origins of intermittency in supersonic, highly magnetized turbulence with diverse modes of driving

The probability density function (PDF) of the logarithmic density contrast, s = ln (ρ/ρ 0 ), with gas density ρ and mean density ρ 0 , for hydrodynamical supersonic turbulence is well known to have significant non-Gaussian (intermittent) features that monotonically increase with the turbulent Mach number, M. By studying the mass- and volume-weighted s-PDF for an ensemble of 36 sub-to-trans-Alfvenic mean-field, supersonic, isothermal turbulence simulations with different modes of driving, relevant to molecular gas in the cool interstellar medium, we show that a more intricate picture emerges for the non-Gaussian nature of s. Using four independent measures of the non-Gaussian components, we find hydrodynamical-like structure in the highly magnetized plasma for M≲4. However, for M≳4, the non-Gaussian signatures disappear, leaving approximately Gaussian s-statistics – exactly the opposite of hydrodynamical turbulence in the high-M limit. We also find that the non-Gaussian components of the PDF increase monotonically with more compressive driving modes. To understand the M≲4 non-Gaussian features, we use one-dimensional pencil beams to explore the dynamics along and across the large-scale magnetic field, B 0 . Here we discuss kinetic, density, and magnetic field fluctuations from the pencil beams, and identify physical sources of non-Gaussian components to the PDF as single, strong shocks coupled to fast magnetosonic compressions that form along B 0 . We discuss the Gaussianization of the M≳4 s-fields through the lens of two phenomenologies: the self-similarity of the s-field and homogenization of the dynamical time-scales between the over- and underdense regions in the compressible gas.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Cytochrome b5 diversity in green lineages preceded the evolution of syringyl lignin biosynthesis

Abstract Lignin production marked a milestone in vascular plant evolution, and the emergence of syringyl (S) lignin is lineage specific. S-lignin biosynthesis in angiosperms, mediated by ferulate 5-hydroxylase (F5H, CYP84A1), has been considered a recent evolutionary event. F5H uniquely requires the cytochrome b5 protein CB5D as an obligatory redox partner for catalysis. However, it remains unclear how CB5D functionality originated and whether it coevolved with F5H. We reveal here the ancient evolution of CB5D-type function supporting F5H-catalyzed S-lignin biosynthesis. CB5D emerged in charophyte algae, the closest relatives of land plants, and is conserved and proliferated in embryophytes, especially in angiosperms, suggesting functional diversification of the CB5 family before terrestrialization. A sequence motif containing acidic amino residues in Helix 5 of the CB5 heme-binding domain contributes to the retention of CB5D function in land plants but not in algae. Notably, CB5s in the S-lignin–producing lycophyte Selaginella lack these residues, resulting in no CB5D-type function. An independently evolved S-lignin biosynthetic F5H (CYP788A1) in Selaginella relies on NADPH-dependent cytochrome P450 reductase as sole redox partner, distinct from angiosperms. These results suggest that angiosperm F5Hs coopted the ancient CB5D, forming a modern cytochrome P450 monooxygenase system for aromatic ring meta-hydroxylation, enabling the reemergence of S-lignin biosynthesis in angiosperms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Secreted Effector Proteins of Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways

We report fungal effectors play critical roles in manipulating plant immune responses and promoting colonization. Sphaerulina musiva is a heterothallic ascomycete fungus that causes Septoria leaf spot and stem canker disease in poplar (Populus spp.) plantations. This disease can result in premature defoliation, branch and stem breakage, increased mortality, and plantation failure. However, little is known about the interaction between S. musiva and poplar. Previous work predicted 142 candidate secreted effector proteins in S. musiva (SmCSEPs), 19 of which were selected for further functional characterization in this study. SmCSEP3 induced plant cell death in Nicotiana benthamiana, while 8 out of 19 tested SmCSEPs suppressed cell death. The signal peptides of these eight SmCSEPs exhibited secretory activity in a yeast signal sequence trap assay. Confocal microscopy revealed that four of these eight SmCSEPs target both the cytoplasm and the nucleus, whereas four predominantly localize to discrete punctate structures. Pathogen challenge assays in N. benthamiana demonstrated that the transient expression of six SmCSEPs promoted Fusarium proliferatum infection. The expression of these six SmCSEP genes were induced during infection. SmCSEP2, SmCSEP13, and SmCSEP25 suppressed chitin-triggered reactive oxygen species burst and callose deposition in N. benthamiana. The candidate secreted effector proteins of S. musiva target multiple compartments in the plant cell and modulate different pattern-triggered immunity pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗
DOE OSTI2022

Synthetic diversity in the preparation of metallic uranium

Uranium metal is associated with several aspects of nuclear technology; it is used as fuel for research and power reactors, targets for medical isotope productions, explosive for nuclear weapons and precursors in synthetic chemistry. The study of uranium metal at the laboratory scale presents the opportunity to evaluate metallic nuclear fuels, develop new methods for metallic spent fuel reprocessing and advance the science relevant to nuclear forensics and medical isotope production. Since its first isolation in 1841, from the reaction of uranium chloride and potassium metal, uranium metal has been prepared by solid-state reactions and in solution by electrochemical, chemical and radiochemical methods. The present review summarizes the methods outlined above and describes the chemistry associated with each preparation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Diverse magnetic phase diagram and anomalous Hall effect in antiferromagnetic LuMn 6⁢ Sn 6

The interactions between conduction electrons and magnetism can significantly enhance the Hall signal, a phenomenon known as the anomalous Hall effect (AHE). While the AHE is generally not expected in antiferromagnets, a large AHE is observed in certain antiferromagnets with noncollinear spin textures and nonvanishing Berry curvature. In this work, we present a rich temperature and magnetic phase diagram with eight distinct magnetic phases for the antiferromagnetic kagome compound LuMn 6 Sn 6 . The Hall effect analysis in LuMn 6 Sn 6 reveals both intriguing physical phenomena and methodological challenges. In the coplanar canted antiferromagnetic phase, we observe an AHE, which likely originates from the intrinsic effects. At low temperatures, upon entering the ferromagnetic phase, the AHE sharply increases and exceeds the conventional limits expected from intrinsic mechanisms. We also demonstrate the limitations of standard experimental methods in extracting the topological contribution to the Hall effect data. In particular, we show that accounting for magnetoresistance anisotropy helps reduce spurious contribution that can mimic topological Hall signals, although it does not fully resolve it. Furthermore, these shortcomings in current approaches in partitioning the Hall response necessitate new tools to interpret transport results in complex magnetic materials such as LuMn 6 Sn 6 .

Anomalous Hall effect↗
DOE OSTI2026

Spectral Similarity Masks Structural Diversity at Hydrophobic Water Interfaces

The air-water and graphene-water interfaces represent quintessential examples of the liquid-gas and liquid-solid boundaries, respectively. While the sum-frequency generation (SFG) spectra of these interfaces show similarities, a consensus on their signals and interpretations has yet to be reached. Leveraging deep learning, we computed first-principles SFG spectra for both systems, addressing experimental discrepancies. Here, our findings reveal that similarities in SFG signals do not translate into comparable interfacial microscopic properties. Instead, graphene-water and air-water interfaces exhibit fundamental differences in SFG-active thicknesses, hydrogen-bonding networks, and surface dynamics. These distinctions underscore roughness suppression and electronic interactions present at the solid-liquid interface but absent at the gas-liquid interface.

Wang, Yong [Princeton Univ., NJ (United States)] (↗