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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A genomic perspective on fungal diversity and evolution

Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different ‘species’ and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute’s MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, in this study, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.

Mondo, Stephen J. [USDOE Joint Genome Institute (J↗
DOE OSTI2020

Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples

Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a method implementing TruSeq high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant gene targets representing a full-spectrum of antibiotic resistance classes common to environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within complex environmental samples originated from manure, soil, and livestock feces, in addition to a mock-community reference to assess sensitivity and specificity. DARTE-QM offers a new approach to studying antibiotic resistance in environmental microbiomes, showing advantages in efficiency and the ability to scale for many samples. This method provides a means of data acquisition that will alleviate some of the obstacles that many researchers in this area currently face.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Protection of U.S. streams is insufficient to safeguard stream diversity and prevent habitat impairment

Despite covering a small portion of Earth’s surface, streams support a disproportionate amount of biodiversity. Here, we measure progress against the Global Biodiversity Framework 30×30 protection target for streams within the conterminous U.S., in terms of quantity, representation, and effectiveness of habitat protection under primarily land-based protection strategies. We evaluated the geophysical and biogeographical diversity of streams falling under protection measures. Additionally, we expose a paradox of streams being protected yet simultaneously impaired from human disturbances. Without considering impairment, approximately 30% of streams are currently protected through land-based conservation of their local or upstream watersheds; when considering impairment, only 9% to 28% of streams are truly protected from disturbances depending on impairment thresholds and protection criteria. Furthermore, despite protection approaching 30×30 targets, only 5% of the most prevalent physical stream habitat types are protected. We provide a targeted protection strategy, overcoming the impairment paradox and ensuring adequate representation of streams.

Biogeography↗
DOE OSTI2022

Synthesis of bacteriochlorins bearing diverse β-substituents

Synthetic bacteriochlorins, analogues of native bacteriochlorophylls, provide absorption in the near-infrared spectral region and hence are valuable for fundamental studies in photochemistry and applications ranging from solar energy conversion to photomedicine. The full realization of such opportunities hinges on access to synthetically malleable bacteriochlorins. Here, two established routes that rely on self-condensation of a dihydrodipyrrin-acetal or dihydrodipyrrin-carboxaldehyde have been exploited to prepare 6 bacteriochlorins (2 new, 4 known in improved fashion). Each bacteriochlorin contains a gem-dimethyl group in the reduced, pyrroline ring to ensure stability toward adventitious dehydrogenation. These and related synthetic bacteriochlorins have been derivatized to tailor the perimeter of the macrocycle with diverse groups, affording 9 additional new bacteriochlorins and 4 known bacteriochlorins. By direct installation and/or derivatization, the scope of attached entities in this collection includes alkyl, amino, aryl, bromo, carboethoxy, oxo, phenylethynyl, and pyridyl. Furthermore, the bacteriochlorins are suited for surface attachment, bioconjugation, water-solubilization, vibrational studies, and elaboration into multichromophore arrays. Altogether the synthesis of 25 new compounds (11 bacteriochlorins, 14 precursors) is described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Luminescent hybrid halides with various centering metal cations (Zn, Cd and Pb) and diverse structures

Organic–inorganic hybrid metal halides have been extensively studied because of their great potential in optoelectronics. Herein, we report three hybrid metal halides (Bmpip) 2 ZnBr 4 , (Bmpip) 2 CdBr 4 , and (Bmpip) 8 Pb 11 Br 30 (where Bmpip + is 1-butyl-1-methyl-piperidinium, C 10 H 22 N + ). (Bmpip) 2 ZnBr 4 and (Bmpip) 2 CdBr 4 crystallize in the P2 1 /c space group with zero-dimensional crystal structures with [MBr 4 ] 2− (M = Zn, Cd) tetrahedra isolated by Bmpip + . (Bmpip) 8 Pb 11 Br 30 crystallizes in the triclinic space group P$\overline{1}$ with combining macron] with one-dimensional corrugated chains constructed from face-sharing [PbBr 6 ] 4− octahedra. Furthermore, all of the compounds exhibit excellent ambient and thermal stability. Under UV excitation, all three compounds exhibit very broad emissions. Temperature-dependent photoluminescence measurements indicate that the broad emissions of (Bmpip) 2 ZnBr 4 and (Bmpip) 2 CdBr 4 can be attributed to both the organic cations and self-trapped excitons (STEs) and that the emission of (Bmpip) 8 Pb 11 Br 30 is assigned to STEs. Density functional theory calculations reveal that the three compounds adopt a direct band gap. This work enriches our understanding of the structure types of hybrid metal halides while revealing their diverse emission mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Plant glycosyltransferases for expanding bioactive glycoside diversity

Glycosylation is a successful strategy to alter the pharmacological properties of small molecules, and it has emerged as a unique approach to expand the chemical space of natural products that can be explored in drug discovery. Traditionally, most glycosylation events have been carried out chemically, often requiring many protection and deprotection steps to achieve a target molecule. Further, enzymatic glycosylation by glycosyltransferases could provide an alternative strategy for producing new glycosides. In particular, the glycosyltransferase family has greatly expanded in plants, representing a rich enzymatic resource to mine and expand the diversity of glycosides with novel bioactive properties. This article highlights previous and prospective uses for plant glycosyltransferases in generating bioactive glycosides and altering their pharmacological properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Intermolecular C–H silylations of arenes and heteroarenes with mono-, bis-, and tris(trimethylsiloxy)hydrosilanes: control of silane redistribution under operationally diverse approaches

Operationally diverse C–H silylations of (hetero) arenes with a broad silane scope are reported. The control of silane redistribution improves overall catalytic efficiency, affording the various arylsiloxysilanes useful for polysiloxane materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Visualizing diverse lithium growth and stripping behaviors in anode-free solid-state batteries with operando X-ray tomography

Anode-free solid-state batteries (SSBs), which eliminate the need for lithium metal use during cell assembly, have the potential to enable high energy densities and simplified manufacturing. However, the factors that control lithium growth/stripping at the anode current collector are not well understood. Here, we use operando X-ray microcomputed tomography to comprehensively image and quantify lithium deposition and stripping under various conditions in three different Li|Li 6 PS 5 Cl|current collector cells, revealing diverse behavior that depends on interface morphology, cell resistance, and solid-state electrolyte (SSE) microstructure. A cell with high resistance exhibits extensive lithium filament growth across the entire current collector interface, with filaments that grow around pre-existing pores in the SSE rather than lithium filling these pores. Lithium filament formation is partially reversible, with the cracks shrinking as lithium metal is stripped. Uniform lithium deposition is achievable at low current densities in low-resistance cells, whereas higher current densities in these cells cause an increase in interfacial roughness, which is correlated with subsequent filamentary growth at the edges of the cell. These results provide insight into filamentary vs. planar lithium growth and highlight that the evolution of lithium is sensitively dependent on SSE microstructure and electrochemical processes.

25 ENERGY STORAGE↗
DOE OSTI2025

From the laboratory to space: unveiling isomeric diversity of C 5 H 2 in the reaction of tricarbon (C 3 , X 1 Σ g + ) with the vinyl radical (C 2 H 3 , X 2 A′)

By connecting laboratory dynamics with cosmic observables, this work highlights the critical role of reactions between highly reactive species in shaping the molecular inventory of the interstellar medium and opens new windows into the spectroscopically elusive corners of astrochemical complexity. The gas phase formation of distinct C 5 H 2 isomers is explored through the bimolecular reaction of tricarbon (C 3 , X 1 Σ + g ) with the vinyl radical (C 2 H 3 , X 2 A′) at a collision energy of 44 ± 1 kJ mol −1 employing the crossed molecular beam technique augmented by electronic structure and Rice–Ramsperger–Kassel–Marcus (RRKM) calculations. This barrierless and exoergic reaction follows indirect dynamics and is initiated by the addition of tricarbon to the radical center of the vinyl radical forming a Cs symmetric doublet collisional complex (CCCCHCH 2 ). Subsequent low-barrier isomerization steps culminate in the resonantly stabilized 2,4-pentadiynyl-1 radical (CHCCCCH 2 ), which decomposes via atomic hydrogen loss. Statistical calculations identify linear, triplet pentadiynylidene (p2, X 3 Σ − g ) as the dominant product, while singlet carbenes ethynylcyclopropenylidene (p1, X 1 A′), pentatetraenylidene (p3, X 1 A 1 ), and ethynylpropadienylidene (p4, X 1 A′) are formed with lower branching ratios. The least stable isomer, 2-cyclopropen-1-ylidenethenylidene (‘eiffelene’; p5, X 1 A 1 ), remains thermodynamically feasible, but exhibits negligible branching ratios. Two isomers detected in TMC-1 to date (p1 and p3) possess significant dipole moments making them amenable to radio telescopic observations, whereas linear pentadiynylidene (p2; D ∞h ) is only traceable via infrared spectroscopy or through its cyanopentadiynylidene derivative (HCCCCCCN). This study highlights the isomer diversity accessed in the low temperature hydrocarbon chemistry of barrierless and exoergic bimolecular reactions involving two unstable, reactants in cold molecular clouds.

Medvedkov, Iakov A. [University of Hawai'i at Mano↗
DOE OSTI2021

Diverse simulations of time-resolved photoluminescence in thin-film solar cells: A SnO 2 /CdSe y Te 1-y case study

Time-resolved photoluminescence (TRPL) is widely used to measure carrier lifetime in thin-film solar cell absorbers. However, the injection dependence of data and frequent non-exponential decay shapes complicate the interpretation. Here, we develop a numerical model to simulate injection-dependent TRPL measurements in a SnO 2 /CdSe y Te 1-y case study solar cell structure, considering parameters of interest to researchers in industry and academia. Previous simulations have shown that, in low injection, excess electrons and holes injected by the laser pulse are rapidly separated in the electric field formed by the pn junction. As a result, at early times, the PL signal can decay faster than the Shockley-Read-Hall lifetime in the absorber bulk (t_bulk). Prior simulations have shown that the charge stored in the junction can slowly leak out to affect decays at late times. However, it has not been clear if and to what degree charge storage can affect the slopes extracted from TRPL decays - t_2 - commonly cited as the TRPL-measured lifetime. Here, we show that charge storage can, in some cases, result in t_2 values that substantially overestimate t_bulk. Previous simulations indicate that high injection conditions can screen the junction field and minimize charge separation. Here, we show that continued injection increases can drive down t_2 below t_bulk as radiative recombination becomes dominant. We catalog charge storage and radiative recombination impacts for a diverse set of material parameters and compare results to double-heterostructure models.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,S↗
DOE OSTI2022

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. Here, we identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Respiration-driven methanotrophic growth of diverse marine methanogens

Anaerobic marine environments are the third largest producer of the greenhouse gas methane. The release to the atmosphere is prevented by anaerobic ‘methanotrophic archaea (ANME) dependent on a symbiotic association with sulfate-reducing bacteria or direct reduction of metal oxides. Metagenomic analyses of ANME are consistent with a reverse methanogenesis pathway, although no wild-type isolates have been available for validation and biochemical investigation. Herein is reported the characterization of methanotrophic growth for the diverse marine methanogens Methanosarcina acetivorans C2A and Methanococcoides orientis sp. nov. Growth was dependent on reduction of either ferrihydrite or humic acids revealing a respiratory mode of energy conservation. Acetate and/or formate were end products. In conclusion, reversal of the well-characterized methanogenic pathways is remarkably like the consensus pathways for uncultured ANME based on extensive metagenomic analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Diversity and evolution of nitric oxide reduction in bacteria and archaea

Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.

Science & Technology - Other Topics↗
DOE OSTI2025

High-density CRISPRi screens reveal diverse routes to improved acclimation in cyanobacteria

Cyanobacteria are the oldest form of photosynthetic life on Earth and contribute to primary production in nearly every habitat, from permafrost to hot springs. Despite longstanding interest in the acclimation of these microbes, it remains poorly understood and challenging to rewire. Here, this study uses a high-density, genome-wide CRISPR interference screen to examine the influence of gene-specific transcriptional variation on the growth of Synechococcus sp. PCC 7002 under environmental extremes. Surprisingly, many partial knockdowns enhanced fitness under cold monochromatic conditions. Transcriptional repression of genes for core subunits of the NDH-1 complex, which are important for photosynthesis and carbon uptake, improved growth rates under both red and blue light but at distinct, color-specific optima. Most genes with fitness-improving knockdowns were distinct to each light color, and dual-target transcriptional repression produced nonadditive effects. Findings reveal diverse routes to improved acclimation in cyanobacteria (e.g., attenuation of genes involved in CO 2 uptake, light harvesting, translation, and purine metabolism) and provide an approach for using gradients in sgRNA activity to pinpoint biochemically influential transcriptional changes in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Growth instabilities shape morphology and genetic diversity of microbial colonies

Abstract Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Golden, Alexander↗
DOE OSTI2020

Simulating Diverse HEP Workflows on Heterogeneous Architectures

We evaluate key patterns and estimate throughput bounds of simulated transformation of conventional high energy physics (HEP) data processing workflows to heterogeneous equivalents. The simulation parameter space includes the number of offloaded tasks, CPU/accelerator ratios of intra-task computations, offload latencies, and run time efficiency of offloaded computations. The simulation is performed for a diverse set of state-of-the-art event reconstruction scenarios from ATLAS, LHCb and CMS - the frontier HEP experiments of the Large Hadron Collider project.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Climate change alters flood magnitudes and mechanisms in climatically-diverse headwaters across the northwestern United States

Abstract Flooding caused by high streamflow events poses great risk around the world and is projected to increase under climate change. This paper assesses how climate change will alter high streamflow events by changing both the prevalence of different driving mechanisms (i.e. ‘flood generating processes’) and the magnitude of differently generated floods. We present an analysis of simulated changes in high streamflow events in selected basins in the hydroclimatically diverse Pacific Northwestern United States, classifying the events according to their mechanism. We then compare how the different classes of events respond to changes in climate at the annual scale. In a warmer future, high flow events will be caused less frequently by snowmelt and more frequently by precipitation events. Also, precipitation-driven high flow events are more sensitive to increases in precipitation than are snowmelt-driven high flow events, so the combination of the increase in both frequency and magnitude of precipitation-driven high flow events leads to higher flood likelihood than under each change alone. Our comparison of the results from two emissions pathways shows that a reduction in global emissions will limit the increase in magnitude and prevalence of these precipitation-driven events.

S Chegwidden, Oriana (ORCID:0000000313763835)↗