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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The effect of annealing on kink band formation in Ag/Fe nanolaminates

Kink banding is a common, though not well understood, failure mechanism in anisotropic materials such as nano metallic laminates (NMLs). In this work, we investigate the effect of annealing on kink band (KB) formation in Ag/Fe NMLs prepared by accumulative roll bonding (ARB) using in situ micropillar compression, scanning/transmission electron microscopy (S/TEM), and transmission Kikuchi diffraction (TKD) analyses. Our results show that annealing increases the KB initiation strain, decreases the probability of KB formation, and decreases the load drop magnitude accompanying kink banding in Ag/Fe NMLs. Post-compression analyses reveal that annealing facilitates more uniform deformation of pillars and affects the formation of geometrically necessary grain boundaries (GNBs) near the kink band boundary (KBB). Compared to its as-rolled counterpart, annealed Ag/Fe has wider KBs with blunter KBBs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Superionic Surface Li-Ion Transport in Carbonaceous Materials

Unlike Li-ion transport in the bulk of carbonaceous materials, little is known about Li-ion diffusion on their surface. Here, in this study, we have discovered an ultrafast Li-ion transport phenomenon on the surface of carbonaceous materials with limited reversible Li insertion capacity and high surface area. An ionic conductivity of 18.1 mS cm –1 at room temperature is observed in lithiated Ketjen black (KB), far exceeding those of most solid-state ion conductors. Theoretical calculations reveal low diffusion barriers for the surface Li species. As a result, lithiated KB functions effectively as an interlayer between Li and solid-state electrolytes (SSEs) to mitigate dendrite growth. Further, lithiated KB acts as a high-performance mixed ionic–electronic conductor and replaces solid electrolytes to enhance graphite anode performance, demonstrating full utilization with ∼85% capacity retention over 300 cycles. The discovery of this surface-mediated ultrafast Li-ion transport mechanism provides new directions for the design of solid-state ion conductors and solid-state batteries.

Li metal batteries↗
DOE OSTI2022

Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages

Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991–3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses—amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Enterprise , a massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

CRISPR-Cas9/Cas12a systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding the feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 and Cas12a are widely used in genetic and metabolic engineering. In filamentous fungi, both Cas9 and Cas12a have been utilized as CRISPR nucleases. In this work we first compared efficacies and types of genetic edits for CRISPR-Cas9 and -Cas12a systems at the polyketide synthase (albA) gene locus in Aspergillus niger. By employing a tRNA-based gRNA polycistronic cassette, both Cas9 and Cas12a have demonstrated equally remarkable editing efficacy. Cas12a showed potential superiority over Cas9 protein when one gRNA was used for targeting, achieving an editing efficiency of 86.5% compared to 31.7% for Cas9. Moreover, when employing two gRNAs for targeting, both systems achieved up to 100% editing efficiency for single gene editing. In addition, the CRISPR-Cas9 system has been reported to induce large genomic deletions in various species. However, its use for engineering large chromosomal segments deletions in filamentous fungi still requires optimization. Here, we engineered Cas9 and -Cas12a-induced large genomic fragment deletions by targeting various genomic regions of A. niger ranging from 3.5 kb to 40 kb. Our findings demonstrate that targeted engineering of large chromosomal segments can be achieved, with deletions of up to 69.1% efficiency. Furthermore, by targeting a secondary metabolite gene cluster, we show that fragments over 100 kb can be efficiently and specifically deleted using the CRISPR-Cas9 or -Cas12a system. Overall, in this paper, we present an efficient multi-gRNA genome editing system utilizing Cas9 or Cas12a that enables highly efficient targeted editing of genes and large chromosomal regions in A. niger.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

KBKit: A Python Toolkit for Kirkwood–Buff Theory from Molecular Dynamics

Thermodynamic properties of liquid mixtures govern processes that range from drug delivery to energy storage, yet extracting these properties from molecular simulations remains challenging. Kirkwood–Buff (KB) theory offers a rigorous route by linking microscopic pair distribution functions to macroscopic free energies, but practical use of the theory has been hindered by two obstacles: (i) the long simulations needed to obtain well-converged Kirkwood-Buff integrals (KBIs) and (ii) the specialized corrections required to translate finite-size data to the thermodynamic limit. $\texttt{KBKit}$ is an open-source Python package that removes these barriers. It automatically computes KBIs and derived thermodynamic quantities from GROMACS input files, applies state-of-the-art finite-size corrections, and provides built-in diagnostic tools to quantify statistical uncertainty. Written with modern software-engineering practices—continuous integration, extensive unit testing, and thorough documentation—$\texttt{KBKit}$ is both reliable and easy to extend. By condensing complex KBI analysis into a few intuitive commands, $\texttt{KBKit}$ enables researchers to incorporate KB theory into routine simulation workflows and accelerate the discovery of solution-phase thermodynamics.

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

Relation between the Hydrated Electron Solvation Structure and Its Partial Molar Volume

It is now generally accepted that the hydrated electron occupies a cavity in water, but the size of the cavity and the arrangements of the solvating water molecules are not fully characterized. Here, we use the Kirkwood-Buff (KB) approach to examine how the partial molar volume (V M ) provides insight into these issues. The KB method relates V M to an integral of the electron-water radial distribution function, a key measure of the hydrated electron structure. Here we have applied it to three widely-used pseudopotentials and the results show that V M is a sensitive measure of the fidelity of hydrated electron descriptions. Thus, the measured V M places constraints on the hydrated electron structure that are important in developing and evaluating model descriptions. Importantly, we find that V M does not reflect only the cavity size (and thus should not be used to infer the cavity radius), but is strongly dependent on the extended solvation structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ketjenblack-Supported and Unsupported ZrO 2 –ZrN Nanoparticle Systems for Enabling Efficient Electrochemical Nitrogen Reduction to Ammonia

Artificial N 2 fixation via the electrocatalytic nitrogen (N 2 ) reduction reaction (NRR) has been recently promoted as a rational route toward reducing energy consumption and CO 2 emission as compared with the traditional Haber–Bosch process. Nevertheless, optimizing NRR relies on developing highly efficient electrocatalysts. Herein, we report on the reliable and reproducible synthesis of two promising electrocatalysts in either the presence or absence of Ketjenblack (KB), namely, ZrO 2 –ZrN@KB and ZrO 2 –ZrN systems, synthesized through the nitriding of Zr. Both materials had never previously been considered for NRR, to the best of our knowledge. Nevertheless, both of these electrocatalysts incorporated a combination of tetragonal ZrO 2 , ZrON, and cubic ZrN and showed excellent activity and durability toward NH 3 formation. Moreover, the maximum NH3 production rate of 84.1 μg h –1 mg –1 at -0.7 V vs a reversible hydrogen electrode (RHE) was achieved with the ZrO 2 –ZrN electrocatalyst with an impressive Faradaic efficiency of 21.2% at -0.6 V vs RHE, indicating a high selectivity associated with the NRR. Additionally, the catalysts demonstrated excellent stability during the electrolysis process and recycling tests. Here we postulate that the combination of exposed active sites of ZrN and ZrO 2 likely contributes to the enhanced NRR performance attributed to ZrO 2 –ZrN.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9

Targeted insertion of transgenes at pre-determined plant genomic safe harbors provides a desirable alternative to insertions at random sites achieved through conventional methods. Most existing cases of targeted gene insertion in plants have either relied on the presence of a selectable marker gene in the insertion cassette or occurred at low frequency with relatively small DNA fragments (<1.8 kb). Here, we report the use of an optimized CRISPR-Cas9-based method to achieve the targeted insertion of a 5.2 kb carotenoid biosynthesis cassette at two genomic safe harbors in rice. We obtain marker-free rice plants with high carotenoid content in the seeds and no detectable penalty in morphology or yield. Whole-genome sequencing reveals the absence of off-target mutations by Cas9 in the engineered plants. These results demonstrate targeted gene insertion of marker-free DNA in rice using CRISPR-Cas9 genome editing, and offer a promising strategy for genetic improvement of rice and other crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reactivation of a developmentally silenced embryonic globin gene

The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large freshwater phages with the potential to augment aerobic methane oxidation

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host–phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Extreme dimensions — how big (or small) can tailed phages be?

Bacteriophages (phages), that is, viruses that infect bacteria, represent an extremely diverse, yet under-characterized, group of viruses. Although most known phages harbour genomes that are shorter than 200 kb packaged into capsids with a diameter under 100 Å, more and more ‘extremely large’ phages are being discovered. Early reports of phages with genomes larger than 200 kb defined them as ‘jumbo phages’1. Phylogenetic analysis of these jumbo phages revealed that they form distinct and cohesive groups with multiple independent origins. This suggested that jumbo phages are not merely mistakes or aberrations of smaller phages that got too big, but that large genome size is generally a stable trait. In fact, a larger genome can be advantageous; almost all jumbo phages encode their own specific transcription factors, at least some parts of the replication machinery, and many also have their own tRNA genes, which enables increased independence from their host. Here, large genomes also provide more flexibility in terms of transcription strategy; smaller phage genomes tend to have a strict modular genome structure to increase efficiency, whereas jumbo phage genomes may be much less organized in the absence of a strong selection pressure to maintain a compact genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Range extender mediates long-distance enhancer activity

Although most mammalian transcriptional enhancers regulate their cognate promoters over distances of tens of kilobases, some enhancers act over distances in the megabase range1. The sequence features that enable such long-distance enhancer–promoter interactions remain unclear. Here we used in vivo enhancer-replacement experiments at the mouse Shh locus to show that short- and medium-range limb enhancers cannot initiate gene expression at long-distance range. We identify a cis-acting element, range extender (REX), that confers long-distance regulatory activity and is located next to a long-range limb enhancer of Sall1. The REX element has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range limb enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of REX increased the range of an enhancer by an order of magnitude from its native 73 kb to 848 kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs that are critical for its activity. These motifs are enriched in long-range limb enhancers genome-wide, including the ZRS (zone of polarizing activity (ZPA) regulatory sequence), a benchmark long-range limb enhancer of Shh2. The ZRS enhancer with mutated [C/T]AATTA motifs maintains limb activity at short range, but loses its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature associated with long-range enhancer–promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer long-distance activation by remote enhancers.

Bower, Grace↗
DOE OSTI2022

Waveform processing using neural network algorithms on the front-end electronics

In a multi-channel radiation detector readout system, waveform sampling, digitization, and raw data transmission to the data acquisition system constitute a conventional processing chain. The deposited energy on the sensor is estimated by extracting peak amplitudes, area under pulse envelopes from the raw data, and starting times of signals or time of arrivals. However, such quantities can be estimated using machine learning algorithms on the front-end Application-Specific Integrated Circuits (ASICs), often termed as “edge computing”. Edge computation offers enormous benefits, especially when the analytical forms are not fully known or the registered waveform suffers from noise and imperfections of practical implementations. In this work, we aim to predict peak amplitude from a single waveform snippet whose rising and falling edges containing only 3 to 4 samples. We thoroughly studied two well-accepted neural network algorithms, Multi-Layer Perceptron (MLP) and Convolutional Neural Network (CNN) by varying their model sizes. Further, to better fit front-end electronics, neural network model reduction techniques, such as network pruning methods and variable-bit quantization approaches, were also studied. By combining pruning and quantization, our best performing model has the size of 1.5 KB, reduced from 16.6 KB of its full model counterpart. It can reach mean absolute error of 0.034 comparing to that of a naive baseline of 0.135. Such parameter-efficient and predictive neural network models established feasibility and practicality of their deployment on front-end ASICs.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Abstract Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

Salgado-Salazar, Catalina↗
DOE OSTI2022

High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water

The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de $D\hat{o}me$ (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Promoter deletion in the soybean Compact mutant leads to overexpression of a gene with homology to the C 20 -gibberellin 2-oxidase family

Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. Furthermore, these results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.

59 BASIC BIOLOGICAL SCIENCES↗