Showing papers by "United States Department of Energy published in 2015"

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.

Abstract: To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

Abstract: Immune systems distinguish “self” from “nonself” to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

Discovery of a Weyl fermion state with Fermi arcs in niobium arsenide

Abstract: Three types of fermions play a fundamental role in our understanding of nature: Dirac, Majorana and Weyl. Whereas Dirac fermions have been known for decades, the latter two have not been observed as any fundamental particle in high-energy physics, and have emerged as a much-sought-out treasure in condensed matter physics. A Weyl semimetal is a novel crystal whose low-energy electronic excitations behave as Weyl fermions. It has received worldwide interest and is believed to open the next era of condensed matter physics after graphene and three-dimensional topological insulators. However, experimental research has been held back because Weyl semimetals are extremely rare in nature. Here, we present the experimental discovery of the Weyl semimetal state in an inversion-symmetry-breaking single-crystalline solid, niobium arsenide (NbAs). Utilizing the combination of soft X-ray and ultraviolet photoemission spectroscopy, we systematically study both the surface and bulk electronic structure of NbAs. We experimentally observe both the Weyl cones in the bulk and the Fermi arcs on the surface of this system. Our ARPES data, in agreement with our theoretical band structure calculations, identify the Weyl semimetal state in NbAs, which provides a real platform to test the potential of Weyltronics. Experiments show that niobium arsenide is a Weyl semimetal.

Strong lithium polysulfide chemisorption on electroactive sites of nitrogen-doped carbon composites for high-performance lithium-sulfur battery cathodes.

Abstract: Despite the high theoretical capacity of lithium–sulfur batteries, their practical applications are severely hindered by a fast capacity decay, stemming from the dissolution and diffusion of lithium polysulfides in the electrolyte. A novel functional carbon composite (carbon-nanotube-interpenetrated mesoporous nitrogen-doped carbon spheres, MNCS/CNT), which can strongly adsorb lithium polysulfides, is now reported to act as a sulfur host. The nitrogen functional groups of this composite enable the effective trapping of lithium polysulfides on electroactive sites within the cathode, leading to a much improved electrochemical performance (1200 mAh g−1 after 200 cycles). The enhancement in adsorption can be attributed to the chemical bonding of lithium ions by nitrogen functional groups in the MNCS/CNT framework. Furthermore, the micrometer-sized spherical structure of the material yields a high areal capacity (ca. 6 mAh cm−2) with a high sulfur loading of approximately 5 mg cm−2, which is ideal for practical applications of the lithium–sulfur batteries.

Minimum Information about a Biosynthetic Gene cluster.

Abstract: A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

The Pierre Auger Cosmic Ray Observatory

Abstract: The Pierre Auger Observatory, located on a vast, high plain in western Argentina, is the world's largest cosmic ray observatory. The objectives of the Observatory are to probe the origin and characteristics of cosmic rays above $10^{17}$ eV and to study the interactions of these, the most energetic particles observed in nature. The Auger design features an array of 1660 water-Cherenkov particle detector stations spread over 3000 km$^2$ overlooked by 24 air fluorescence telescopes. In addition, three high elevation fluorescence telescopes overlook a 23.5 km$^2$, 61 detector infill array. The Observatory has been in successful operation since completion in 2008 and has recorded data from an exposure exceeding 40,000 km$^2$ sr yr. This paper describes the design and performance of the detectors, related subsystems and infrastructure that make up the Auger Observatory.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Abstract: A multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics, determines the phylogenetic composition of the microbial community and assesses its functional potential and activity along a thaw transition from intact permafrost to thermokast bog. The application of the various individual 'omics' tools to the study of microbial ecosystems has dramatically altered our view of their constituents and ecology over the past decade. Here Janet Jansson and colleagues develop an multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics to analyse microbial gene expression in frozen soils that form part of the Alaska Peatland Experiment. The results show that the community shifts along a natural thaw gradient from permafrost to seasonally thawed active layer to thermokarst bog and the authors find that there is a transition in the potential for several biogeochemical cycles with thaw, including those for denitrification, nitrate reduction, iron reduction and methane oxidation. Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere1. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils2,3,4 and a rapid shift in functional gene composition during short-term thaw experiments3. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales5,6. Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes

Abstract: Viruses are infectious particles that can only multiply inside the cells of microbes and other organisms. Little is known about the genetic differences between virus particles (so-called ‘genetic diversity’), especially compared to what we know about the diversity of bacteria, archaea, and other single-celled microbes. This lack of knowledge hampers our understanding of the role viruses play in the evolution of microbial communities and their associated ecosystems. Studying the genetics of the viruses in these communities is challenging. There is no single ‘marker’ gene that can be used to identify all viruses in environmental samples. Also, many of the fragments of viral genomes that have been identified have not yet been linked to their host microbes. Many viruses integrate their genome into the DNA of their host cell, and there are computational tools available that exploit this ability to identify viruses and link them to their host. However, other viruses can live and multiply inside cells without integrating their genome into the host's DNA. Earlier in 2015, researchers developed a new computational tool called VirSorter that can predict virus genome sequences within the DNA extracted from microbes. VirSorter identifies viral genome sequences based on the presence of ‘hallmark’ genes that encode for components found in many virus particles, together with a reference database of genomes from many viruses. Now, Roux et al.—including some of the researchers from the earlier work—use VirSorter to predict viral DNA from publicly available bacteria and archaea genome data. The study identifies over 12,000 viral genomes and links them to their microbial hosts. These data increase the number of viral genome sequences that are publically available by a factor of ten and identify the first viruses associated with 13 new types of bacteria, which include species that are abundant in particular environments. It is possible for several different viruses to infect a single cell at the same time. Some viruses are known to be able to exchange DNA, and if this happens frequently in other viruses, it could have a big impact on how viruses evolve. Roux et al.'s findings suggest that although it is common for several different viruses to infect the same cell, it is relatively rare for these viruses to exchange genetic material. Roux et al.'s findings demonstrate the value of searching publicly available microbial genome data for fragments of viral genomes. These new viral genomes will serve as a useful resource for researchers as they explore the communities of viruses and microbes in natural environments, the human body and in industrial processes.

Cerium: An Unlikely Replacement of Dysprosium in High Performance Nd–Fe–B Permanent Magnets

Abstract: Replacement of Dy and substitution of Nd in NdFeB-based permanent magnets by Ce, the most abundant and lowest cost rare earth element, is important because Dy and Nd are costly and critical rare earth elements. The Ce, Co co-doped alloys have excellent high-temperature magnetic properties with an intrinsic coercivity being the highest known for T ≥ 453 K.

Programmable self-assembly

Abstract: Two conceptual strategies for encoding information into self-assembling building blocks highlight opportunities and challenges in the realization of programmable colloidal nanostructures.

Fabrication of MMMs with improved gas separation properties using externally-functionalized MOF particles

Abstract: Mixed matrix membranes (MMM) have the potential to overcome the limitations of traditional polymeric membranes for gas separation by improving both the permeability and selectivity. The most difficult challenge is accessing defect free and optimized MMM membranes. Defects are generally due to incompatible interfaces between the polymer and the filler particle. Herein, we present a new approach to modify and optimize the surface of UiO-66-NH2 based MOF particles to improve its interaction with Matrimid® polymer. A series of surface modified UiO-66-NH2 particles were synthesized and characterized using 1H NMR spectroscopy, mass spectrometry, XPS, and powder X-ray diffraction. MMMs containing surface optimized MOF particles exhibit improved thermal and mechanical properties. Most importantly, the MMMs show significantly enhanced gas separation properties; CO2 permeability was increased by ∼200% and CO2/N2 ideal selectivity was increased by ∼25%. These results confirm the success of the proposed technique to mitigate defective MOF/Matrimid® interfaces.

Additive loss-of-function proteasome subunit mutations in CANDLE/PRAAS patients promote type I IFN production

Abstract: Autosomal recessive mutations in proteasome subunit β 8 (PSMB8), which encodes the inducible proteasome subunit β5i, cause the immune-dysregulatory disease chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE), which is classified as a proteasome-associated autoinflammatory syndrome (PRAAS). Here, we identified 8 mutations in 4 proteasome genes, PSMA3 (encodes α7), PSMB4 (encodes β7), PSMB9 (encodes β1i), and proteasome maturation protein (POMP), that have not been previously associated with disease and 1 mutation in PSMB8 that has not been previously reported. One patient was compound heterozygous for PSMB4 mutations, 6 patients from 4 families were heterozygous for a missense mutation in 1 inducible proteasome subunit and a mutation in a constitutive proteasome subunit, and 1 patient was heterozygous for a POMP mutation, thus establishing a digenic and autosomal dominant inheritance pattern of PRAAS. Function evaluation revealed that these mutations variably affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. Moreover, defects in proteasome formation and function were recapitulated by siRNA-mediated knockdown of the respective subunits in primary fibroblasts from healthy individuals. Patient-isolated hematopoietic and nonhematopoietic cells exhibited a strong IFN gene-expression signature, irrespective of genotype. Additionally, chemical proteasome inhibition or progressive depletion of proteasome subunit gene transcription with siRNA induced transcription of type I IFN genes in healthy control cells. Our results provide further insight into CANDLE genetics and link global proteasome dysfunction to increased type I IFN production.

Direct Measurement of Polysulfide Shuttle Current: A Window into Understanding the Performance of Lithium-Sulfur Cells

Abstract: The shuttling of polysulfide ions between the electrodes in a lithium-sulfur battery is a major technical issue limiting the self-discharge and cycle life of this high-energy rechargeable battery. Although there have been attempts to suppress the shuttling process, there has not been a direct measurement of the rate of shuttling. We report here a simple and direct measurement of the rate of the shuttling (that we term “shuttle current”), applicable to the study of any type of lithium-sulfur cell. We demonstrate the effectiveness of this measurement technique using cells with and without lithium nitrate (a widely-used shuttle suppressor additive). We present a phenomenological analysis of the shuttling process and simulate the shuttle currents as a function of the state-of-charge of a cell. We also demonstrate how the rate of decay of the shuttle current can be used to predict the capacity fade in a lithium-sulfur cell due to the shuttle process. As a result, we expect that this new ability to directly measure shuttle currents will provide greater insight into the performance differences observed with various additives and electrode modifications that are aimed at suppressing the rate of shuttling of polysulfide ions and increasing the cycle life of lithium-sulfur cells.

Hemichordate genomes and deuterostome origins

Abstract: Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world.

Abstract: Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.

Efficient Electrochemical CO2 Conversion Powered by Renewable Energy

Abstract: The catalytic conversion of CO2 into industrially relevant chemicals is one strategy for mitigating greenhouse gas emissions. Along these lines, electrochemical CO2 conversion technologies are attractive because they can operate with high reaction rates at ambient conditions. However, electrochemical systems require electricity, and CO2 conversion processes must integrate with carbon-free, renewable-energy sources to be viable on larger scales. We utilize Au25 nanoclusters as renewably powered CO2 conversion electrocatalysts with CO2 → CO reaction rates between 400 and 800 L of CO2 per gram of catalytic metal per hour and product selectivities between 80 and 95%. These performance metrics correspond to conversion rates approaching 0.8–1.6 kg of CO2 per gram of catalytic metal per hour. We also present data showing CO2 conversion rates and product selectivity strongly depend on catalyst loading. Optimized systems demonstrate stable operation and reaction turnover numbers (TONs) approaching 6 × 106 molCO2 m...

A More Resilient Grid: The U.S. Department of Energy Joins with Stakeholders in an R&D Plan

Abstract: ELECTRIC DISTRIBUTION GRID RESEARCH AND DEVELOPment (RD however, this focus has primarily been outside the realm of severe climate events. Due to the increasing frequency and intensity of weather-caused grid outages in recent years, the U.S. Department of Energy (DOE) has placed an added emphasis on R&D to enhance resilience to climate change and extreme weather. To forge a focused national R&D effort on grid resilience, the DOE is adopting a public/private partnership approach to join with key stakeholders in developing and implementing a resilient grid R&D plan. This article presents the plan development process and the R&D need areas identified for pursuit.

Multifunctional Cyanate Ester Nanocomposites Reinforced by Hexagonal Boron Nitride after Noncovalent Biomimetic Functionalization

Abstract: Boron nitride (BN) reinforced polymer nanocomposites have attracted a growing research interest in the microelectronic industry for their uniquely thermal conductive but electrical insulating properties. To overcome the challenges in surface functionalization, in this study, hexagonal boron nitride (h-BN) nanoparticles were noncovalently modified with polydopamine in a solvent-free aqueous condition. The strong π–π interaction between the hexagonal structural BN and aromatic dopamine molecules facilitated 15 wt % polydopamine encapsulating the nanoparticles. High-performance bisphenol E cyanate ester (BECy) was incorporated by homogeneously dispersed h-BN at different loadings and functionalities to investigate their effects on thermo-mechanical, dynamic-mechanical, and dielectric properties, as well as thermal conductivity. Different theoretical and empirical models were successfully applied to predict thermal and dielectric properties of h-BN/BECy nanocomposites. Overall, the prepared h-BN/BECy nanocomp...

Engineering Light Outcoupling in 2D Materials

Abstract: When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs a...

Controlled Anisotropic Growth of Co‐Fe‐P from Co‐Fe‐O Nanoparticles

Abstract: A facile approach to bimetallic phosphides, Co-Fe-P, by a high-temperature (300 °C) reaction between Co-Fe-O nanoparticles and trioctylphosphine is presented. The growth of Co-Fe-P from the Co-Fe-O is anisotropic. As a result, Co-Fe-P nanorods (from the polyhedral Co-Fe-O nanoparticles) and sea-urchin-like Co-Fe-P (from the cubic Co-Fe-O nanoparticles) are synthesized with both the nanorod and the sea-urchin-arm dimensions controlled by Co/Fe ratios. The Co-Fe-P structure, especially the sea-urchin-like (Co0.54Fe0.46)2P, shows enhanced catalysis for the oxygen evolution reaction in KOH with its catalytic efficiency surpassing the commercial Ir catalyst. Our synthesis is simple and may be readily extended to the preparation of other multimetallic phosphides for important catalysis and energy storage applications.

Oxidation of CoCrFeMnNi High Entropy Alloys

Abstract: Eight model high entropy alloys (HEAs) in the CoCrFeMnNi family (including one alloy each in the CoCrFeNi and CoFeMnNi subfamilies) were made, prepared, and exposed to laboratory air for 1100 h at 650°C and 750°C. Two commercial alloys, nickel-base superalloy 230 (N06230) and austenitic stainless steel 304H (S30409), were simultaneously exposed for comparison. Mass change oxidation kinetics were measured and cross-sections of exposed samples were observed. Seven of these HEAs contained much more Mn (12–24 wt.%) than is found in commercial heat-resistant stainless steels and superalloys. The oxidation resistance of CoCrFeNi was excellent and comparable to 304H at 650°C and only slightly worse at 750°C. The thin oxide scale on CoCrFeNi was primarily Cr oxide (presumably Cr2O3) with some Mn oxide at the outer part of the scale. The CoCrFeMnNi HEAs all experienced more rapid oxidation than CoCrFeNi and, especially at 750°C, experienced oxide scale spallation. The addition of Y in the alloy to lower S improved the oxidation resistance of these HEAs. Alloy CoFeMnNi, without Cr, experienced much higher oxidation rates and scale spallation than the Cr-containing alloys. A linear regression analysis of the log of the parabolic rate constant, log(kp), as functions of wt.% Cr and Mn found a good correlation for the compositional dependence of the oxidation rate constant, especially at 650°C. Mn was found to be more detrimental increasing log(k p) than Cr was helpful reducing log(k p). If CoCrFeMnNi HEAs are to be used in high temperature oxidizing environments, then examining lower levels of Mn, while maintaining Cr levels, should be pursued.

Tuning the Magic Size of Atomically Precise Gold Nanoclusters via Isomeric Methylbenzenethiols.

Abstract: Toward controlling the magic sizes of atomically precise gold nanoclusters, herein we have devised a new strategy by exploring the para-, meta-, ortho-methylbenzenethiol (MBT) for successful preparation of pure Au130(p-MBT)50, Au104(m-MBT)41 and Au40(o-MBT)24 nanoclusters. The decreasing size sequence is in line with the increasing hindrance of the methyl group to the interfacial Au–S bond. That the subtle change of ligand structure can result in drastically different magic sizes under otherwise similar reaction conditions is indeed for the first time observed in the synthesis of thiolate-protected gold nanoclusters. These nanoclusters are highly stable as they are synthesized under harsh size-focusing conditions at 80–90 °C in the presence of excess thiol and air (i.e., without exclusion of oxygen).