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  1. Abstract Chemical warfare agents (CWAs) are unarguably one of the most feared toxic substances produced by mankind. Their inception in conventional warfare can be traced as far back as the Middle Ages but their full breakthrough as central players in bellic conflicts was not realized until World War I. Since then, more modern CWAs along with efficient methods for their manufacture have emerged and violently shaped the way modern warfare and diplomatic relations are conducted. Owing to their mass destruction ability, counter methods to mitigate their impact appeared almost immediately on par with their development. These efforts have focused onmore » their efficient destruction, development of medical countermeasures and their detection by modern analytical chemistry methods. The following review seeks to provide the reader with a broad introduction on their direct detection by gas chromatography-mass spectrometry (GC-MS) and the various sample derivatization methods available for the analysis of their degradation products. The review concentrates on three of the main CWA classes and includes the nerve agents, the blistering agents and lastly, the incapacitating agents. Each section begins with a brief introduction of the CWA along with discussions of reports dealing with their detection in the intact form by GC-MS. Furthermore, as products arising from their degradation carry as much importance as the agents themselves in the field of forensic analysis, the available derivatization methods of these species are presented for each CWA highlighting some examples from our lab in the Forensic Science Center at the Lawrence Livermore National Laboratory.« less
  2. Background Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota.more » We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. Results The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes ( p  < 0.01) and fewer Proteobacteria ( p  < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g.  Neisseria , Gemella , Rothia , Actinomyces , Fusobacterium , and Leptotrichia , were more abundant in mothers than in infants. Conclusions Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.« less
  3. BackgroundViral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we usedin silicomock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. ResultsTools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, andmore » IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. ConclusionsThese simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.« less
  4. ABSTRACT A recent surprising discovery of the activity of rare earth metals (lanthanides) as enzyme cofactors as well as transcriptional regulators has overturned the traditional assumption of biological inertia of these metals. However, so far, examples of such activities have been limited to alcohol dehydrogenases. Here we describe the physiological effects of a mutation in xoxG , a gene encoding a novel cytochrome, XoxG(4), and compare these to the effects of mutation in XoxF, a lanthanide-dependent methanol dehydrogenase, at the enzyme activity level and also at the community function level, using Methylomonas sp. strain LW13 as a model organism. Throughmore » comparative phenotypic characterization, we establish XoxG as the second protein directly involved in lanthanide-dependent metabolism, likely as a dedicated electron acceptor from XoxF. However, mutation in XoxG caused a phenotype that was dramatically different from the phenotype of the mutant in XoxF, suggesting a secondary function for this cytochrome, in metabolism of methane. We also purify XoxG(4) and demonstrate that this protein is a true cytochrome c , based on the typical absorption spectra, and we demonstrate that XoxG can be directly reduced by a purified XoxF, supporting one of its proposed physiological functions. Overall, our data continue to suggest the complex nature of the interplay between the calcium-dependent and lanthanide-dependent alcohol oxidation systems, while they also suggest that addressing the roles of these alternative systems is essential at the enzyme and community function level, in addition to the gene transcription level. IMPORTANCE The lanthanide-dependent biochemistry of living organisms remains a barely tapped area of knowledge. So far, only a handful of lanthanide-dependent alcohol dehydrogenases have been described, and their regulation by lanthanides has been demonstrated at the transcription level. Little information is available regarding the concentrations of lanthanides that could support sufficient enzymatic activities to support specific metabolisms, and so far, no other redox proteins involved in lanthanide-dependent methanotrophy have been demonstrated. The research presented here provides enzyme activity-level data on lanthanide-dependent methanotrophy in a model methanotroph. Additionally, we identify a second protein important for lanthanide-dependent metabolism in this organism, XoxG(4), a novel cytochrome. XoxG(4) appears to have multiple functions in methanotrophy, one function as an electron acceptor from XoxF and another function remaining unknown. On the basis of the dramatic phenotype of the XoxG(4) mutant, this function must be crucial for methanotrophy.« less
  5. ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.
  6. The emergence of superconductivity upon progressively suppressing the long-range, charge-density-wave (CDW) order characterizes the phase diagram of several materials of interest in the on-going solid-state physics research. Se-doped ZrTe 3 compounds provide the most recent, suitable arena in order to investigate the interplay of otherwise competing orders in layeredlike two-dimensional systems. We present an optical study of the CDW state in ZrTe 3-xSe x at selected Se dopings, based on the measurement of the reflectivity from the far-infrared up to the ultraviolet, as a function of temperature. We particularly focus our attention to the redistribution of the spectral weight, whichmore » images the impact of the CDW state within the optical conductivity across the phase diagram of the title compounds. The electrodynamic response is consistent with a scenario based on a long-range CDW condensate at low Se doping. Upon increasing the Se content, this then gives way to local, short-range order CDW segments. Thus, our spectral weight analysis reveals the presence of a pseudogap phase, as fingerprint of the CDW precursor effects and thus shaping the charge dynamics of the title compounds in their normal state, preceding the onset of superconductivity.« less
  7. Geoscientific models manage myriad and increasingly complex data structures as trans-disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd. We show real-world examples including data structuremore » self-assembly, effortless save/restart and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. In conclusion, embracing emulated reflection allows generically-written codes that are highly re-usable across projects.« less
  8. Abstract This study applies atom probe tomography (APT) to analyze the oxide scales formed on model NiAlCr alloys doped with Hf, Y, Ti, and B. Due to its ability to measure small amounts of alloying elements in the oxide matrix and its ability to quantify segregation, t he technique offers a possibility for detailed studies of the dopant’s fate during high-temperature oxidation. Three model NiAlCr alloys with different additions of Hf, Y, Ti, and B were prepared and oxidized in O 2at 1,100°C for 100 h. All specimens showed an outer region consisting of different spinel oxides with relativelymore » small grains and the protective Al 2O 3-oxide layer below. APT analyses focused mainly on this protective oxide layer. In all the investigated samples segregation of both Hf and Y to the oxide grain boundaries was observed and quantified. Neither B nor Ti were observed in the alumina grains or at the analyzed interfaces. The processes of formation of oxide scales and segregation of the alloying elements are discussed. The experimental challenges of the oxide analyses by APT are also addressed.« less
  9. Abstract
  10. Abstract The convection-enhanced paradigm behind core-collapse supernovae (SNe) invokes a multi-physics model where convection above the proto-neutron star is able to convert the energy released in the collapse to produce the violent explosions observed as SNe. Over the past decade, the evidence in support of this engine has grown, including constraints placed by SN neutrinos, energies, progenitors and remnants. Although considerable theoretical work remains to utilize this data, our understanding of normal SNe is advancing. To achieve a deeper level of understanding, we must find ways to compare detailed simulations with the increasing set of observational data. Here we reviewmore » the current constraints and how we can apply our current understanding to broaden our understanding of these powerful engines.« less

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