64 research outputs found
Common principles and best practices for engineering microbiomes
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps
hinder their efficient use for addressing urgent societal and environmental challenges. We argue
hat structuring research and technology developments around a design-build-test-learn (DBTL)
cycle will advance microbiome engineering and spur new discoveries on the basic scientific
principles governing microbiome function. In this Review, we present key elements of an
iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches,
including top-down and bottom-up design processes, synthetic and self-assembled construction
methods, and emerging tools to analyze microbiome function. These approaches can be used to
harness microbiomes for broad applications related to medicine, agriculture, energy, and the
environment. We also discuss key challenges and opportunities of each approach and synthesize
them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a
DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving
human and animal health, agriculture, and enabling the bioeconomy
Molecular dynamics study of melting of a bcc metal-vanadium II : thermodynamic melting
We present molecular dynamics simulations of the thermodynamic melting
transition of a bcc metal, vanadium using the Finnis-Sinclair potential. We
studied the structural, transport and energetic properties of slabs made of 27
atomic layers with a free surface. We investigated premelting phenomena at the
low-index surfaces of vanadium; V(111), V(001), and V(011), finding that as the
temperature increases, the V(111) surface disorders first, then the V(100)
surface, while the V(110) surface remains stable up to the melting temperature.
Also, as the temperature increases, the disorder spreads from the surface layer
into the bulk, establishing a thin quasiliquid film in the surface region. We
conclude that the hierarchy of premelting phenomena is inversely proportional
to the surface atomic density, being most pronounced for the V(111) surface
which has the lowest surface density
Exchange and the Coulomb blockade: Peak height statistics in quantum dots
We study the effect of the exchange interaction on the Coulomb blockade peak
height statistics in chaotic quantum dots. Because exchange reduces the level
repulsion in the many body spectrum, it strongly affects the fluctuations of
the peak conductance at finite temperature. We find that including exchange
substantially improves the description of the experimental data. Moreover, it
provides further evidence of the presence of high spin states (S>1) in such
systems.Comment: 5 pages, 4 figures. Published version, title change
Experimentally validated reconstruction and analysis of a genome-scale metabolic model of an anaerobic Neocallimastigomycota fungus
Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi
Time-integrated luminosity recorded by the BABAR detector at the PEP-II e+e- collider
This article is the Preprint version of the final published artcile which can be accessed at the link below.We describe a measurement of the time-integrated luminosity of the data collected by the BABAR experiment at the PEP-II asymmetric-energy e+e- collider at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and in a continuum region below each resonance. We measure the time-integrated luminosity by counting e+e-→e+e- and (for the ϒ(4S) only) e+e-→μ+μ- candidate events, allowing additional photons in the final state. We use data-corrected simulation to determine the cross-sections and reconstruction efficiencies for these processes, as well as the major backgrounds. Due to the large cross-sections of e+e-→e+e- and e+e-→μ+μ-, the statistical uncertainties of the measurement are substantially smaller than the systematic uncertainties. The dominant systematic uncertainties are due to observed differences between data and simulation, as well as uncertainties on the cross-sections. For data collected on the ϒ(3S) and ϒ(2S) resonances, an additional uncertainty arises due to ϒ→e+e-X background. For data collected off the ϒ resonances, we estimate an additional uncertainty due to time dependent efficiency variations, which can affect the short off-resonance runs. The relative uncertainties on the luminosities of the on-resonance (off-resonance) samples are 0.43% (0.43%) for the ϒ(4S), 0.58% (0.72%) for the ϒ(3S), and 0.68% (0.88%) for the ϒ(2S).This work is supported by the US Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat à l’Energie Atomique and Institut National de Physique Nucléaire et de Physiquedes Particules (France), the Bundesministerium für Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (The Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Ciencia e Innovación (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A.P. Sloan Foundation (USA)
Observation of the baryonic decay B \uaf 0 \u2192 \u39bc+ p \uaf K-K+
We report the observation of the baryonic decay B\uaf0\u2192\u39bc+p\uafK-K+ using a data sample of 471
7106 BB\uaf pairs produced in e+e- annihilations at s=10.58GeV. This data sample was recorded with the BABAR detector at the PEP-II storage ring at SLAC. We find B(B\uaf0\u2192\u39bc+p\uafK-K+)=(2.5\ub10.4(stat)\ub10.2(syst)\ub10.6B(\u39bc+))
710-5, where the uncertainties are statistical, systematic, and due to the uncertainty of the \u39bc+\u2192pK-\u3c0+ branching fraction, respectively. The result has a significance corresponding to 5.0 standard deviations, including all uncertainties. For the resonant decay B\uaf0\u2192\u39bc+p\uaf\u3c6, we determine the upper limit B(B\uaf0\u2192\u39bc+p\uaf\u3c6)<1.2
710-5 at 90% confidence level
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