8 research outputs found

    The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

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    The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

    Protein production in Saccharomyces cerevisiae for systems biology studies

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    Proteins together with metabolites, nucleic acids, lipids, and other intracellular molecules form biological systems that involve networks of functional and physical interactions. To understand these interactions and the many other characteristics of proteins in the context of biochemical networks and systems biology, research aimed at studying medium and large sets of proteins is required. This either involves an investigation focused on individual protein activities in the mixture (e.g., cell extracts) or a protein characterization in the isolated form. This chapter provides an overview on the currently available resources and strategies for isolation of proteins from Saccharomyces cerevisiae. The use of standardized gene expression systems is discussed, and protein production protocols applied to the data generation pipeline for systems biology are described in detail

    Thermal Variation of Structure and Electrical Conductivity in Bi<sub>4</sub>YbO<sub>7.5</sub>

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    The thermal behavior of the oxide ion-conducting solid electrolyte Bi<sub>4</sub>YbO<sub>7.5</sub> was investigated using a combination of variable temperature X-ray and neutron powder diffraction, thermal analysis (DTA and TGA), and ac impedance spectroscopy. The title compound shows a fluorite-type structure throughout the measured temperature range (20–850 °C), with a phase separation at ca. 600 °C into a cubic δ-type phase and an orthorhombic phase of assumed stoichiometry Bi<sub>17</sub>Yb<sub>7</sub>O<sub>36</sub>. This type of transition is a relatively common feature in bismuth oxide-based systems and can limit their practical application. Here, the transition was carefully studied using isothermal measurements, which showed that it is accompanied by changes in oxide-ion stoichiometry, as well as significant disorder in the oxide ion sublattice in the δ-type phase. These results correlate with the observed electrical behavior. Analysis of the total neutron scattering through reverse Monte Carlo (RMC) modeling reveals details of the coordination environments for both cations. The oxide-ion vacancy distribution seems to be consistent with a favoring of ⟨100⟩ vacancy pairs, although ⟨110⟩ vacancy pairs exhibit the highest frequency as they have the maximum likelihood. A vacancy ordering model based on three vacancies per cell is presented

    Absolute quantification of the glycolytic pathway in yeast : deployment of a complete qconCAT approach

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    The availability of label-free data derived from yeast cells (based on the summed intensity of the three strongest, isoform-specific peptides) permitted a preliminary assessment of protein abundances for glycolytic proteins. Following this analysis, we demonstrate successful application of the QconCAT technology, which uses recombinant DNA techniques to generate artificial concatamers of large numbers of internal standard peptides, to the quantification of enzymes of the glycolysis pathway in the yeast Saccharomyces cerevisiae. A QconCAT of 88 kDa (59 tryptic peptides) corresponding to 27 isoenzymes was designed and built to encode two or three analyte peptides per protein, and after stable isotope labeling of the standard in vivo, protein levels were determined by LCMS, using ultra high performance liquid chromatographycoupled mass spectrometry. We were able to determine absolute protein concentrations between 14,000 and 10 million molecules/cell. Issues such as efficiency of extraction and completeness of proteolysis are addressed, as well as generic factors such as optimal quantotypic peptide selection and expression. In addition, the same proteins were quantified by intensity-based label-free analysis, and both sets of data were compared with other quantification methods

    A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

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    We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a ‘‘cycle of knowledge’’ strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought
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