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Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography

Description: New software tools are introduced to facilitate diffraction experiments involving largenumbers of crystals. While existing programs have long provided a framework for lattice indexing, Bragg spot integration, and symmetry determination, these initial data processing steps often require significant manual effort. This limits the timely availability of data analysis needed for high-throughput procedures, including the selection of the best crystals from a large sample pool, and the calculation of… more
Date: October 10, 2007
Creator: Gonzalez, Ana; Gonzalez, Ana; Moorhead, Penjit; McPhillips, Scott E.; Song, Jinhu; Sharp, Ken et al.
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Partner: UNT Libraries Government Documents Department
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Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

Description: BackgroundIncreasing energy costs and environmental concerns have motivated engineering microbes for the production of ?second generation? biofuels that have better properties than ethanol.Results& ConclusionsSaccharomyces cerevisiae was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number of different organisms (S. cerevisiae, Escherichia coli, Clostridium beijerinckii, and Ralstonia eutropha) were substituted for the Clostridial enzymes and their effect on n-… more
Date: November 25, 2008
Creator: Steen, EricJ.; Chan, Rossana; Prasad, Nilu; Myers, Samuel; Petzold, Christopher; Redding, Alyssa et al.
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Partner: UNT Libraries Government Documents Department
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Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

Description: {sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed… more
Date: June 27, 2008
Creator: Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila & Keasling, Jay D.
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Partner: UNT Libraries Government Documents Department

Discovering and validating biological hypotheses from coherent patterns in functional genomics data

Description: The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data… more
Date: August 12, 2008
Creator: Joachimiak, Marcin Pawel
Item Type: Refine your search to only Presentation
Partner: UNT Libraries Government Documents Department
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Zeaxanthin Radical Cation Formation in Minor Light-Harvesting Complexes of Higher Plant Antenna

Description: Previous work on intact thylakoid membranes showed that transient formation of a zeaxanthin radical cation was correlated with regulation of photosynthetic light-harvesting via energy-dependent quenching. A molecular mechanism for such quenching was proposed to involve charge transfer within a chlorophyll-zeaxanthin heterodimer. Using near infrared (880-1100 nm) transient absorption spectroscopy, we demonstrate that carotenoid (mainly zeaxanthin) radical cation generation occurs solely in isola… more
Date: January 31, 2008
Creator: Avenson, Thomas H.; Ahn, Tae Kyu; Zigmantas, Donatas; Niyogi, Krishna K.; Li, Zhirong; Ballottari, Matteo et al.
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Partner: UNT Libraries Government Documents Department
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Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster from X-ray Spectroscopy

Description: Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria iscatalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes pola… more
Date: October 24, 2007
Creator: Yano, Junko; Yano, Junko & Yachandra, Vittal K.
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Partner: UNT Libraries Government Documents Department
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In-situ Spectroscopy of Water Oxidation at Ir Oxide Nanocluster Drivenby Visible TiOCr Charge-Transfer Chromophore in Mesoporous Silica

Description: An all-inorganic photocatalytic unit consisting of a binuclear TiOCr charge-transfer chromophore coupled to an Ir oxide nanocluster has been assembled on the pore surface of mesoporous silica AlMCM-41. In situ FT-Raman and EPR spectroscopy of an aqueous suspension of the resulting IrxOy-TiCr-AlMCM-41 powder reveal the formation of superoxide species when exciting the Ti(IV)OCr(III) --> Ti(III)OCr(IV) metal-to-metal charge-transfer chromophore with visible light. Use of H218O confirms that th… more
Date: June 3, 2008
Creator: Frei, Heinz; Han, Hongxian & Frei, Heinz
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Partner: UNT Libraries Government Documents Department
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Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Description: Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide… more
Date: September 2, 2007
Creator: Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol et al.
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Partner: UNT Libraries Government Documents Department
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Membrane proteomics of phagosomes suggests a connection to autophagy

Description: Phagocytosis is the central process by which macrophage cellsinternalize and eliminate infectious microbes as well as apoptoticcells. During maturation, phagosomes containing engulfed particlesfuse with various endosomal compartments through theaction of regulatory molecules on the phagosomal membrane. Inthis study, we performed a proteomic analysis of the membranefraction from latex bead-containing (LBC) phagosomes isolatedfrom macrophages. The profile, which comprised 546 proteins,suggests di… more
Date: November 25, 2008
Creator: Shui, Wenqing; Sheu, Leslie; Liu, Jun; Smart, Brian; Petzold, Christopher J.; Hsieh, Tsung-yen et al.
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Partner: UNT Libraries Government Documents Department

Application of Proteomics and Lipid Studies in Environmental Biotechnology

Description: The overview of changes in protein levels or states in response to a growth condition, stress, mutation or metabolic engineering is invaluable in understanding the physiology of a microbial system. The lipid profile of the cell is similarly a valuable diagnostic of the cellular response and health, especially in context of survival in a fluctuating environment. To obtain comprehensive cellular models, post-transcriptional cell wide surveys at the levels of proteins and lipids are required. Both… more
Date: August 12, 2008
Creator: Mukhopadhyay, Aindrila
Item Type: Refine your search to only Presentation
Partner: UNT Libraries Government Documents Department
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ARCHITECTURE OF A CHARGE-TRANSFER STATE REGULATING LIGHT HARVESTING IN A PLANT ANTENNA PROTEIN

Description: Energy-dependent quenching of excess absorbed light energy (qE) is a vital mechanism for regulating photosynthetic light harvesting in higher plants. All of the physiological characteristics of qE have been positively correlated with charge-transfer between coupled chlorophyll and zeaxanthin molecules in the light-harvesting antenna of photosystem II (PSII). In this work, we present evidence for charge-transfer quenching in all three of the individual minor antenna complexes of PSII (CP29, CP26… more
Date: April 2, 2008
Creator: Fleming, Graham; Ahn, Tae Kyu; Avenson, Thomas J.; Ballottari, Matteo; Cheng, Yuan-Chung; Niyogi, Krishna K. et al.
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Partner: UNT Libraries Government Documents Department
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Direct Observation of the Kinetically Relevant Site of CO Hydrogenation on Supported Ru Catalyst at 700 K by Time-Resolved FT-IR Spectroscopy

Description: Time-resolved FT-IR spectra of carbon monoxide hydrogenation over alumina-supported ruthenium particles were recorded on themillisecond time scale at 700 K using pulsed release of CO and a continuous flow of H2/N2 (ratio 0.067 or 0.15, 1 atm total pressure). Adsorbed carbon monoxide was detected along with gas phase products methane (3016 and 1306 cm-1), water (1900 +- 1300 cm-1), and carbon dioxide (2348 cm-1). Aside from adsorbed CO, no other surface species were observed. The rate of formati… more
Date: June 4, 2008
Creator: Frei, Heinz; Wasylenko, Walter & Frei, Heinz
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Partner: UNT Libraries Government Documents Department

Information Dashboards

Description: "A dashboard is a visual interface that provides at-a-glance views into key measures relevant to a particular objective or business process." Key Attributes: Graphical to focus attention on key trends, comparisons and exceptions, Display only relevant data, Inherently contain predefined conclusions. Note: Collecting user requirements is KEYfrom'Excel 2007 Dashboards& Reports for Dummies' by Michael Alexander
Date: April 11, 2008
Creator: Shutkin, Amy; Shutkin, Amy & Shutkin, Amy
Item Type: Refine your search to only Presentation
Partner: UNT Libraries Government Documents Department
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High-Resolution Structure of the Photosynthetic Mn4Ca Catalyst from X-ray Spectroscopy

Description: The application of high-resolution X-ray spectroscopy methods to study the photosynthetic water oxidizing complex, which contains a unique hetero-nuclear catalytic Mn4Ca cluster, are described. Issues of X-ray damage especially at the metal sites in the Mn4Ca cluster are discussed. The structure of the Mn4Ca catalyst at high-resolution which has so far eluded attempts of determination by X-ray diffraction, EXAFS and other spectroscopic techniques has been addressed using polarized EXAFS techniq… more
Date: August 1, 2007
Creator: Yachandra, Vittal; Yano, Junko; Kern, Jan; Pushkar, Yulia; Sauer, Kenneth; Glatzel, Pieter et al.
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Partner: UNT Libraries Government Documents Department
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Visualization of Excitonic Structure in the Fenna-Matthews-OlsonPhotosynthetic Complex by Polarization-Dependent Two-DimensionalElectronic Spectroscopy

Description: Photosynthetic light-harvesting proceeds by the collection and highly efficient transfer of energy through a network of pigment-protein complexes. Inter-chromophore electronic couplings and interactions between pigments and the surrounding protein determine energy levels of excitonic states and dictate the mechanism of energy flow. The excitonic structure (orientation of excitonic transition dipoles) of pigment-protein complexes is generally deduced indirectly from x-ray crystallography in comb… more
Date: May 26, 2008
Creator: Department of Chemistry, The University of Chicago; Department of Biology, Department of Chemistry, Washington University; Fleming, Graham; Read, Elizabeth L.; Schlau-Cohen, Gabriela S.; Engel, Gregory S. et al.
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Partner: UNT Libraries Government Documents Department
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Focussing the view on Nature's water-splitting catalyst

Description: About 3 billion years ago Nature invented a catalyst that splits water with highefficiency into molecular oxygen and hydrogen equivalents (protons and electrons). This reaction is energetically driven by sun light and the active centre contains relatively cheap and abundant metals: manganese and calcium. This biological system therefore forms the paradigm for all man made attempts for direct solar fuel production and several studies are underway to determine the electronic and geometric structu… more
Date: January 1, 2008
Creator: Messinger, Johannes & Yano, Junko
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Partner: UNT Libraries Government Documents Department
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Structural Genomics of Minimal Organisms: Pipeline and Results

Description: The initial objective of the Berkeley Structural Genomics Center was to obtain a near complete three-dimensional (3D) structural information of all soluble proteins of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter has fewer than 700 genes. A semiautomated structural genomics pipeline was set up from target selection, cloning, expression, purification, and ultimately structural determination. At the ti… more
Date: September 14, 2007
Creator: Kim, Sung-Hou; Shin, Dong-Hae; Kim, Rosalind; Adams, Paul & Chandonia, John-Marc
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
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Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

Description: A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our f… more
Date: January 20, 2009
Creator: Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David et al.
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Partner: UNT Libraries Government Documents Department
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Spin Spectrometer at the ALS and APS

Description: A spin-resolving photoelectron spectrometer, the"Spin Spectrometer," has been designed and built. It has been utilized at both the Advanced Light Source in Berkeley, CA, and the Advanced Photon Source in Argonne, IL. Technical details and an example of experimental results are presented here.
Date: April 20, 2007
Creator: Laboratory, Lawrence Livermore National; Missouri-Rolla, University of; Technologies, Boyd; Morton, Simon A; Morton, Simon A; Tobin, James G et al.
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Partner: UNT Libraries Government Documents Department
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NMR structure of the N-terminal domain of the replication initiator protein DnaA

Description: DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone ang… more
Date: August 7, 2007
Creator: Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao et al.
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Partner: UNT Libraries Government Documents Department
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Comparing Patterns of Natural Selection Across Species Using Selective Signatures

Description: Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and… more
Date: December 18, 2007
Creator: Alm, Eric J.; Shapiro, B. Jesse & Alm, Eric J.
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Partner: UNT Libraries Government Documents Department
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On the Jarzynski relation for dissipative quantumdynamics

Description: In this note, we will discuss how to compactly express the Jarzynski identity for an open quantum system with dissipative dynamics. In quantum dynamics we must avoid explicitly measuring the work directly, which is tantamount to continuously monitoring the state of the system, and instead measure the heat ?ow from the environment. These measurements can be concisely represented with Hermitian map superoperators, which provide a convenient and compact representations of correlation functions and… more
Date: October 30, 2008
Creator: Crooks, Gavin E
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Partner: UNT Libraries Government Documents Department
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Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis

Description: Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called signal to both standard deviations ratio (SSDR) was developed, and evaluated along with other two methods, signal to standard deviation ratio (SSR), and signal to background ratio (SBR). At a low stringency, the thresholds of … more
Date: March 6, 2008
Creator: Zhou, Jizhong; He, Zhili & Zhou, Jizhong
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Partner: UNT Libraries Government Documents Department
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Far-from-equilibrium measurements of thermodynamic length

Description: Thermodynamic length is a path function that generalizes the notion of length to the surface of thermodynamic states. Here, we show how to measure thermodynamic length in far-from-equilibrium experiments using the work fluctuation relations. For these microscopic systems, it proves necessary to define the thermodynamic length in terms of the Fisher information. Consequently, the thermodynamic length can be directly related to the magnitude of fluctuations about equilibrium. The work fluctuation… more
Date: November 5, 2008
Creator: Feng, Edward H. & Crooks, Gavin E.
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Partner: UNT Libraries Government Documents Department
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