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Documenting the Physical Universe:Preserving the Record of SLAC from 1962 to 2005 (open access)

Documenting the Physical Universe:Preserving the Record of SLAC from 1962 to 2005

Since 1905, Albert Einstein's ''miraculous year'', modern physics has advanced explosively. In 2005, the World Year of Physics, a session at the SAA Annual meeting discusses three institutional initiatives--Einstein's collected papers, an international geophysical program, and a research laboratory--to examine how physics and physicists are documented and how that documentation is being collected, preserved, and used. This paper provides a brief introduction to the research laboratory (SLAC), discusses the origins of the SLAC Archives and History Office, its present-day operations, and the present and future challenges it faces in attempting to preserve an accurate historical record of SLAC's activities.
Date: March 10, 2006
Creator: Deken, Jean Marie
System: The UNT Digital Library
Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions (open access)

Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions

Sulphate-reducing bacteria are anaerobes readily found in oxic-anoxic interfaces. Multiple defence pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that sulphate-reducing bacteria are likely to encounter in natural habitats, and the global transcriptomic response was determined. 307 genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism is up-regulated, involving the [NiFeSe]hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defence response concentrates on damage repair by metal-free enzymes. These data, together with the down regulation of the Fur operon, which restricts the availability of iron, and the lack of response of the PerR operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.
Date: March 12, 2008
Creator: Pereira, Patricia M.; He, Qiang; Xavier, Antonio V.; Zhou, Jizhong; Pereira, Ines A.C. & Louro, Ricardo O.
System: The UNT Digital Library
High-Resolution UV Relay Lens for Particle Size Distribution Measurements Using Holography (open access)

High-Resolution UV Relay Lens for Particle Size Distribution Measurements Using Holography

Shock waves passing through a metal sample can produce ejecta particulates at a metal-vacuum interface. Holography records particle size distributions by using a highpower, short-pulse laser to freeze particle motion. The sizes of the ejecta particles are recorded using an in-line Fraunhofer holography technique. Because the holographic plate would be destroyed in this energetic environment, a high-resolution lens has been designed to relay the interference fringes to a safe environment. Particle sizes within a 12-mm-diameter, 5-mm-thick volume are recorded on holographic film. To achieve resolution down to 0.5 microns, ultraviolet (UV) light (in this case supplied by a tripled Nd:YAG laser) is needed. The design and assembly of a nine-element lens that achieves >2000 lp/mm resolution and operates at f/0.85 will be described. To set up this lens system, a doublet lens is temporarily attached that enables operation with 532-nm (green) light and 1100 lp/mm resolution. Thus, the setup and alignment is performed with green light, but the dynamic recording is done with UV light. During setup, the 532-nm beam provides enough focus shift to accommodate the placement of a resolution pattern outside the ejecta volume; this resolution pattern does not interfere with the calibrated wires and pegs surrounding the …
Date: March 1, 2008
Creator: Malone, Robert M.; Frogget, Brent C.; Kaufman, Morris I.; Tibbits, Aric; Capelle, Gene A.; Grover, Mike et al.
System: The UNT Digital Library
Use of Gene Probes to Assess the Impact and Effectiveness of Aerobic in Situ Bioremediation of Tce (open access)

Use of Gene Probes to Assess the Impact and Effectiveness of Aerobic in Situ Bioremediation of Tce

Gene probe hybridization was used to determine distribution and expression of co-metabolic genes at a contaminated site as it underwent in situ methanotrophic bioremediation of trichloroethylene (TCE). The bioremediation strategies tested included a series of air, air:methane, and air:methane:nutrient pulses of the test plot using horizontal injection wells. During the test period, the levels of TCE reduced drastically in almost all test samples. Sediment core samples (n = 367) taken from 0 m (surface)-43 m depth were probed for gene coding for methanotrophic soluble methane monooxygenase (sMMO) and heterotrophic toluene dioxygenase (TOD), which are known to co-metabolize TCE. The same sediment samples were also probed for genes coding for methanol dehydrogenase (MDH) (catalyzing the oxidation of methanol to formaldehyde) to assess specifically changes in methylotrophic bacterial populations in the site. Gene hybridization results showed that the frequency of detection of sMMO genes were stimulated approximately 250% following 1% methane:air (v/v) injection. Subsequent injection of 4% methane:air (v/v) resulted in an 85% decline probably due to nutrient limitations, since addition of nutrients (gaseous nitrogen and phosphorus) thereafter caused an increase in the frequency of detection of sMMO genes. Detection of TOD genes declined during the process, and eventually they were non-detectable …
Date: March 15, 2009
Creator: Hazen, T. C.; Chakraborty, R.; Fleming, J. M.; Gregory, I. R.; Bowman, J. P.; Jimenez, L. et al.
System: The UNT Digital Library
Security issues at the Department of Energy and records management (open access)

Security issues at the Department of Energy and records management

In order to discuss the connection between security issues within the Department of Energy and records management, the author covers a bit of security history and talks about what she calls ``the Amazing Project''. Initiated in late May 1999, it was to be a tri-laboratory (Lawrence Livermore National Laboratory of Livermore, California, Los Alamos National Laboratory of Los Alamos, New Mexico, and Sandia National Laboratories of Albuquerque, New Mexico, and Livermore, California) project. The team that formed was tasked to develop the best set of security solutions that still enabled weapon mission work to get done and the security solutions were to be the same set for everyone. The amazing project was called ''The Integrated Security Management Project'', or ''ISecM' for short. She'll describe why she thinks this project was so amazing and what it accomplished. There's a bit of sad news about the project, but then she'll move onto discuss what was learned at Sandia as a result of the project and what they're currently doing in records management.
Date: March 13, 2000
Creator: NUSBAUM,ANNA W.
System: The UNT Digital Library
A Newly Discovered 1722 Letter by Fan- and Miniature Painter Louis Goupy (1675? - 1747) (open access)

A Newly Discovered 1722 Letter by Fan- and Miniature Painter Louis Goupy (1675? - 1747)

Article discussing a newly discovered 1722 letter by fan- and miniature painter Louis Goupy (1675-1747).
Date: March 2009
Creator: Kaplan, Marijn S.
System: The UNT Digital Library
[Publicity Articles for Brilliant Magazine] (open access)

[Publicity Articles for Brilliant Magazine]

Press kit containing articles about the launching of Brilliant Magazine by Brilliance Media in Austin, Texas.
Date: 2003-03/2004-01
Creator: unknown
System: The UNT Digital Library
Proposal for a High Energy Nuclear Database (open access)

Proposal for a High Energy Nuclear Database

We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac and AGS to RHIC to CERN-LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.
Date: March 31, 2005
Creator: Brown, David A. & Vogt, Ramona
System: The UNT Digital Library
Proposal for a High Energy Nuclear Database (open access)

Proposal for a High Energy Nuclear Database

The authors propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac, AGS and SPS to RHIC and CERN-LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, they propose periodically performing evaluations of the data and summarizing the results in topical reviews.
Date: March 31, 2005
Creator: Brown, D. A. & Vogt, R.
System: The UNT Digital Library
Integrating Records Management (RM) and Information Technology (IT) (open access)

Integrating Records Management (RM) and Information Technology (IT)

Records Managers are continually exploring ways to integrate their services with those offered by Information Technology-related professions to capitalize on the advantages of providing customers a total solution to managing their records and information. In this day and age, where technology abounds, there often exists a fear on the part of records management that this integration will result in a loss of identity and the focus of one's own mission - a fear that records management may become subordinated to the fast-paced technology fields. They need to remember there is strength in numbers and it benefits RM, IT, and the customer when they can bring together the unique offerings each possess to reach synergy for the benefit of all the corporations. Records Managers, need to continually strive to move ''outside the records management box'', network, expand their knowledge, and influence the IT disciplines to incorporate the concept of ''management'' into their customer solutions.
Date: March 2, 2000
Creator: NUSBAUM,ANNA W. & CUSIMANO,LINDA J.
System: The UNT Digital Library
Migrating birds : assessment of impact on 915-MHz radar wind profiler performance at the Atmospheric Radiation Measurement Program's southern great plains. (open access)

Migrating birds : assessment of impact on 915-MHz radar wind profiler performance at the Atmospheric Radiation Measurement Program's southern great plains.

The U. S. Department of Energy's Atmospheric Radiation Measurement Program is running a small network of 915-MHz radar wind profilers (RWPs) at its Southern Great Plains Cloud and Radiation Testbed site in northern Oklahoma and southern Kansas. Seasonal migration of passerines may cause significant interference with the operation of 915-MHz RWPs. The extent of this ''bird jamming'' depends on the radar's parameters, the place of deployment, the season, and the time of day. This poster presents a new diagnostic method for detecting possible bird contamination in RWP data, along with an evaluation of the method using a three-year data set for two RWPs.
Date: March 13, 2002
Creator: Pekour, M. S.
System: The UNT Digital Library
Renewable Energy Deployment in the Federal Sector: A Status Report (Preprint) (open access)

Renewable Energy Deployment in the Federal Sector: A Status Report (Preprint)

Executive Order 13123 directs Federal agencies to expand their use of renewable energy at Federal facilities. It also requires the Secretary of Energy to develop goals for the amount of energy generated from renewable resources-such as solar, wind, and biomass-that will be used at those facilities by a certain year. This paper lists key provisions of the Executive Order dealing with renewable energy. It also describes (1) the Federal sector's extensive prior experience with renewable resources and energy systems, and (2) progress up to date (Spring 2000) in meeting the goals of the Executive Order. This progress included a Federal Working Group tasked with developing goals and guidelines for Federal use of renewable energy systems. The next step was to submit a draft goal and plan to the Secretary of Energy for approval and implementation among Federal agencies.
Date: March 1, 2000
Creator: Carlisle, N.
System: The UNT Digital Library
SOFTWARE TOOLS THAT ADDRESS HAZARDOUS MATERIAL ISSUES DURING NUCLEAR FACILITY D and D (open access)

SOFTWARE TOOLS THAT ADDRESS HAZARDOUS MATERIAL ISSUES DURING NUCLEAR FACILITY D and D

The 49-year-old Chemistry and Metallurgy Research (CMR) Facility is where analytical chemistry and metallurgical studies on samples of plutonium and nuclear materials are conduct in support of the Department of Energy's nuclear weapons program. The CMR Facility is expected to be decontaminated and decommissioned (D and D) over the next ten to twenty years. Over the decades, several hazardous material issues have developed that need to be address. Unstable chemicals must be properly reassigned or disposed of from the workspace during D and D operation. Materials that have critical effects that are primarily chronic in nature, carcinogens, reproductive toxin, and materials that exhibit high chronic toxicity, have unique decontamination requirements, including the decontrolling of areas where these chemicals were used. Certain types of equipment and materials that contain mercury, asbestos, lead, and polychlorinated biphenyls have special provisions that must be addressed. Utilization of commercially available software programs for addressing hazardous material issues during D and D operations such as legacy chemicals and documentation are presented. These user-friendly programs eliminate part of the tediousness associated with the complex requirements of legacy hazardous materials. A key element of this approach is having a program that inventories and tracks all hazardous materials. Without …
Date: March 1, 2001
Creator: COURNOYER, M. & GRUNDEMANN, R.
System: The UNT Digital Library
Specification and implementation of IFC based performance metrics to support building life cycle assessment of hybrid energy systems (open access)

Specification and implementation of IFC based performance metrics to support building life cycle assessment of hybrid energy systems

Minimizing building life cycle energy consumption is becoming of paramount importance. Performance metrics tracking offers a clear and concise manner of relating design intent in a quantitative form. A methodology is discussed for storage and utilization of these performance metrics through an Industry Foundation Classes (IFC) instantiated Building Information Model (BIM). The paper focuses on storage of three sets of performance data from three distinct sources. An example of a performance metrics programming hierarchy is displayed for a heat pump and a solar array. Utilizing the sets of performance data, two discrete performance effectiveness ratios may be computed, thus offering an accurate method of quantitatively assessing building performance.
Date: March 29, 2004
Creator: Morrissey, Elmer; O'Donnell, James; Keane, Marcus & Bazjanac, Vladimir
System: The UNT Digital Library
Motion control design of the SDSS 2.5 mts. telescope (open access)

Motion control design of the SDSS 2.5 mts. telescope

This paper describes the control system analysis and design for the three principal axes of the 2.5 mts SDSS Telescope. The telescope requirements are good tracking performance with errors lower than 165 arcsec rms in the speed range between 0 to 45 arcsec/sec for all the axes. The pointing error is about 2 arcsec rms per axis with a maximum absolute value of 5 arcsec. The telescope has the additional requirements of slewing, between tracking areas, with maximum speed of 3 degree/sec. The dynamical model of the telescope including the friction is analyzed and based on that, the design of a PID controller for each axis is presented. The specifications for pointing and tracking mode are achieved with this design in all the range of velocities and the performance in slew-mode is acceptable. Simulations and experimental results depict the behavior of the telescope in slewing, tracking and pointing.
Date: March 24, 2000
Creator: Rivetta, C.; Briegel, C. & Czarapata, P.
System: The UNT Digital Library
Microbial co-habitation and lateral gene transfer: what transposases can tell us (open access)

Microbial co-habitation and lateral gene transfer: what transposases can tell us

Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with? All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections. We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable …
Date: March 1, 2009
Creator: Hooper, Sean D.; Mavromatis, Konstantinos & Kyrpides, Nikos C.
System: The UNT Digital Library
Reconstruction of mechanically recorded sound by image processing (open access)

Reconstruction of mechanically recorded sound by image processing

Audio information stored in the undulations of grooves in a medium such as a phonograph record may be reconstructed, with no or minimal contact, by measuring the groove shape using precision metrology methods and digital image processing. The effects of damage, wear, and contamination may be compensated, in many cases, through image processing and analysis methods. The speed and data handling capacity of available computing hardware make this approach practical. Various aspects of this approach are discussed. A feasibility test is reported which used a general purpose optical metrology system to study a 50 year old 78 r.p.m. phonograph record. Comparisons are presented with stylus playback of the record and with a digitally re-mastered version of the original magnetic recording. A more extensive implementation of this approach, with dedicated hardware and software, is considered.
Date: March 26, 2003
Creator: Fadeyev, Vitaliy & Haber, Carl
System: The UNT Digital Library
Cross-language search: The case of Google Language Tools (open access)

Cross-language search: The case of Google Language Tools

Article on cross-language searching and a case study of Google Language Tools, especially its cross-language search service.
Date: March 2, 2009
Creator: Chen, Jiangping & Bao, Yu
System: The UNT Digital Library
Molecular stress response in the CNS of mice after systemic exposureto interferon-alpha, ionizing radiation and ketamine (open access)

Molecular stress response in the CNS of mice after systemic exposureto interferon-alpha, ionizing radiation and ketamine

We previously showed that the expression of troponin T1 (Tnnt 1) was induced in the central nervous system (CNS) of adultmice 30 min after treatment with ketamine, a glutamate N-methyl-D-aspartic acid (NMDA) receptor antagonist. We hypothesized that Tnnt 1 expression may be an early molecular biomarker of stress response in the CNS of mice. To further evaluate this hypothesis, we investigated the regional expression of Tnnt 1 in the mouse brain using RNA in situ hybridization 4 h after systemic exposure to interferon-a (IFN-a) and gamma ionizing radiation, both of which have be associated with wide ranges of neuropsychiatric complications. Adult B6C3F1 male mice were treated with either human IFN-a (a single i.p. injection at 1 x 105 IU/kg) or whole body gamma-radiation (10 cGy or 2 Gy). Patterns of Tnnt 1 transcript expression were compared in various CNS regions after IFN-a, radiation and ketamine treatments (previous study). Tnnt 1 expression was consistently induced in pyramidal neurons of cerebral cortex and hippocampus after all treatment regimens including 10 cGy of ionizing radiation. Regional expression of Tnnt 1 was induced in Purkinje cells of cerebellum after ionizing radiation and ketamine treatment; but not after IFN-a treatment. None of the three treatments …
Date: March 3, 2009
Creator: Lowe, Xiu R.; Marchetti, Francesco; Lu, Xiaochen & Wyrobek, Andrew J.
System: The UNT Digital Library
The Impact of Glucuronidation on the Bioactivation and DNA Adduction of the Cooked-Food Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b] pyridine in vivo (open access)

The Impact of Glucuronidation on the Bioactivation and DNA Adduction of the Cooked-Food Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5-b] pyridine in vivo

UDP-glucuronosyltransferases (UGTs) catalyze the glucuronidation of many different chemicals. Glucuronidation is especially important for detoxifying reactive intermediates from metabolic reactions, which otherwise can be biotransformed into highly reactive cytotoxic or carcinogenic species. Detoxification of certain food-borne carcinogenic heterocyclic amines (HAs) is highly dependent on UGT1A-mediated glucuronidation. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), the most mass abundant carcinogenic HA found in well-done cooked meat, is extensively glucuronidated by UGT1A proteins. In humans, CYP1A2 catalyzed N-hydroxylation and subsequent UGT1A-mediated glucuronidation is a dominant pathway in the metabolism of PhIP. Therefore, changes in glucuronidation rates could significantly alter PhIP metabolism. To determine the importance of UGT1A-mediated glucuronidation in the biotransformation of PhIP, UGT1A proficient Wistar and UGT1A deficient Gunn rats were exposed to a single 100 {micro}g/kg oral dose of [{sup 14}C]-PhIP. Urine was collected over 24 h and the PhIP urinary metabolite profiles were compared between the two strains. After the 24 h exposure, livers and colon were removed and analyzed for DNA adduct formation by accelerator mass spectrometry. Wistar rats produced several PhIP and N-hydroxy-PhIP glucuronides that accounted for {approx}25% of the total amount of recovered urinary metabolites. In the Gunn rats, PhIP and N-hydroxy-PhIP glucuronides were reduced by 68-92%, compared to the Wistar rats, …
Date: March 31, 2005
Creator: Malfatti, M A; Ubick, E A & Felton, J S
System: The UNT Digital Library
Integration of the predictions of two models with dose measurements in a case study of children exposed to the emissions of a lead smelter (open access)

Integration of the predictions of two models with dose measurements in a case study of children exposed to the emissions of a lead smelter

The predictions of two source-to-dose models are systematically evaluated with observed data collected in a village polluted by a currently operating secondary lead smelter. Both models were built up from several sub-models linked together and run using Monte-Carlo simulation, to calculate the distribution children's blood lead levels attributable to the emissions from the facility. The first model system is composed of the CalTOX model linked to a recoded version of the IEUBK model. This system provides the distribution of the media-specific lead concentrations (air, soil, fruit, vegetables and blood) in the whole area investigated. The second model consists of a statistical model to estimate the lead deposition on the ground, a modified version of the model HHRAP and the same recoded version of the IEUBK model. This system provides an estimate of the concentration of exposure of specific individuals living in the study area. The predictions of the first model system were improved in terms of accuracy and precision by performing a sensitivity analysis and using field data to correct the default value provided for the leaf wet density. However, in this case study, the first model system tends to overestimate the exposure due to exposed vegetables. The second model …
Date: March 1, 2009
Creator: Bonnard, R. & McKone, T.E.
System: The UNT Digital Library
Massive Star Formation in a Gravitationally-Lensed H II Galaxy at z = 3.357 (open access)

Massive Star Formation in a Gravitationally-Lensed H II Galaxy at z = 3.357

The Lynx arc, with a redshift of 3.357, was discovered during spectroscopic follow-up of the z = 0.570 cluster RX J0848+4456 from the ROSAT Deep Cluster Survey. The arc is characterized by a very red R - K color and strong, narrow emission lines. Analysis of HST WFPC 2 imaging and Keck optical and infrared spectroscopy shows that the arc is an H II galaxy magnified by a factor of {approx} 10 by a complex cluster environment. The high intrinsic luminosity, the emission line spectrum, the absorption components seen in Ly{alpha} and C IV, and the restframe ultraviolet continuum are all consistent with a simple H II region model containing {approx} 10{sup 6} hot O stars. The best fit parameters for this model imply a very hot ionizing continuum (T{sub BB} {approx} 80, 000 K), high ionization parameter (log U {approx} -1), and low nebular metallicity (Z/Z{sub {circle_dot}} {approx} 0.05). The narrowness of the emission lines requires a low mass-to-light ratio for the ionizing stars, suggestive of an extremely low metallicity stellar cluster. The apparent overabundance of silicon in the nebula could indicate enrichment by past pair instability supernovae, requiring stars more massive than {approx}140M{sub {circle_dot}}.
Date: March 2, 2004
Creator: Villar-Martin, M.; Stern, D.; Hook, R. N.; Rosati, P.; Lombardi, M.; Humphrey, A. et al.
System: The UNT Digital Library
Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins (open access)

Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this …
Date: March 1, 2008
Creator: Gaucher, S. P.; Redding, A. M.; Mukhopadhyay, A.; Keasling, J. D. & Singh, A. K.
System: The UNT Digital Library
Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites (open access)

Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites

Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, …
Date: March 25, 2008
Creator: Bishop, James K.B. & Wood, T.J.
System: The UNT Digital Library