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Sample records for site-specific natural geochemical

  1. Site-specific estimation of peak-streamflow frequency using generalized least-squares regression for natural basins in Texas

    USGS Publications Warehouse

    Asquith, William H.; Slade, R.M.

    1999-01-01

    The U.S. Geological Survey, in cooperation with the Texas Department of Transportation, has developed a computer program to estimate peak-streamflow frequency for ungaged sites in natural basins in Texas. Peak-streamflow frequency refers to the peak streamflows for recurrence intervals of 2, 5, 10, 25, 50, and 100 years. Peak-streamflow frequency estimates are needed by planners, managers, and design engineers for flood-plain management; for objective assessment of flood risk; for cost-effective design of roads and bridges; and also for the desin of culverts, dams, levees, and other flood-control structures. The program estimates peak-streamflow frequency using a site-specific approach and a multivariate generalized least-squares linear regression. A site-specific approach differs from a traditional regional regression approach by developing unique equations to estimate peak-streamflow frequency specifically for the ungaged site. The stations included in the regression are selected using an informal cluster analysis that compares the basin characteristics of the ungaged site to the basin characteristics of all the stations in the data base. The program provides several choices for selecting the stations. Selecting the stations using cluster analysis ensures that the stations included in the regression will have the most pertinent information about flooding characteristics of the ungaged site and therefore provide the basis for potentially improved peak-streamflow frequency estimation. An evaluation of the site-specific approach in estimating peak-streamflow frequency for gaged sites indicates that the site-specific approach is at least as accurate as a traditional regional regression approach.

  2. Geologic, geophysical, and geochemical aspects of site-specific studies of the geopressured-geothermal energy resource of southern Louisiana. Final report

    SciTech Connect

    Pilger, R.H. Jr.

    1985-01-01

    The report consists of four sections dealing with progress in evaluating geologic, geochemical, and geophysical aspects of geopressured-geothermal energy resources in Louisiana. Separate abstracts have been prepared for the individual sections. (ACR)

  3. Experimental investigations and geochemical modelling of site-specific fluid-fluid and fluid-rock interactions in underground storage of CO2/H2/CH4 mixtures: the H2STORE project

    NASA Astrophysics Data System (ADS)

    De Lucia, Marco; Pilz, Peter

    2015-04-01

    work packages hosted at the German Research Centre for Geosciences (GFZ) focus on the fluid-fluid and fluid-rock interactions triggered by CO2, H2 and their mixtures. Laboratory experiments expose core samples to hydrogen and CO2/hydrogen mixtures under site-specific conditions (temperatures up to 200 °C and pressure up to 300 bar). The resulting qualitative and, whereas possible, quantitative data are expected to ameliorate the precision of predictive geochemical and reactive transport modelling, which is also performed within the project. The combination of experiments, chemical and mineralogical analyses and models is needed to improve the knowledge about: (1) solubility model and mixing rule for multicomponent gas mixtures in high saline formation fluids: no data are namely available in literature for H2-charged gas mixtures in the conditions expected in the potential sites; (2) chemical reactivity of different mineral assemblages and formation fluids in a broad spectrum of P-T conditions and composition of the stored gas mixtures; (3) thermodynamics and kinetics of relevant reactions involving mineral dissolution or precipitation. The resulting amelioration of site characterization and the overall enhancement in understanding the potential processes will benefit the operational reliability, the ecological tolerance, and the economic efficiency of future energy storing plants, crucial aspects for public acceptance and for industrial investors.

  4. Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

    PubMed Central

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.

    2015-01-01

    ABSTRACT Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. PMID:25968645

  5. Natural bacterial communities serve as quantitative geochemical biosensors

    SciTech Connect

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Techtmann, Steve M.; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.; Hazen, Terry C.

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.

  6. Natural bacterial communities serve as quantitative geochemical biosensors

    DOE PAGESBeta

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; et al

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more » even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

  7. Determination of geochemical and natural radioactivity characteristics in Bilecik Marble, Turkey

    NASA Astrophysics Data System (ADS)

    Yerel Kandemir, Suheyla; Ozbay, Nurgul

    2014-05-01

    Natural stones are one of the oldest known building materials. There are more than 400 natural stone in Turkey. Recently, the demand for the natural stone types in markets has been increasing rapidly. For this reason, the geochemical and natural radioactivity characteristics of natural stone are very important. Bilecik province is located at the northwest part of Turkey and it is surrounded by Sakarya, Bursa, Eskisehir and Kutahya city. Bilecik is one of the important marble industry regions of Turkey. Thus, the geochemical and natural radioactivity characteristics of Bilecik marble are very important. In this study, Bilecik marble was collected to determine the geochemistry and natural radioactivity. Then, analyses of geochemical and natural radioactivity in the marble samples are interpreted. ACKNOWLEDGMENT This study is supported by Bilecik Seyh Edebali University scientific project (Project Number =2011-02-BIL.03-04).

  8. Geochemical history of Chesapeake Bay: Natural and anthropogenic influences

    SciTech Connect

    Hill, J.M.; Park, J.; Brush, G.

    1995-12-31

    Sediment cores, 4--5 m in length were collected at six sites in the mainstem Chesapeake Bay, as part of the NOAA National Status and Trends Program. The cores were described, X-rayed, optically scanned, and analyzed for textural parameters, Si and Al, trace metals, AVS, soluble iron, total carbon, nitrogen and sulfur. In addition, the cores were dated using Pb 210, C 14, and high temporal resolution pollen dating techniques. The cores indicate changes in the geochemical environment of the northern Chesapeake Bay, from an environment dominated by marine geochemical processes to one dominated by estuarine processes; this transition occurred approximately in the late 1930`s. Accompanying this transition is enrichment of the trace metals, as normalized to Al. Data from the cores also indicate periodic anoxic events have occurred in the main stem of the Chesapeake Bay since the time from European settlement, based on sulfur speciation and the behavior of Mn in the sediments. The behavior of the trace metals, in regard to changes through time, is strongly dependent on location in the Bay, reflecting different sources materials, and differences in geochemical environments of deposition. Changes in geochemistry of most of the cores, at approximately the same date, tentatively indicate events with Baywide influence are recorded in the sediments of these cores.

  9. Analysis of the site-specific carbon isotope composition of propane by gas source isotope ratio mass spectrometer

    NASA Astrophysics Data System (ADS)

    Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Neto, E. V. Santos; Eiler, John M.

    2016-09-01

    Site-specific isotope ratio measurements potentially provide valuable information about the formation and degradation of complex molecules-information that is lost in conventional bulk isotopic measurements. Here we discuss the background and possible applications of such measurements, and present a technique for studying the site-specific carbon isotope composition of propane at natural abundance based on mass spectrometric analysis of the intact propane molecule and its fragment ions. We demonstrate the feasibility of this approach through measurements of mixtures of natural propane and propane synthesized with site-specific 13C enrichment, and we document the limits of precision of our technique. We show that mass balance calculations of the bulk δ13C of propane based on our site-specific measurements is generally consistent with independent constraints on bulk δ13C. We further demonstrate the accuracy of the technique, and illustrate one of its simpler applications by documenting the site-specific carbon isotope signature associated with gas phase diffusion of propane, confirming that our measurements conform to the predictions of the kinetic theory of gases. This method can be applied to propane samples of moderate size (tens of micromoles) isolated from natural gases. Thus, it provides a means of studying the site-specific stable isotope systematics of propane at natural isotope abundances on sample sizes that are readily recovered from many natural environments. This method may also serve as a model for future techniques that apply high-resolution mass spectrometry to study the site-specific isotopic distributions of larger organic molecules, with potential applications to biosynthesis, forensics and other geochemical subjects.

  10. Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues.

    PubMed

    Santini, Talitha C; Warren, Lesley A; Kendra, Kathryn E

    2015-08-01

    Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

  11. Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

    PubMed Central

    Warren, Lesley A.; Kendra, Kathryn E.

    2015-01-01

    Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

  12. Site-Specific Carbon Isotopes in Organics

    NASA Astrophysics Data System (ADS)

    Piasecki, A.; Eiler, J. M.

    2012-12-01

    Natural organic molecules exhibit a wide range of internal site-specific isotope variation (i.e., molecules with same isotopic substitution type but different site). Such variations are generally unconstrained by bulk isotopic measurements. If known, site-specific variations might constrain temperatures of equilibrium, mechanisms of formation or consumption reactions, and possibly other details. For example, lipids can exhibit carbon isotope differences of up to 30‰ between adjacent carbon sites as a result of fractionations arising during decarboxylation of pyruvate and other steps in lipid biosynthesis(1). We present a method for site-specific carbon isotope analysis of propane, based on high-resolution, multi-collector gas source mass spectrometry, using a novel prototype instrument - the Thermo MAT 253 Ultra. This machine has an inlet system and electron bombardment ion source resembling those in conventional stable isotope gas source mass spectrometers, and the energy filter, magnet, and detector array resembling those in multi-collector ICPMS and TIMS. The detector array has 7 detector positions, 6 of which are movable, and each of which can collect ions with either a faraday cup (read through amplifiers ranging from 107-1012 ohms) or an SEM. High mass resolving power (up to 27,000, MRP = M/dM definition) is achieved through a narrow entrance slit, adjustable from 250 to 5 μm. Such resolution can cleanly separate isobaric interferences between isotopologues of organic molecules having the same cardinal mass (e.g., 13CH3 and 12CH2D). We use this technology to analyze the isotopologues and fragments of propane, and use such data to solve for the site-specific carbon isotope fractionation. By measuring isotopologues of both the one-carbon (13CH3) and the two-carbon (13C12CH4) fragment ion, we can solve for both bulk δ13C and the difference in δ13C between the terminal and central carbon position. We tested this method by analyzing mixtures between natural

  13. [Reproduction of European bank vole (Myodes glareolus, Rodentia) under conditions of natural geochemical anomalies].

    PubMed

    Baĭtimirova, E A; Mamina, V P; Zhigal'skiĭ, O A

    2010-01-01

    Estimates of abundance, morpho-functional state of ovaries, potential and actual fecundity of European bank vole, Myodes glareolus, inhabiting the territories of natural geochemical anomalies that are situated over ultra-basic rock and have an excess content of chrome, nickel, and cobaltare obtained. The population adaptive response to extreme geochemical conditions that facilitates the species survival under unfavorable environmental conditions and is manifested through an increase in potential and actual fecundity, decline of pre-implantation mortality, and decrease in proportion of females with pre-implantation losses is revealed. It is shown that in anomalous areas the intensity of folliculogenesis in mature voles is independent of the population cycle phase. As for immature animals residing within geochemical anomalies, an increase in size and numbers of follicles in ovaries is observed which is indicative of maturation fastening. An increase in potential and actual fecundity, as well as changes in morpho-functional state of ovaries, can be interpreted as means of birth rate accelerating which is supposed to compensate high postnatal mortality and maintain population abundance.

  14. DOE site-specific threat assessment

    SciTech Connect

    West, D.J.; Al-Ayat, R.A.; Judd, B.R.

    1985-07-12

    A facility manager faced with the challenges of protecting a nuclear facility against potential threats must consider the likelihood and consequences of such threats, know the capabilities of the facility safeguards and security systems, and make informed decisions about the cost-effectivness of safeguards and security upgrades. To help meet these challenges, the San Francisco Operations Office of the Department of Energy, in conjunction with the Lawrence Livermore Laboratory, has developed a site-specific threat assessment approach and a quantitative model to improve the quality and consistency of site-specific threat assessment and resultant security upgrade decisions at sensitive Department of Energy facilities. 5 figs.

  15. Site-Specific Infrared Probes of Proteins

    PubMed Central

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-01-01

    Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

  16. Natural geochemical analogues of the near field of high-level nuclear waste repositories

    SciTech Connect

    Apps, J.A.

    1995-09-01

    United States practice has been to design high-level nuclear waste (HLW) geological repositories with waste densities sufficiently high that repository temperatures surrounding the waste will exceed 100{degrees}C and could reach 250{degrees}C. Basalt and devitrified vitroclastic tuff are among the host rocks considered for waste emplacement. Near-field repository thermal behavior and chemical alteration in such rocks is expected to be similar to that observed in many geothermal systems. Therefore, the predictive modeling required for performance assessment studies of the near field could be validated and calibrated using geothermal systems as natural analogues. Examples are given which demonstrate the need for refinement of the thermodynamic databases used in geochemical modeling of near-field natural analogues and the extent to which present models can predict conditions in geothermal fields.

  17. Geochemical Responses to Anthropogenic and Natural Influences in Ebinur Lake Sediments of Arid Northwest China.

    PubMed

    Ma, Long; Wu, Jinglu; Abuduwaili, Jilili; Liu, Wen

    2016-01-01

    Geochemical concentrations were extracted for a short sediment core from Ebinur Lake, located in arid northwest China, and mathematical methods were used to demonstrate the complex pattern of the geochemical anomalies resulting from the temporal changes in natural and anthropogenic forces on the lake sediments. The first element assemblage (C1) (aluminum, potassium, iron, magnesium, beryllium, etc.) was predominantly terrigenous; among the assemblage, total phosphorus and titanium were generally consistent with aluminum except with regards to their surface sequences, which inferred the differences of source regions for terrigenous detrital material led to this change around ca. 2000AD. The second assemblage (C2) (calcium and strontium) was found to have a negative relationship with aluminum through a cluster analysis. The third assemblage (C3) included sodium and magnesium, which were influenced by the underwater lake environment and deposited in the Ebinur depression. The concentration ratio of C1/(C1+C2) was used as an indicator for denudation amount of detrital materials, which was supported by the values of magnetic susceptibility. The enrichment factors for heavy metals suggested that the influence of human activities on heavy-metal enrichment in Ebinur Lake region was not severe over the past century. Prior to the 1960s, geochemical indicators suggested a stable lacustrine environment with higher water levels. Beginning in the 1960s, high agricultural water demand resulted in rapid declines in lake water level, with subsequent increases of lake water salinity, as evidenced by enhanced sodium concentration in lake core sediments. During this period, anthropogenic activity also enhanced the intensity of weathering and the denudation of the Ebinur watershed. PMID:27176765

  18. Geochemical Responses to Anthropogenic and Natural Influences in Ebinur Lake Sediments of Arid Northwest China

    PubMed Central

    Wu, Jinglu; Abuduwaili, Jilili; Liu, Wen

    2016-01-01

    Geochemical concentrations were extracted for a short sediment core from Ebinur Lake, located in arid northwest China, and mathematical methods were used to demonstrate the complex pattern of the geochemical anomalies resulting from the temporal changes in natural and anthropogenic forces on the lake sediments. The first element assemblage (C1) (aluminum, potassium, iron, magnesium, beryllium, etc.) was predominantly terrigenous; among the assemblage, total phosphorus and titanium were generally consistent with aluminum except with regards to their surface sequences, which inferred the differences of source regions for terrigenous detrital material led to this change around ca. 2000AD. The second assemblage (C2) (calcium and strontium) was found to have a negative relationship with aluminum through a cluster analysis. The third assemblage (C3) included sodium and magnesium, which were influenced by the underwater lake environment and deposited in the Ebinur depression. The concentration ratio of C1/(C1+C2) was used as an indicator for denudation amount of detrital materials, which was supported by the values of magnetic susceptibility. The enrichment factors for heavy metals suggested that the influence of human activities on heavy-metal enrichment in Ebinur Lake region was not severe over the past century. Prior to the 1960s, geochemical indicators suggested a stable lacustrine environment with higher water levels. Beginning in the 1960s, high agricultural water demand resulted in rapid declines in lake water level, with subsequent increases of lake water salinity, as evidenced by enhanced sodium concentration in lake core sediments. During this period, anthropogenic activity also enhanced the intensity of weathering and the denudation of the Ebinur watershed. PMID:27176765

  19. Nanoparticles for Site Specific Genome Editing

    NASA Astrophysics Data System (ADS)

    McNeer, Nicole Ali

    Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to

  20. Geochemical evidence for possible natural migration of Marcellus Formation brine to shallow aquifers in Pennsylvania.

    PubMed

    Warner, Nathaniel R; Jackson, Robert B; Darrah, Thomas H; Osborn, Stephen G; Down, Adrian; Zhao, Kaiguang; White, Alissa; Vengosh, Avner

    2012-07-24

    The debate surrounding the safety of shale gas development in the Appalachian Basin has generated increased awareness of drinking water quality in rural communities. Concerns include the potential for migration of stray gas, metal-rich formation brines, and hydraulic fracturing and/or flowback fluids to drinking water aquifers. A critical question common to these environmental risks is the hydraulic connectivity between the shale gas formations and the overlying shallow drinking water aquifers. We present geochemical evidence from northeastern Pennsylvania showing that pathways, unrelated to recent drilling activities, exist in some locations between deep underlying formations and shallow drinking water aquifers. Integration of chemical data (Br, Cl, Na, Ba, Sr, and Li) and isotopic ratios ((87)Sr/(86)Sr, (2)H/H, (18)O/(16)O, and (228)Ra/(226)Ra) from this and previous studies in 426 shallow groundwater samples and 83 northern Appalachian brine samples suggest that mixing relationships between shallow ground water and a deep formation brine causes groundwater salinization in some locations. The strong geochemical fingerprint in the salinized (Cl > 20 mg/L) groundwater sampled from the Alluvium, Catskill, and Lock Haven aquifers suggests possible migration of Marcellus brine through naturally occurring pathways. The occurrences of saline water do not correlate with the location of shale-gas wells and are consistent with reported data before rapid shale-gas development in the region; however, the presence of these fluids suggests conductive pathways and specific geostructural and/or hydrodynamic regimes in northeastern Pennsylvania that are at increased risk for contamination of shallow drinking water resources, particularly by fugitive gases, because of natural hydraulic connections to deeper formations.

  1. Geochemical evidence for possible natural migration of Marcellus Formation brine to shallow aquifers in Pennsylvania

    PubMed Central

    Warner, Nathaniel R.; Jackson, Robert B.; Darrah, Thomas H.; Osborn, Stephen G.; Down, Adrian; Zhao, Kaiguang; White, Alissa; Vengosh, Avner

    2012-01-01

    The debate surrounding the safety of shale gas development in the Appalachian Basin has generated increased awareness of drinking water quality in rural communities. Concerns include the potential for migration of stray gas, metal-rich formation brines, and hydraulic fracturing and/or flowback fluids to drinking water aquifers. A critical question common to these environmental risks is the hydraulic connectivity between the shale gas formations and the overlying shallow drinking water aquifers. We present geochemical evidence from northeastern Pennsylvania showing that pathways, unrelated to recent drilling activities, exist in some locations between deep underlying formations and shallow drinking water aquifers. Integration of chemical data (Br, Cl, Na, Ba, Sr, and Li) and isotopic ratios (87Sr/86Sr, 2H/H, 18O/16O, and 228Ra/226Ra) from this and previous studies in 426 shallow groundwater samples and 83 northern Appalachian brine samples suggest that mixing relationships between shallow ground water and a deep formation brine causes groundwater salinization in some locations. The strong geochemical fingerprint in the salinized (Cl > 20 mg/L) groundwater sampled from the Alluvium, Catskill, and Lock Haven aquifers suggests possible migration of Marcellus brine through naturally occurring pathways. The occurrences of saline water do not correlate with the location of shale-gas wells and are consistent with reported data before rapid shale-gas development in the region; however, the presence of these fluids suggests conductive pathways and specific geostructural and/or hydrodynamic regimes in northeastern Pennsylvania that are at increased risk for contamination of shallow drinking water resources, particularly by fugitive gases, because of natural hydraulic connections to deeper formations. PMID:22778445

  2. Site-Specific PEGylation of Therapeutic Proteins

    PubMed Central

    Dozier, Jonathan K.; Distefano, Mark D.

    2015-01-01

    The use of proteins as therapeutics has a long history and is becoming ever more common in modern medicine. While the number of protein-based drugs is growing every year, significant problems still remain with their use. Among these problems are rapid degradation and excretion from patients, thus requiring frequent dosing, which in turn increases the chances for an immunological response as well as increasing the cost of therapy. One of the main strategies to alleviate these problems is to link a polyethylene glycol (PEG) group to the protein of interest. This process, called PEGylation, has grown dramatically in recent years resulting in several approved drugs. Installing a single PEG chain at a defined site in a protein is challenging. Recently, there is has been considerable research into various methods for the site-specific PEGylation of proteins. This review seeks to summarize that work and provide background and context for how site-specific PEGylation is performed. After introducing the topic of site-specific PEGylation, recent developments using chemical methods are described. That is followed by a more extensive discussion of bioorthogonal reactions and enzymatic labeling. PMID:26516849

  3. Site-Specific Covalent Labeling of RNA by Enzymatic Transglycosylation.

    PubMed

    Alexander, Seth C; Busby, Kayla N; Cole, Christian M; Zhou, Cun Yu; Devaraj, Neal K

    2015-10-14

    We demonstrate the site-specific incorporation of nucleobase derivatives bearing fluorophores or affinity labels into a short RNA stem loop recognition motif by exchange of a guanine residue. The RNA-TAG (transglycosylation at guanosine) is carried out by a bacterial (E. coli) tRNA guanine transglycosylase (TGT), whose natural substrate is the nitrogenous base PreQ1. Remarkably, we have successfully incorporated large functional groups including biotin, BODIPY, thiazole orange, and Cy7 through a polyethylene glycol linker attached to the exocyclic amine of PreQ1. Larger RNAs, such as mRNA transcripts, can be site-specifically labeled if they possess the 17-nucleotide hairpin recognition motif. The RNA-TAG methodology could facilitate the detection and manipulation of RNA molecules by enabling the direct incorporation of functional artificial nucleobases using a simple hairpin recognition element. PMID:26393285

  4. Using Natural Geochemical Tracers to Discern the Dominant Sources of Freshwater into Biscayne Bay, Southeast Florida

    NASA Astrophysics Data System (ADS)

    Stalker, J. C.; Price, R. M.; Swart, P. K.

    2005-05-01

    Biscayne Bay is a sub-tropical estuary located on the carbonate platform of south Florida. The water occupying Biscayne Bay is a balance of saltwater influx from the open ocean and freshwater inputs from precipitation, surface water runoff, and submarine groundwater discharge. The bays watershed includes a total of 3 million inhabitants, the major urban centers of Miami and Ft. Lauderdale, as well as the Everglades system. With the development of south Florida, the natural diffuse groundwater and stream flow into the bay has been replaced by a large system of canals and levees in an effort to control flooding and drain swampland. The Comprehensive Everglades Restoration Plan includes changes in the freshwater deliveries to Biscayne Bay from point-source discharges via canals to non-point source discharges via wetlands and groundwater flow. The balance of salinity in Biscayne Bay effects sensitive seagrass and tidal ecosystems including numerous species of corals and other biota. A comprehensive understanding of the flow of freshwater into the bay is crucial to future planned developments and restorations. The goal of this study is to use naturally occurring geochemical constituents as tracers to identify and quantify the sources of freshwater, i.e. rainfall, canal flow, and groundwater, discharge to Biscayne Bay. In this study, discrete samples of precipitation, canal water, terrestrial groundwater, marine groundwater, and bay surface water are collected monthly and analyzed for the stable isotopes of hydrogen and oxygen as well as for major cations and anions. Initial results indicate that fresh groundwater has an isotopic signature (del 18O = -2.66 per mil, del D, -7.60 per mil) similar to rainfall (del 18O = -2.86 per mil, del D =-4.78 per mil). In contrast canal water has a heavy isotopic signature (del 18O = -0.46 per mil, del D = -2.48 per mil) due to evaporation. Thus it is possible to use stable isotopes of oxygen and hydrogen to separate canal water from

  5. Savannah River Site's Site Specific Plan

    SciTech Connect

    Not Available

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  6. The effect of sterilization on biological, organic geochemical and morphological information in natural samples

    NASA Technical Reports Server (NTRS)

    Hochstein, L. I.; Kvenvolden, K. A.; Philpott, D. E.

    1974-01-01

    The loss of biological, organic geochemical, and morphological science information that may occur should a Mars surface sample be sterilized prior to return to earth is examined. Results of experimental studies are summarized.

  7. The Connectivity Between Site-Specific Life Cycle Impact Assessment and Site-Specific Weighting

    EPA Science Inventory

    The goal of many LCIAs is to come to a single score with all of the impacts from a wide variety of impact assessments weighted to form this single score. My past experiences with developing site-specific impact assessment methodologies and how this can change the valuation porti...

  8. Geochemical Processes During Geological Carbon Storage: Lessons from Natural Analogues and Field Experiments (Invited)

    NASA Astrophysics Data System (ADS)

    Bickle, M. J.; Kampman, N.; Wigley, M.; Dubacq, B.

    2013-12-01

    that fluid-mineral reactions are initially fast, are important in buffering fluid compositions and may cause important beneficial changes to formation and caprock permeabilities. However much more needs to be learnt. Many of the inferences on mineral dissolution and precipitation reactions are derived from modal decomposition calculations based on changes in sampled fluid chemistry and these suffer ambiguities arising from the limited number of soluble cations present in stoichiometric proportions in minerals and from the uncertainties in mineral compositions. The reservoirs and caprocks in natural analogues contain an inadequately sampled and exploited record of the fluid-mineral reactions but deciphering this requires careful petrographic, mineralogical and geochemical work to distinguish the response to CO2-charged fluids from earlier diagenetic episodes.

  9. Statistical and Economic Techniques for Site-specific Nematode Management.

    PubMed

    Liu, Zheng; Griffin, Terry; Kirkpatrick, Terrence L

    2014-03-01

    Recent advances in precision agriculture technologies and spatial statistics allow realistic, site-specific estimation of nematode damage to field crops and provide a platform for the site-specific delivery of nematicides within individual fields. This paper reviews the spatial statistical techniques that model correlations among neighboring observations and develop a spatial economic analysis to determine the potential of site-specific nematicide application. The spatial econometric methodology applied in the context of site-specific crop yield response contributes to closing the gap between data analysis and realistic site-specific nematicide recommendations and helps to provide a practical method of site-specifically controlling nematodes.

  10. RESRAD. Site-Specific Residual Radioactivity

    SciTech Connect

    Yu, C.

    1989-06-01

    RESRAD is designed to derive site-specific guidelines for allowable residual concentrations of radionuclides in soil. A guideline is defined as a radionuclide concentration or a level of radiation or radioactivity that is acceptable if a site is to be used without radiological restrictions. Guidelines are expressed as (1) concentrations of residual radionuclides in soil, (2) concentrations of airborne radon decay products, (3) levels of external gamma radiation, (4) levels of radioactivity from surface contamination, and (5) concentrations of residual radionuclides in air and water. Soil is defined as unconsolidated earth material, including rubble and debris that may be present. The controlling principles of all guidelines are (1) the annual radiation dose received by a member of the critical population group from the residual radioactive material - predicted by a realistic but reasonably conservative analysis and averaged over a 50 year period - should not exceed 100 mrem/yr, and (2) doses should be kept as low as reasonably achievable. All significant exposure pathways for the critical population group are considered in deriving soil guidelines. These pathways include direct exposure to external radiation from the contaminated soil material; internal radiation from inhalation of airborne radionuclides; and internal radiation from ingestion of plant foods grown in the contaminated soil, meat and milk from livestock fed with contaminated fodder and water, drinking water from a contaminated well, and fish from a contaminated pond.

  11. Determination of transport rates in the Yellow River Bohai Sea mixing zone via natural geochemical tracers

    NASA Astrophysics Data System (ADS)

    Peterson, Richard N.; Burnett, William C.; Taniguchi, Makoto; Chen, Jianyao; Santos, Isaac R.; Misra, Sambuddha

    2008-11-01

    In light of the current problems facing the Yellow River and surrounding areas (e.g., periods of zero river discharge, increasing nitrate concentrations of the Bohai Sea), we examined the coastal mixing dynamics around the mouth of the Yellow River. Naturally occurring radium isotopes ( 223Ra, 224Ra, 226Ra, and 228Ra) and other geochemical tracers (Ba, Si, and salinity) were employed to determine river plume transport scales and rates. Barium and radium exhibit elevated concentrations within the salinity gradient where they are desorbed from particles via ion-exchange. Once they are added to the system, they decrease offshore from dilution with lower concentration Bohai Sea water, and in the case of 224Ra and 223Ra, by radioactive decay. Using radium "ages" to assess the dissolved material transport scales and rates proved to be a useful tool in this environment. The ages based on the 224Ra/ 228Ra activity ratio increased gradually until salinities reached ˜25 when they rapidly increased due to decreased mixing at higher salinities. Integrated net transport rates through the salinity front ranged from 1.4 to 1.6 cm/s and did not vary significantly with river discharge. Thus, tidal mixing appears to dominate in this system, at least over the range of discharges investigated (80-600 m 3/s). Determining the temporal scale of flow across the coastal zone in this region is a valuable first step toward examining whether the Yellow River is contributing to the increasing inorganic nitrogen concentrations in the central Bohai Sea.

  12. Site-Specific, Climate-Friendly Farming

    NASA Astrophysics Data System (ADS)

    Brown, D. J.; Brooks, E. S.; Eitel, J.; Huggins, D. R.; Painter, K.; Rupp, R.; Smith, J. L.; Stockle, C.; Vierling, L. A.

    2011-12-01

    Of the four most important atmospheric greenhouse gasses (GHG) enriched through human activities, only nitrous oxide (N2O) emissions are due primarily to agriculture. However, reductions in the application of synthetic N fertilizers could have significant negative consequences for a growing world population given the crucial role that these fertilizers have played in cereal yield increases since WWII. Increasing N use efficiency (NUE) through precision management of agricultural N in space and time will therefore play a central role in the reduction of agricultural N2O emissions. Precision N management requires a greater understanding of the spatio-temporal variability of factors supporting N management decisions such as crop yield, water and N availability, utilization and losses. We present an overview of a large, collaborative, multi-disciplinary project designed to improve our basic understanding of nitrogen (N), carbon (C) and water (H2O) spatio-temporal dynamics for wheat-based cropping systems on complex landscapes, and develop management tools to optimize water- and nitrogen-use efficiency for these systems and landscapes. Major components of this project include: (a) cropping systems experiments addressing nitrogen application rate and seeding density for different landscape positions; (b) GHG flux experiments and monitoring; (c) soil microbial genetics and stable isotope analyses to elucidate biochemical pathways for N2O production; (d) proximal soil sensing for construction of detailed soil maps; (e) LiDAR and optical remote sensing for crop growth monitoring; (f) hydrologic experiments, monitoring, and modeling; (g) refining the CropSyst simulation model to estimate biophysical processes and GHG emissions under a variety of management and climatic scenarios; and (h) linking farm-scale enterprise budgets to simulation modeling in order to provide growers with economically viable site-specific climate-friendly farming guidance.

  13. Site-specific features influence sediment stability of intertidal flats

    NASA Astrophysics Data System (ADS)

    Defew, Emma C.; Tolhurst, Trevor J.; Paterson, David M.

    The factors that influence the sediment stability and the transport of estuarine mudflats are not yet fully understood but knowledge of them is essential in coastal engineering applications and pollution ecology studies. The suggestion that variation in predictive models of sediment stability might be due to site-specific characteristics is investigated using data from four estuarine mudflats (Eden Estuary, Scotland, the Biezelingsche Ham, Zandkreek, and Molenplaat mudflats in The Netherlands). These estuaries differ in their environmental conditions, macrofaunal species composition and local features (e.g. Enteromorpha mats, migratory biofilms). Stable and unstable sediments were compared, and mean chlorophyll-a concentrations and granulometry of the sediments were significantly different between the two groups. Step-wise multiple linear regressions were applied to the sediment stability data of all sites to establish the influences on erosion threshold of microphytobenthic biomass, water content, granulometry, organic carbon content and the abundance of dominant macrofaunal species. The stability of each site was influenced by different factors. Sediment stability of the Eden Estuary was affected by the Enteromorpha bloom; Biezelingsche Ham was influenced by the highly migratory nature of the diatom biofilms and the abundance of Corophium volutator; the polychaete worm Arenicola marina had a net negative effect on sediment stability of the Zandkreek; and the Molenplaat was influenced by microphytobenthic biomass. This research highlights the need for site-specific calibration of models and suggests that a universal proxy parameter for sediment stability is unlikely to be obtained.

  14. Preliminary delineation of natural geochemical reactions, Snake River Plain aquifer system, Idaho National Engineering Laboratory and vicinity, Idaho

    SciTech Connect

    Knobel, L.L.; Bartholomay, R.C.; Orr, B.R.

    1997-05-01

    The U.S. Geological Survey, in cooperation with the U.S. Department of Energy, is conducting a study to determine the natural geochemistry of the Snake River Plain aquifer system at the Idaho National Engineering Laboratory (INEL), Idaho. As part of this study, a group of geochemical reactions that partially control the natural chemistry of ground water at the INEL were identified. Mineralogy of the aquifer matrix was determined using X-ray diffraction and thin-section analysis and theoretical stabilities of the minerals were used to identify potential solid-phase reactants and products of the reactions. The reactants and products that have an important contribution to the natural geochemistry include labradorite, olivine, pyroxene, smectite, calcite, ferric oxyhydroxide, and several silica phases. To further identify the reactions, analyses of 22 representative water samples from sites tapping the Snake River Plain aquifer system were used to determine the thermodynamic condition of the ground water relative to the minerals in the framework of the aquifer system. Principal reactions modifying the natural geochemical system include congruent dissolution of olivine, diopside, amorphous silica, and anhydrite; incongruent dissolution of labradorite with calcium montmorillonite as a residual product; precipitation of calcite and ferric oxyhydroxide; and oxidation of ferrous iron to ferric iron. Cation exchange reactions retard the downward movement of heavy, multivalent waste constituents where infiltration ponds are used for waste disposal.

  15. Methods for generating phosphorylation site-specific immunological reagents

    DOEpatents

    Anderson, Carl W.; Appella, Ettore; Sakaguchi, Kazuyasu

    2001-01-01

    The present invention provides methods for generating phosphorylation site-specific immunological reagents. More specifically, a phosphopeptide mimetic is incorporated into a polypeptide in place of a phosphorylated amino acid. The polypeptide is used as antigen by standard methods to generate either monoclonal or polyclonal antibodies which cross-react with the naturally phosphorylated polypeptide. The phosphopeptide mimetic preferably contains a non-hydrolyzable linkage from the appropriate carbon atom of the amino acid residue to a phosphate group. A preferred linkage is a CF.sub.2 group. Such a linkage is used to generate the phosphoserine mimetic F.sub.2 Pab, which is incorporated into a polypeptide sequence derived from p53 to produce antibodies which recognize a specific phosphorylation state of p53. A CF.sub.2 group linkage is also used to produce the phosphothreonine mimetic F.sub.2 Pmb, and to produce the phosphotyrosine mimetic, F.sub.2 Pmp.

  16. Site-specific recombinases: molecular machines for the Genetic Revolution.

    PubMed

    Olorunniji, Femi J; Rosser, Susan J; Stark, W Marshall

    2016-03-15

    The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.

  17. Site-specific development plan: Carlin, Nevada

    SciTech Connect

    Fiore, J.H.

    1980-01-01

    The conditions for developing the geothermal resource near Carlin appear favorable. The resource has a favorable temperature range for direct applications (174/sup 0/F or 79/sup 0/C), the geothermal fluid has low total dissolved solids, no objectionable constituents that would result in costly scaling or corrosion problems and the resource is conveniently located within two miles from town. Direct space heating is the most realistic application and is recommended. Several clusters of homes are located less than 2 miles away. The project could be developed on a larger scale than this study proposes. The engineering and economic models are proposed on a small scale here for simplicity in evaluating the feasibility of pursuing development. Conceivably the producing well will provide sufficient hot water to accommodate more homes than the models include. The town of Carlin seems receptive to development and there does not appear to be any major barriers to exploration or development. The regulatory climate in both the state and county is conducive to geothermal development at this level. No major regulatory or environmental obstacles are noted which would severely curtail utilization for space heating. The prospect of replacing natural gas heat with geothermal heat for 60 or more homes is economically attractive. Geothermal rates for hot water are not expected to increase as rapidly as the price of natural gas to the consumer over the next 10 years. The increases for hot water from geothermal are primarily a function of power costs for the pumps plus inflation affecting maintenance costs. Individual homeowners can expect payback on retrofitting costs within two to three years.

  18. Global and site specific multimedia (field) studies

    SciTech Connect

    Cutshall, N.H.; Guerin, M.R.

    1987-01-01

    Experience with radioactive fallout, with organic contaminants and with heavy metals has amply demonstrated that cross-media transfers are common and that understanding the transport, cycling, and fate of these contaminants requires a multimedia approach. Nonetheless, pollutants with similar physical and chemical attributes may follow markedly different pathways. The frequency of exceptions to predictions based on simplistic models is also sufficient to show that direct investigation of environmental contamination is essential to confirm validity of models used for conceptualizing a problem or for control. Modeling based on multimedia premises and regulatory controls that encompass multimedia considerations are challenged by a dilemma, however. First, the development of multimedia models or regulatory frameworks represents simplification and generalization. This is true for several reasons: (1) inadequate understanding of physical and environmental factors which control specific cross-media transfer; (2) the absence of specific data on certain multimedia pollutant concentrations; (3) even the most powerful computers do not have sufficient speed and capacity to deal with the known complexities of natural systems. On the other hand, for contaminants such as mercury, it may be necessary to include great detail; the overall distribution in the environment may be less important than the rate of some minor process. With sufficient experience and good judgment of what can be ignored, the simplifications and generalizations can be made. For the present, and for the foreseeable future, however, they absolutely must be accompanied by thorough field validation and monitoring.

  19. Site Specific Management of Cotton Production in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific management or precision agriculture, as it is evolving in large-scale crop production, offers promising new methods for managing cotton production for optimized yields, maximized profitability, and minimized environmental pollution. However, adaptation of site-specific theory and meth...

  20. SITE-SPECIFIC CHARACTERIZATION OF SOIL RADON POTENTIALS

    EPA Science Inventory

    The report presents a theoretical basis for measuring site-specific radon potentials. However, the empirical measurements suggest that the precision of such measurements is marginal, leaving an uncertainty of about a factor of 2 in site-specific estimates. Although this may be us...

  1. Site-specific crop management using geophysical proximal sensors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Key components of site-specific crop management are (i) identifying the site-specific factors that influence within-field crop yield variation and (ii) spatially characterizing those factors. Geo-referenced measurements of apparent soil electrical conductivity (ECa) provide a potential means of cha...

  2. Enhancing adoption of site-specific variable rate sprinkler systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than twenty years of private and public research on site-specific variable-rate sprinkler irrigation (SS-VRI) has resulted in very limited commercial adoption of the technology. Documented and proven water conservation strategies using site-specific irrigation are quite limited, and its cost-ef...

  3. Geochemical processes controlling water salinization in an irrigated basin in Spain: identification of natural and anthropogenic influence.

    PubMed

    Merchán, D; Auqué, L F; Acero, P; Gimeno, M J; Causapé, J

    2015-01-01

    Salinization of water bodies represents a significant risk in water systems. The salinization of waters in a small irrigated hydrological basin is studied herein through an integrated hydrogeochemical study including multivariate statistical analyses and geochemical modeling. The study zone has two well differentiated geologic materials: (i) Quaternary sediments of low salinity and high permeability and (ii) Tertiary sediments of high salinity and very low permeability. In this work, soil samples were collected and leaching experiments conducted on them in the laboratory. In addition, water samples were collected from precipitation, irrigation, groundwater, spring and surface waters. The waters show an increase in salinity from precipitation and irrigation water to ground- and, finally, surface water. The enrichment in salinity is related to the dissolution of soluble mineral present mainly in the Tertiary materials. Cation exchange, precipitation of calcite and, probably, incongruent dissolution of dolomite, have been inferred from the hydrochemical data set. Multivariate statistical analysis provided information about the structure of the data, differentiating the group of surface waters from the groundwaters and the salinization from the nitrate pollution processes. The available information was included in geochemical models in which hypothesis of consistency and thermodynamic feasibility were checked. The assessment of the collected information pointed to a natural control on salinization processes in the Lerma Basin with minimal influence of anthropogenic factors. PMID:25262295

  4. Geochemical processes controlling water salinization in an irrigated basin in Spain: identification of natural and anthropogenic influence.

    PubMed

    Merchán, D; Auqué, L F; Acero, P; Gimeno, M J; Causapé, J

    2015-01-01

    Salinization of water bodies represents a significant risk in water systems. The salinization of waters in a small irrigated hydrological basin is studied herein through an integrated hydrogeochemical study including multivariate statistical analyses and geochemical modeling. The study zone has two well differentiated geologic materials: (i) Quaternary sediments of low salinity and high permeability and (ii) Tertiary sediments of high salinity and very low permeability. In this work, soil samples were collected and leaching experiments conducted on them in the laboratory. In addition, water samples were collected from precipitation, irrigation, groundwater, spring and surface waters. The waters show an increase in salinity from precipitation and irrigation water to ground- and, finally, surface water. The enrichment in salinity is related to the dissolution of soluble mineral present mainly in the Tertiary materials. Cation exchange, precipitation of calcite and, probably, incongruent dissolution of dolomite, have been inferred from the hydrochemical data set. Multivariate statistical analysis provided information about the structure of the data, differentiating the group of surface waters from the groundwaters and the salinization from the nitrate pollution processes. The available information was included in geochemical models in which hypothesis of consistency and thermodynamic feasibility were checked. The assessment of the collected information pointed to a natural control on salinization processes in the Lerma Basin with minimal influence of anthropogenic factors.

  5. Protein assemblies by site-specific avidin-biotin interactions.

    PubMed

    Mori, Yutaro; Minamihata, Kosuke; Abe, Hiroki; Goto, Masahiro; Kamiya, Noriho

    2011-08-21

    Exploiting self-assembly systems with biological building blocks is of significant interest in the fabrication of advanced biomaterials. We assessed the potential use of site-specific ligand labeling of protein building blocks in designing functional protein self-assemblies by combining site-specifically biotinylated bacterial alkaline phosphatase (as a bidentate or tetradentate ligand unit) and streptavidin (as a tetrameric receptor). PMID:21731938

  6. Geochemical Signature of Natural Water Recharge in the Jungar Basin and Its Response to Climate.

    PubMed

    Zhu, Bingqi; Yu, Jingjie; Rioual, Patrick

    2016-01-01

    This paper analyzed the physico-chemical characteristics of natural waters in a drainage system of the Jungar Basin, northwestern China to identify chemical evolution and recharge mechanisms of natural waters in an arid environment. The waters studied are different in mineralization, but are typically carbonate rivers and alkaline in nature. No Cl-dominated water type occurs, indicating an early stage of water evolution. Regolith and geomorphological parameters controlling ground-surface temperature may play a large role in the geological evolution of the water. Three main morphological and hydrological units are reflected in water physico-chemistry. Climate influences the salinization of natural waters substantially. Direct recharge from seasonal snow and ice-melt water and infiltration of rain to the ground are significant recharge processes for natural waters, but recharge from potential deep groundwater may be less important. The enrichment of ions in lakes has been mainly caused by evaporation rather than through the quality change of the recharged water.

  7. A readily synthesized cyclic pyrrolysine analogue for site-specific protein "click" labeling.

    PubMed

    Hao, Ziyang; Song, Yanqun; Lin, Shixian; Yang, Maiyun; Liang, Yujie; Wang, Jing; Chen, Peng R

    2011-04-21

    A concise route was developed for the facile synthesis of a cyclic pyrrolysine analogue bearing an azide handle. Directed evolution enabled the encoding of this non-natural amino acid in both prokaryotic and eukaryotic cells, which offers a highly efficient approach for the site-specific protein labeling using click chemistry.

  8. Putting the Fizz in the Fissure: Geochemical and Geomechanical Effects of Carbonated Brine in a Natural Fracture

    NASA Astrophysics Data System (ADS)

    Smith, M. M.; Walsh, S. D.; Carroll, S.

    2012-12-01

    The increased mobility and buoyancy of CO2, coupled with rising demands for renewable energy production, make it an attractive alternative heat-exchange fluid in lieu of water for use in enhanced geothermal systems (EGS). However, the geochemical impact of elevated CO2 levels on these engineered systems and the consequent effects on reservoir capacity and system permeability are poorly-constrained at present, leading to uncertainty in predictions of longer-term reservoir performance. For example, consistently high levels of aqueous CO2 cycling through the subsurface may result in relatively rapid and extensive dissolution of pH-sensitive minerals, with an increased risk of secondary alteration phase precipitation (e.g., oxides, clays, and/or carbonate minerals) and adverse effects on EGS resource productivity. If, however, injected CO2-rich fluids traverse the system primarily through fracture networks, other factors such as accessibly reactive surface areas, fracture asperity susceptibility, and fracture surface/wallrock exchange may also factor into the ultimate evolution of reservoir permeability. To evaluate the comparative impacts of both geochemistry and geomechanics in sustaining fracture network flow under conditions relevant to CO2-EGS, a 60-day core-flooding experiment was conducted on a naturally fractured and chemically complex greywacke core sample exposed to CO2-acidified brine at 200C and 25MPa. The objective of this study was to investigate the potential effects of using CO2 as a heat-exchange fluid on fracture flow and reaction within a pre-existing well-characterized fracture representative of reactivated fractures targeted for stimulation in many EGS projects. Over the course of the experiment, changes in solution chemistry and pressure/permeability were monitored. In addition, pre- and post-reaction three-dimensional high-resolution X-ray computed tomography (XRCT) imaging was used to determine changes in fracture aperture and geometry as well

  9. The geochemical nature of the Archean Ancient Gneiss Complex and Granodiorite Suite, Swaziland: a preliminary study

    USGS Publications Warehouse

    Hunter, D.R.; Barker, F.; Millard, H.T., Jr.

    1978-01-01

    The Ancient Gneiss Complex (AGC) of Swaziland, an Archean gray gneiss complex, lies southeast and south of the Barberton greenstone belt and includes the most structurally complex and highly metamorphosed portions of the eastern Kaapvaal craton. The AGC is not precisely dated but apparently is older than 3.4 Ga. The AGC consists of three major units: (a) a bimodal suite of closely interlayered siliceous, low-K gneisses and metabasalt; (b) homogeneous tonalite gneiss; and (c) interlayered siliceous microcline gneiss, metabasalt, and minor metasedimentary rocks - termed the metamorphite suite. A geologically younger gabbro-diorite-tonalite-trondhjemite suite, the Granodiorite Suite, is spatially associated with the AGC and intrusive into it. The bimodal suite consists largely of two types of low-K siliceous gneiss: one has SiO2 14%, low Rb/Sr ratios, and depleted heavy rare earth elements (REE's); the other has SiO2 > 75%, Al2O3 < 13%, high Rb/Sr ratios, and relatively abundant REE's except for negative Eu anomalies. The interlayered metabasalt ranges from komatiitic to tholeiitic compositions. Lenses of quartz monzonitic gneiss of K2O/Na2O close to 1 form a minor part of the bimodal suite. Tonalitic to trondhjemitic migmatite locally is abundant and has major-element abundances similar to those of non-migmatitic varieties. The siliceous gneisses of the metamorphic suite show low Al2O, K2O/Na2O ratios of about 1, high Rb/Sr ratios, moderate REE abundances and negative Eu anomalies. K/Rb ratios of siliceous gneisses of the bimodal suite are very low (???130); of the tonalitic gneiss, low (???225); of the siliceous gneiss of the metamorphite suite, moderate (???300); and of the Granodiorite Suite, high (???400). Rocks of the AGC differ geochemically in several ways from the siliceous volcanic and hypabyssal rocks of the Upper Onverwacht Group and from the diapirs of tonalite and trondhjemite that intrude the Swaziland Group. ?? 1978.

  10. Geochemical Signature of Natural Water Recharge in the Jungar Basin and Its Response to Climate.

    PubMed

    Zhu, Bingqi; Yu, Jingjie; Rioual, Patrick

    2016-01-01

    This paper analyzed the physico-chemical characteristics of natural waters in a drainage system of the Jungar Basin, northwestern China to identify chemical evolution and recharge mechanisms of natural waters in an arid environment. The waters studied are different in mineralization, but are typically carbonate rivers and alkaline in nature. No Cl-dominated water type occurs, indicating an early stage of water evolution. Regolith and geomorphological parameters controlling ground-surface temperature may play a large role in the geological evolution of the water. Three main morphological and hydrological units are reflected in water physico-chemistry. Climate influences the salinization of natural waters substantially. Direct recharge from seasonal snow and ice-melt water and infiltration of rain to the ground are significant recharge processes for natural waters, but recharge from potential deep groundwater may be less important. The enrichment of ions in lakes has been mainly caused by evaporation rather than through the quality change of the recharged water. PMID:26803030

  11. Site-specific recombinases as tools for heterologous gene integration.

    PubMed

    Hirano, Nobutaka; Muroi, Tetsurou; Takahashi, Hideo; Haruki, Mitsuru

    2011-10-01

    Site-specific recombinases are the enzymes that catalyze site-specific recombination between two specific DNA sequences to mediate DNA integration, excision, resolution, or inversion and that play a pivotal role in the life cycles of many microorganisms including bacteria and bacteriophages. These enzymes are classified as tyrosine-type or serine-type recombinases based on whether a tyrosine or serine residue mediates catalysis. All known tyrosine-type recombinases catalyze the formation of a Holliday junction intermediate, whereas the catalytic mechanism of all known serine-type recombinases includes the 180° rotation and rejoining of cleaved substrate DNAs. Both recombinase families are further subdivided into two families; the tyrosine-type recombinases are subdivided by the recombination directionality, and the serine-type recombinases are subdivided by the protein size. Over more than two decades, many different site-specific recombinases have been applied to in vivo genome engineering, and some of them have been used successfully to mediate integration, deletion, or inversion in a wide variety of heterologous genomes, including those from bacteria to higher eukaryotes. Here, we review the recombination mechanisms of the best characterized recombinases in each site-specific recombinase family and recent advances in the application of these recombinases to genomic manipulation, especially manipulations involving site-specific gene integration into heterologous genomes. PMID:21822899

  12. Oxygen as a site specific structural probe in neutron diffraction

    SciTech Connect

    Neuefeind, Joerg C; Simonson, J Michael {Mike}; Salmon, Phil; Zeidler, Anita; Fischer, Henry E; Rauch, Helmut; Markland, Thomas; Lemmel, Hartmut

    2011-01-01

    Oxygen is a ubiquitous element, playing an essential role in most scientific and technological disciplines, and is often incorporated within a structurally disordered material where examples include molten silicates in planetary science, glasses used for lasers and optical communication, and water in biological processes. Establishing the structure of a liquid or glassy oxide and thereby its relation to the functional properties of a material is not, however, a trivial task owing to the complexity associated with atomic disorder. Here we approach this challenge by measuring the bound coherent neutron scattering lengths of the oxygen isotopes with the sensitive technique of neutron interferometry. We find that there is a small but finite contrast of 0.204(6) fm between the scattering lengths of the isotope 18O and oxygen of natural isotopic abundance natO, contrary to tables of recommended values. This has enabled us to investigate the structure of both light and heavy water by exploiting, for the first time, the method of oxygen isotope substitution in neutron diffraction, thus circumventing many of the significant problems associated with more traditional methods in which hydrogen is substituted by deuterium. We find a difference of ~0.5% between the O-H and O-D intra-molecular bond distances which is much smaller than recent estimates based on diffraction data and is found to be in excellent agreement with path integral molecular dynamics simulations made with a flexible polarisable water model. Our results demonstrate the potential for using oxygen isotope substitution as a powerful and effective site specific probe in a plethora of materials, of pertinence as instrumentation at next generation neutron sources comes online

  13. Utilization of Site-Specific Recombination in Biopharmaceutical Production.

    PubMed

    Ahmadi, Maryam; Damavandi, Narges; Akbari Eidgahi, Mohammad Reza; Davami, Fatemeh

    2016-01-01

    Mammalian expression systems, due to their capacity in post-translational modification, are preferred systems for biopharmaceutical protein production. Several recombinant protein systems have been introduced to the market, most of which are under clinical development. In spite of significant improvements such as cell line engineering, introducing novel expression methods, gene silencing and process development, expression level is unpredictable and unstable because of the random location of integration in the genome. Site-specific recombination techniques are capable of producing stable and high producer clonal cells; therefore, they are gaining more importance in the biopharmaceutical production. Site-specific recombination methods increase the recombinant protein production by specifically inserting a vector at a locus with specific expression trait. The present review focused on the latest developments in site-specific recombination techniques, their specific features and comparisons.

  14. Utilization of Site-Specific Recombination in Biopharmaceutical Production

    PubMed Central

    Ahmadi, Maryam; Damavandi, Narges; Akbari, Mohammad Reza; Davami, Fatemeh

    2016-01-01

    Mammalian expression systems, due to their capacity in post-translational modification, are preferred systems for biopharmaceutical protein production. Several recombinant protein systems have been introduced to the market, most of which are under clinical development. In spite of significant improvements such as cell line engineering, introducing novel expression methods, gene silencing and process development, expression level is unpredictable and unstable because of the random location of integration in the genome. Site-specific recombination techniques are capable of producing stable and high producer clonal cells; therefore, they are gaining more importance in the biopharmaceutical production. Site-specific recombination methods increase the recombinant protein production by specifically inserting a vector at a locus with specific expression trait. The present review focused on the latest developments in site-specific recombination techniques, their specific features and comparisons. PMID:26602035

  15. Naturally occurring arsenic in groundwater and identification of the geochemical sources in the Duero Cenozoic Basin, Spain

    NASA Astrophysics Data System (ADS)

    Gómez, J. J.; Lillo, J.; Sahún, B.

    2006-09-01

    Arsenic concentrations surpassing potability limit of 10 μg/L in the groundwater supplies of an extensive area in the Duero Cenozoic Basin (central Spain) have been detected and the main sources of arsenic identified. Arsenic in 514 samples of groundwater, having mean values of 40.8 μg/L, is natural in origin. Geochemical analysis of 553 rock samples, assaying arsenic mean values of 23 mg/kg, was performed. Spatial coincidence between the arsenic anomaly in groundwater and the arsenic lithogeochemical distribution recorded in the Middle Miocene clayey organic-rich Zaratan facies illustrates that the rocks of this unit are the main source of arsenic in groundwater. The ferricretes associated to the Late Cretaceous-Middle Miocene siliciclastics also constitute a potential arsenic source. Mineralogical study has identified the presence of arsenic in iron oxides, authigenic pyrite, manganese oxides, inherited titanium-iron oxides, phyllosilicates and organomineral compounds. Arsenic mobilization to groundwater corresponds to arsenic desorption from iron and manganese oxides and from organic matter.

  16. The geochemical behavior of natural radionuclides in coastal waters: A modeling study for the Huelva estuary

    NASA Astrophysics Data System (ADS)

    Periáñez, Raúl; Hierro, Almudena; Bolívar, Juan Pedro; Vaca, Federico

    2013-10-01

    A numerical model to study the behavior and distribution of natural radionuclides in sediments of an estuary (Odiel and Tinto rivers, SW Spain) affected by acid mine drainage and industrial activities has been developed. The model solves water circulation due to tides and river stream flows. The dispersion model includes uptake/release reactions of radionuclides between the dissolved phase and bed sediments in a dynamic way, using kinetic transfer coefficients. Seasonal pH and chlorinity distributions are simulated, and a formulation has been developed to consider these seasonal variations on kinetic coefficients. Calculated concentrations of 226Ra and 238U in sediments have been compared with measurements from four seasonal sampling campaigns. Numerical experiments have been carried out to study the relative significance of the different radionuclides sources into the estuary as well as the effect of the two components of water circulation (tides are river flows) on radionuclide dispersion patterns.

  17. Improving and testing geochemical speciation predictions of metal ions in natural waters.

    PubMed

    Ahmed, Imad A M; Hamilton-Taylor, John; Bieroza, Magdalena; Zhang, Hao; Davison, William

    2014-12-15

    The ability of WHAM VII and NICA-Donnan models to predict free-ion activities of Cu in natural waters was examined from two perspectives, (i) the presence of EDTA and NTA contaminants, (ii) the need to improve estimates of HA and FA concentrations. Potentiometric responses of a Cu(II) ion-selective electrode were investigated in five assays containing dissolved organic matter (DOM) isolated from a series of polluted (urban) and relatively unpolluted (upland) streams in northern England. The [Cu]/[DOC] ratio in these assays spanned an environmentally realistic range of ∼1-500 μmol/g. Reasonably good agreement between measured and predicted Cu(2+) activities was obtained with both WHAM VII and NICA-Donnan models, assuming 65% of DOM as fulvic acid and including the measured EDTA and NTA concentrations, but generally the models overestimated the activities by a factor of ∼2. In contrast, the models over-predicted the Cu(2+) activities by up to 2 orders of magnitude at low [Cu]/[DOC] ratios in urban waters if anthropogenic ligands were not included in the model simulations. Three-dimensional fluorescence excitation-emission matrix (EEM) spectroscopy was used to measure the functional properties of the isolated DOM and to estimate the fractions of FA and HA present. Using these fractions in the models gave improvements in predictions compared to the 65% FA assumption, as shown by higher correlations, reduced error and reduced bias. These results highlight various issues with the use of the available speciation models for predicting free ion concentrations in natural waters, such as the use of the Biotic Ligand Model (BLM) for the derivation of environmental standards. It is clearly necessary to measure EDTA and NTA in waters with urban influences, while fluorescence measurements offer the possibility of appreciably improving the accuracy of predictions.

  18. Uncertainty Analysis with Site Specific Groundwater Models: Experiences and Observations

    SciTech Connect

    Brewer, K.

    2003-07-15

    Groundwater flow and transport predictions are a major component of remedial action evaluations for contaminated groundwater at the Savannah River Site. Because all groundwater modeling results are subject to uncertainty from various causes; quantification of the level of uncertainty in the modeling predictions is beneficial to project decision makers. Complex site-specific models present formidable challenges for implementing an uncertainty analysis.

  19. Adoption of site-specific variable rate sprinkler irrigation systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than twenty years of private and public research on site-specific variable-rate sprinkler irrigation (SS-VRI) technology has resulted in limited commercial adoption of the technology. Competing patents, liability and proprietary software have affected industry’s willingness to move into a new t...

  20. Geochemical Evidence for Possible Natural Migration of Marcellus Formation Brine to Shallow Aquifers in Pennsylvania

    NASA Astrophysics Data System (ADS)

    Warner, N. R.; Darrah, T. H.; Jackson, R. B.; Osborn, S.; Down, A.; Vengosh, A.

    2012-12-01

    The acceleration in production of natural gas from shale formations through horizontal drilling and hydraulic fracturing has altered the landscape of domestic energy production in the USA. Yet shale gas exploration has generated an increased awareness of risks to drinking water quality amid concerns for the possible migration of stray gas or hydraulic fracturing fluid and/or flowback brine to shallow drinking water aquifers. The degree to which shallow drinking water is at risk from hydraulic fracturing could depend upon the hydraulic connectivity between the shale gas formations and the surface. In this study, we analyzed the geochemistry of over 400 water samples located across six counties of northeastern Pennsylvania in the three principle aquifers, two Upper Devonian Age bedrock aquifers (Catskill and Lock Haven) and one Quaternary Age (Alluvium) that overlie the Marcellus Formation. Based on a detailed analysis of major (Br, Cl, Na, Mg, Ba, and Sr) and trace (Li) element geochemistry, coupled with utilization of a specific spectrum of isotopic tracers (87Sr/86Sr, 228Ra/ 226Ra, 2H/H, 18O/16O), we identify a salinized (Cl> 20 mg/L) shallow groundwater type which suggests conservative mixing relationships between fresh shallow groundwater and an underlying brine. Identification of the brine source is complicated as many of the brines in the northern Appalachian Basin likely share a common origin as the expelled remnants of the formation of the Silurian Salina evaporate deposits. To determine the ultimate source of the diluted brine we compared the observed geochemistry to over 80 brines produced from northern Appalachian Basin formations. The shallow salinized groundwater most closely resembles diluted produced water from the Middle Devonian Marcellus Formation. The 18O/16O and 2H/H of the salinized groundwater indicate that the brine is likely diluted with post-glacial (<10,000 ybp) meteoric water. Combined, these data indicate that hydraulic connections

  1. IMPACTS OF SOLUBILITY AND OTHER GEOCHEMICAL PROCESSES ON RADIONUCLIDE RETARDATION IN THE NATURAL SYSTEM

    SciTech Connect

    B. Arnold

    2005-08-02

    This report documents results and findings of a study of solubility/co-precipitation effects and enhanced sorption due to variations in redox conditions on radionuclide transport in the natural system (BSC 2005 [DIRS 173951]; BSC 2005 [DIRS 173859]) conducted in response to DOE Contracting Officer Authorization Letter 05-001, Item d (Mitchell 2005 [DIRS 173265]). The purpose of this study is to assess the potential impacts of precipitation and enhanced sorption due to variations in redox conditions on radionuclide transport in the saturated zone (SZ) at Yucca Mountain. The information presented in this report is intended to aid in assessing the conservatism in the SZ transport model for supporting the total system performance assessment (TSPA) calculations. A similar study was performed for the impact of solubility/precipitation on radionuclide transport in the unsaturated zone (UZ). However, because the unsaturated zone is under predominantly oxidizing conditions and that the radionuclides released from the engineered barrier system are not expected to precipitate in the UZ for the reasons described below, it was concluded that the effect on unsaturated zone transport is not significant to warrant a detailed study. Solubility limiting conditions for neptunium in the UZ are expected to be similar to the conditions for neptunium solubility in the waste emplacement drift invert, where Np{sub 2}O{sub 5} is recommended as the controlling solid phase (BSC 2005 [DIRS 174566], Section 6.6.1). Solubility limits for neptunium inside the waste package, however, are expected to be controlled by NpO{sub 2} (BSC 2005 [DIRS 174566], Section 6.6.1). The solubility limits for Np2O5 are generally much higher than for NpO{sub 2} (BSC 2005 [DIRS 174566], Tables 6.6-4 and 6.6-7). Therefore, the low concentrations of neptunium releases from waste packages are unlikely to be affected by solubility limits in the unsaturated zone. The SZ is part of the Lower Natural Barrier to the

  2. Geochemical and Strontium Isotope Characterization of Produced Waters from Marcellus Shale Natural Gas Extraction

    SciTech Connect

    Elizabeth C. Chapman,† Rosemary C. Capo,† Brian W. Stewart,*,† Carl S. Kirby,‡ Richard W. Hammack,§ Karl T. Schroeder,§ and Harry M. Edenborn

    2012-02-24

    Extraction of natural gas by hydraulic fracturing of the Middle Devonian Marcellus Shale, a major gas-bearing unit in the Appalachian Basin, results in significant quantities of produced water containing high total dissolved solids (TDS). We carried out a strontium (Sr) isotope investigation to determine the utility of Sr isotopes in identifying and quantifying the interaction of Marcellus Formation produced waters with other waters in the Appalachian Basin in the event of an accidental release, and to provide information about the source of the dissolved solids. Strontium isotopic ratios of Marcellus produced waters collected over a geographic range of ∼375 km from southwestern to northeastern Pennsylvania define a relatively narrow set of values (εSr SW = +13.8 to +41.6, where εSr SW is the deviation of the 87Sr/86Sr ratio from that of seawater in parts per 104); this isotopic range falls above that of Middle Devonian seawater, and is distinct from most western Pennsylvania acid mine drainage and Upper Devonian Venango Group oil and gas brines. The uniformity of the isotope ratios suggests a basin-wide source of dissolved solids with a component that is more radiogenic than seawater. Mixing models indicate that Sr isotope ratios can be used to sensitively differentiate between Marcellus Formation produced water and other potential sources of TDS into ground or surface waters.

  3. Natural flow and vertical heterogeneities in a sedimentary geothermal reservoir (Paris Basin, France): Geochemical investigations

    SciTech Connect

    Criaud, Annie, Fouassier, Philippe; Fouillac, Christian; Brach, Michel

    1988-01-01

    Three geothermal wells tapping the Dogger aquifer were studied in detail for their variations in chemical composition with time or conditions of exploitation. Analytical improvements for the determination of Cl, SO{sub 4}, Ca, Mg, Na and K make it possible to detect variations respectively of 0.15, 0.8, 0.6, 1.8, 1.8 and 1.4 %. Despite the fact that the natural flow may be important in some parts of the basin aquifer, we conclude that this factor is not responsible for the small variations noticed in mineralization within the one year survey period. The results concerning reactive and nonreactive species are best explained if a vertical heterogeneity of the chemistry of the fluid is assumed. A number of calcareous sub-layers, already demonstrated by geological studies, contribute to varying degrees to the production of the hot water. The changes in pumping rates, which are fixed according to external requirements, play a major role in the hydrodynamic and chemical disequilibrium of the wells. The consequences for the geothermal exploitations are emphasized.

  4. Geochemical and Strontium Isotope Characterization of Produced Waters from Marcellus Shale Natural Gas Extraction

    SciTech Connect

    Chapman, Elizabeth C; Capo, Rosemary C.; Stewart, Brian W.; Kirby, Carl S.; Hammack, Richard W.; Schroeder, Karl T.; Edenborn, Harry M.

    2012-03-20

    Extraction of natural gas by hydraulic fracturing of the Middle Devonian Marcellus Shale, a major gas-bearing unit in the Appalachian Basin, results in significant quantities of produced water containing high total dissolved solids (TDS). We carried out a strontium (Sr) isotope investigation to determine the utility of Sr isotopes in identifying and quantifying the interaction of Marcellus Formation produced waters with other waters in the Appalachian Basin in the event of an accidental release, and to provide information about the source of the dissolved solids. Strontium isotopic ratios of Marcellus produced waters collected over a geographic range of 375 km from southwestern to northeastern Pennsylvania define a relatively narrow set of values (ε{sub Sr}{sup SW} = +13.8 to +41.6, where ε{sub Sr}{sup SW} is the deviation of the {sup 87}Sr/{sup 86}Sr ratio from that of seawater in parts per 10{sup 4}); this isotopic range falls above that of Middle Devonian seawater, and is distinct from most western Pennsylvania acid mine drainage and Upper Devonian Venango Group oil and gas brines. The uniformity of the isotope ratios suggests a basin-wide source of dissolved solids with a component that is more radiogenic than seawater. Mixing models indicate that Sr isotope ratios can be used to sensitively differentiate between Marcellus Formation produced water and other potential sources of TDS into ground or surface waters.

  5. Geochemical and strontium isotope characterization of produced waters from Marcellus Shale natural gas extraction.

    PubMed

    Chapman, Elizabeth C; Capo, Rosemary C; Stewart, Brian W; Kirby, Carl S; Hammack, Richard W; Schroeder, Karl T; Edenborn, Harry M

    2012-03-20

    Extraction of natural gas by hydraulic fracturing of the Middle Devonian Marcellus Shale, a major gas-bearing unit in the Appalachian Basin, results in significant quantities of produced water containing high total dissolved solids (TDS). We carried out a strontium (Sr) isotope investigation to determine the utility of Sr isotopes in identifying and quantifying the interaction of Marcellus Formation produced waters with other waters in the Appalachian Basin in the event of an accidental release, and to provide information about the source of the dissolved solids. Strontium isotopic ratios of Marcellus produced waters collected over a geographic range of ~375 km from southwestern to northeastern Pennsylvania define a relatively narrow set of values (ε(Sr)(SW) = +13.8 to +41.6, where ε(Sr) (SW) is the deviation of the (87)Sr/(86)Sr ratio from that of seawater in parts per 10(4)); this isotopic range falls above that of Middle Devonian seawater, and is distinct from most western Pennsylvania acid mine drainage and Upper Devonian Venango Group oil and gas brines. The uniformity of the isotope ratios suggests a basin-wide source of dissolved solids with a component that is more radiogenic than seawater. Mixing models indicate that Sr isotope ratios can be used to sensitively differentiate between Marcellus Formation produced water and other potential sources of TDS into ground or surface waters. PMID:22360406

  6. Geochemical gradients in soil O-horizon samples from southern Norway: Natural or anthropogenic?

    USGS Publications Warehouse

    Reimann, C.; Englmaier, P.; Flem, B.; Gough, L.; Lamothe, P.; Nordgulen, O.; Smith, D.

    2009-01-01

    Forty soil O- and C-horizon samples were collected along a south-to-north transect extending inland for approximately 200 km from the southern tip of Norway. The elements As, Au, Bi, Cd, Cu, Ga, Ge, Hf, Hg, In, Mg, Mn, Mo, Na, Ni, Pb, Sb, Se, V, W, Zn and Zr all show a distinct decrease in concentration in soil O-horizons with increasing distance from the coast. The elements showing the strongest coastal enrichment, some by more than an order of magnitude compared to inland samples, are Au, Bi, As, Pb, Sb and Sn. Furthermore, the elements Cd (median O-/median C-horizon = 31), C, Sb, Ag, K, S, Ge (10), Hg, Pb, As, Bi, Sr (5), Se, Au, Ba, Na, Zn, P, Cu and Sn (2) are all strongly enriched in the O-horizon when compared to the underlying C-horizon. Lead isotope ratios, however, do not show any gradient with distance from the coast (declining Pb concentration). Along a 50 km topographically steep east-west transect in the centre of the survey area, far from the coast but crossing several vegetation zones, similar element enrichment patterns and concentration gradients can be observed in the O-horizon. Lead isotope ratios in the O-horizon correlate along both transects with pH and the C/N-ratio, both proxies for the quality of the organic material. Natural conditions in southern Norway, related to climate and vegetation, rather than long range atmospheric transport of air pollutants (LRT), cause the observed features. ?? 2008 Elsevier Ltd.

  7. Highly efficient site-specific transgenesis in cancer cell lines

    PubMed Central

    2012-01-01

    Background Transgenes introduced into cancer cell lines serve as powerful tools for identification of genes involved in cancer. However, the random nature of genomic integration site of a transgene highly influences the fidelity, reliability and level of its expression. In order to alleviate this bottleneck, we characterized the potential utility of a novel PhiC31 integrase-mediated site-specific insertion system (PhiC31-IMSI) for introduction of transgenes into a pre-inserted docking site in the genome of cancer cells. Methods According to this system, a “docking-site” was first randomly inserted into human cancer cell lines and clones with a single copy were selected. Subsequently, an “incoming” vector containing the gene of interest was specifically inserted in the docking-site using PhiC31. Results Using the Pc-3 and SKOV-3 cancer cell lines, we showed that transgene insertion is reproducible and reliable. Furthermore, the selection system ensured that all surviving stable transgenic lines harbored the correct integration site. We demonstrated that the expression levels of reporter genes, such as green fluorescent protein and luciferase, from the same locus were comparable among sister, isogenic clones. Using in vivo xenograft studies, we showed that the genetically altered cancer cell lines retain the properties of the parental line. To achieve temporal control of transgene expression, we coupled our insertion strategy with the doxycycline inducible system and demonstrated tight regulation of the expression of the antiangiogenic molecule sFlt-1-Fc in Pc-3 cells. Furthermore, we introduced the luciferase gene into the insertion cassette allowing for possible live imaging of cancer cells in transplantation assays. We also generated a series of Gateway cloning-compatible intermediate cassettes ready for high-throughput cloning of transgenes and demonstrated that PhiC31-IMSI can be achieved in a high throughput 96-well plate format. Conclusions The novel

  8. Geochemical variability of natural soils and reclaimed minespoil soils in the San Juan Basin, New Mexico

    USGS Publications Warehouse

    Gough, L.P.; Severson, R.C.

    1981-01-01

    An inventory of total-and extractable-element concentrations in soils was made for three areas of the San Juan Basin in New Mexico: (1) the broad area likely to be affected by energy-related development. (2) an area of soils considered to have potential for use as topsoil in mined-land reclamation. and (3) an area of the San Juan coal mine that has been regraded. topsoiled, and revegetated. Maps made of concentrations of 16 elements in area 1 soils show no gradational pattern across the region. Further. these maps do not correspond to those showing geology or soil types. Sodic or saline problems, and a possible but unproven deficiency of zinc available to plants. may make some of the soils in this area undesirable for use as topsoil in mined-land reclamation. Taxonomic great groups of soil in this area cannot be distinguished because each great group tends to have a large within-group variability if compared to the between-group variability. In area 2 the major soils sampled were of the Sheppard. Shiprock. and Doak association. These soils are quite uniform in chemical composition and are not greatly saline or sodic. As in area 1 soils. zinc deficiency may cause a problem in revegetating most of these soils. It is difficult to distinguish soil taxonomic families by using their respective chemical compositions. because of small between-family variability. Topsoil from a reclaimed area of the San Juan mine (area 3) most closely resembles the chemical composition of natural C horizons of soil from area 1. Spoil material that has not been topsoiled is likely to cause sodic-and saline-related problems in revegetation and may cause boron toxicity in plants. Topsoiling has apparently ameliorated these potential problems for plant growth on mine spoil. Total and extractable concentrations for elements and other parameters for each area of the San Juan Basin provide background information for the evaluation of the chemical quality of soils in each area.

  9. Stratigraphic and geochemical controls on naturally occurring arsenic in groundwater, eastern Wisconsin, USA

    NASA Astrophysics Data System (ADS)

    Schreiber, M. E.; Simo, J. A.; Freiberg, P. G.

    High arsenic concentrations (up to 12,000μg/L) have been measured in groundwater from a confined sandstone aquifer in eastern Wisconsin. The main arsenic source is a sulfide-bearing secondary cement horizon (SCH) that has variable thickness, morphology, and arsenic concentrations. Arsenic occurs in pyrite and marcasite as well as in iron oxyhydroxides but not as a separate arsenopyrite phase. Nearly identical sulfur isotopic signatures in pyrite and dissolved sulfate and the correlation between dissolved sulfate, iron, and arsenic concentrations suggest that sulfide oxidation is the dominant process controlling arsenic release to groundwater. However, arsenic-bearing oxyhydroxides can potentially provide another arsenic source if reducing conditions develop or if they are transported as colloids in the aquifer. Analysis of well data indicates that the intersection of the SCH with static water levels measured in residential wells is strongly correlated with high concentrations of arsenic in groundwater. Field and laboratory data suggest that the most severe arsenic contamination is caused by localized borehole interactions of air, water, and sulfides. Although arsenic contamination is caused by oxidation of naturally occurring sulfides, it is influenced by water-level fluctuations caused by municipal well pumping or climate changes, which can shift geographic areas in which contamination occurs. Résumé De fortes concentrations en arsenic, jusqu'à 12000μg/L, ont été mesurées dans l'eau souterraine d'un aquifère gréseux captif, dans l'est du Wisconsin. La principale source d'arsenic est un horizon à cimentation secondaire (SCH) comportant des sulfures, dont l'épaisseur, la morphologie et les concentrations en arsenic sont variables. L'arsenic est présent dans la pyrite et dans la marcassite, de même que dans des oxy-hydroxydes de fer, mais non pas dans une phase séparée d'arsénopyrite. Les signatures isotopiques du soufre presque identiques dans la

  10. Site-Specific Biomolecule Labeling with Gold Clusters

    PubMed Central

    Ackerson, Christopher J.; Powell, Richard D.; Hainfeld, James F.

    2013-01-01

    Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: Linker-mediated bioconjugation, direct gold–biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (His)-tagged proteins. PMID:20887859

  11. Pretargeted PET Imaging Using a Site-Specifically Labeled Immunoconjugate.

    PubMed

    Cook, Brendon E; Adumeau, Pierre; Membreno, Rosemery; Carnazza, Kathryn E; Brand, Christian; Reiner, Thomas; Agnew, Brian J; Lewis, Jason S; Zeglis, Brian M

    2016-08-17

    In recent years, both site-specific bioconjugation techniques and bioorthogonal pretargeting strategies have emerged as exciting technologies with the potential to improve the safety and efficacy of antibody-based nuclear imaging. In the work at hand, we have combined these two approaches to create a pretargeted PET imaging strategy based on the rapid and bioorthogonal inverse electron demand Diels-Alder reaction between a (64)Cu-labeled tetrazine radioligand ((64)Cu-Tz-SarAr) and a site-specifically modified huA33-trans-cyclooctene immunoconjugate ((ss)huA33-PEG12-TCO). A bioconjugation strategy that harnesses enzymatic transformations and strain-promoted azide-alkyne click chemistry was used to site-specifically append PEGylated TCO moieties to the heavy chain glycans of the colorectal cancer-targeting huA33 antibody. Preclinical in vivo validation studies were performed in athymic nude mice bearing A33 antigen-expressing SW1222 human colorectal carcinoma xenografts. To this end, mice were administered (ss)huA33-PEG12-TCO via tail vein injection and-following accumulation intervals of 24 or 48 h-(64)Cu-Tz-SarAr. PET imaging and biodistribution studies reveal that this strategy clearly delineates tumor tissue as early as 1 h post-injection (6.7 ± 1.7%ID/g at 1 h p.i.), producing images with excellent contrast and high tumor-to-background activity concentration ratios (tumor:muscle = 21.5 ± 5.6 at 24 h p.i.). Furthermore, dosimetric calculations illustrate that this pretargeting approach produces only a fraction of the overall effective dose (0.0214 mSv/MBq; 0.079 rem/mCi) of directly labeled radioimmunoconjugates. Ultimately, this method effectively facilitates the high contrast pretargeted PET imaging of colorectal carcinoma using a site-specifically modified immunoconjugate. PMID:27356886

  12. Geochemical evidence concerning the nature of the source region to the Middle Proterozoic Granite-Rhyolite Province

    SciTech Connect

    Shuster, R.D. . Dept. Geography Mueller, P.A.; Heatherington, A.L. . Dept. Geology)

    1992-01-01

    The mostly buried 1.5--1.3 Ga old Granite-Rhyolite Province of the midcontinent of North America, is characterized by extensive, undeformed silicic volcanic rocks and related epizonal granitic plutons. Thirty-three previously dated samples from a wide geographic range (Michigan to Colorado) have been analyzed to determine their chemical and Nd and Pb isotopic compositions in order to constrain source regions and processes involved in the formation of these rocks. Major and trace element analyses of these rocks indicate their anorogenic nature, with relatively high Ce/Nb and Y/Nb ratios, as well as relatively high Ga/Al ratios. Geochemically, these rocks are similar to the A2 granites of Eby (1992), which are thought to be generated from the melting of crust which has experienced at least one cycle of subduction-related magmatism. Rare earth element and Pb isotopic data suggest melting at middle to shallow depths. The isotopic data (Nd and Pb) indicate little to no contribution of Archean crust to the source of these rocks. Initial Pb isotopic ratios (208Pb/204Pb) suggest a low Th/U ratio in the source, which contrasts strongly with high Th/U ratios of the Wyoming Province. The Pb isotopic ratios for these rocks are variable, but cluster about the orogene plumbotectonics curve. The variability in the data suggest sources which are variable in their U/Pb ratios and/or ages. The isotopic data are consistent with the existence of a proposed lithospheric boundary which trend NE-SW through the Granite-Rhyolite Province and separates 1.65 Ga old lithosphere (to the NW) from 1.5 Ga old lithosphere (to the SE). Samples analyzed from either side of this boundary have different isotopic signatures. Many of the samples appear to be derived from sources which are only slightly older than the crystallization ages of the granites themselves.

  13. Formation and geochemical significance of micrometallic aggregates including fissiogenic platinum group elements in the Oklo natural reactor, Gabon

    NASA Astrophysics Data System (ADS)

    Kikuchi, Makiko; Hidaka, Hiroshi; Gauthier-Lafaye, François

    2010-08-01

    Metallic aggregates with a size of a few tens μm and consisting mainly of Ru, Rh, Pd, Te, Pb, As, Sb, S and Bi were found in the acid residue of SD37-S2/CD uraninite taken from Oklo natural reactor zone (RZ) 13. Quantitative analyses of major elements using an electron probe microanalyzer and in situ isotopic analyses of Zr, Mo, Ru, Pb and U using a sensitive high-resolution ion microprobe were performed on the metallic aggregates to determine the geochemical behaviors of fission products and actinides and to ascertain the processes of formation of the aggregates in the RZs. The chemical compositions of the aggregates investigated in this study are significantly different from those reported previously, showing lower Pb content and no correlation between the contents of Pb and S in the individual grains. The 235U/ 238U ratios in metallic aggregates vary significantly from 0.00478 to 0.01466, indicating chemical fractionation between U and Pu during the formation of the aggregates. The Pb isotopic data indicate that most of the Pb in the aggregates decayed from 2.05 Ga-old uraninite that existed in the RZ originally and that there was chemical fractionation between U and Pb in some aggregates. The Zr and Mo isotopic ratios, 90Zr/ 91Zr and 95Mo/ 97Mo, for most of the aggregates had small variations, which can be simply explained by constant separate mixing of fissiogenic and nonfissiogenic components. On the other hand, a large variation in the 99Ru/ 101Ru ratio (0.324-1.73) cannot be explained only by a two component mixing theory; thus, chemical fractionation between Tc and Ru during the reactor criticality is suggested. The large variations in the 235U/ 238U and 99Ru/ 101Ru isotopic ratios suggest that the aggregates formed under various redox conditions owing to the radiolysis of water.

  14. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    SciTech Connect

    Zope, Rajendra R. Baruah, Tunna; Bhusal, Shusil; Basurto, Luis; Jackson, Koblar

    2015-08-28

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C{sub 60}@C{sub 240} and C{sub 60}@C{sub 180} onions shows that, compared to the polarizability of isolated C{sub 60} fullerene, the encapsulation of the C{sub 60} in C{sub 240} and C{sub 180} fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C{sub 60} in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  15. Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

    NASA Astrophysics Data System (ADS)

    Zope, Rajendra R.; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

    2015-08-01

    We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

  16. Site Specific Probable Maximum Precipitation Estimates and Professional Judgement

    NASA Astrophysics Data System (ADS)

    Hayes, B. D.; Kao, S. C.; Kanney, J. F.; Quinlan, K. R.; DeNeale, S. T.

    2015-12-01

    State and federal regulatory authorities currently rely upon the US National Weather Service Hydrometeorological Reports (HMRs) to determine probable maximum precipitation (PMP) estimates (i.e., rainfall depths and durations) for estimating flooding hazards for relatively broad regions in the US. PMP estimates for the contributing watersheds upstream of vulnerable facilities are used to estimate riverine flooding hazards while site-specific estimates for small water sheds are appropriate for individual facilities such as nuclear power plants. The HMRs are often criticized due to their limitations on basin size, questionable applicability in regions affected by orographic effects, their lack of consist methods, and generally by their age. HMR-51 for generalized PMP estimates for the United States east of the 105th meridian, was published in 1978 and is sometimes perceived as overly conservative. The US Nuclear Regulatory Commission (NRC), is currently reviewing several flood hazard evaluation reports that rely on site specific PMP estimates that have been commercially developed. As such, NRC has recently investigated key areas of expert judgement via a generic audit and one in-depth site specific review as they relate to identifying and quantifying actual and potential storm moisture sources, determining storm transposition limits, and adjusting available moisture during storm transposition. Though much of the approach reviewed was considered a logical extension of HMRs, two key points of expert judgement stood out for further in-depth review. The first relates primarily to small storms and the use of a heuristic for storm representative dew point adjustment developed for the Electric Power Research Institute by North American Weather Consultants in 1993 in order to harmonize historic storms for which only 12 hour dew point data was available with more recent storms in a single database. The second issue relates to the use of climatological averages for spatially

  17. Site-specific polymer modification of therapeutic proteins.

    PubMed

    Kochendoerfer, Gerd G

    2005-12-01

    Recent advances in chemoselective ligation technology have made possible the modification of proteins with polymers in a site-specific and controlled manner. These approaches rely on the incorporation of chemoselective anchors into the protein backbone by either chemical or recombinant means, and subsequent modification with a polymer carrying a complementary linker. As a result, the assembly process and the covalent structure of the resulting protein-polymer conjugate are completely controlled, enabling the rational optimization of drug properties, in particular efficacy and pharmacokinetic properties. Application of chemoselective ligation technologies to cytokines and chemokines has led to the generation of new lead proteins for use as erythropoietic agents and HIV fusion inhibitors.

  18. Chemical tags for site-specific fluorescent labeling of biomolecules.

    PubMed

    Freidel, Christoph; Kaloyanova, Stefka; Peneva, Kalina

    2016-06-01

    This review focuses on the various approaches to covalently attach a chromophore to a biomolecule of interest in site-specific manner. Novel methods like inverse electron-demand Diels-Alder reaction, Pictet-Spengler ligation and enzyme tags like SNAP and Halo-tags are critically discussed and compared to established techniques like copper-free click reaction and native chemical ligation. Selected examples in which the tags have been exploited for in vitro or in vivo imaging are reviewed and evaluated. PMID:26969255

  19. IRON PRECIPITATION AND ARSENIC ATTENUATION - ASSESSMENT OF ARSENIC NATURAL ATTENUATION OF THE SUBSURFACE USING A GEOCHEMICAL MODEL (PHREEQC)

    EPA Science Inventory

    Laboratory experiments show that amorphous and poorly crystallized ferric iron hydroxides have much greater capacity to attenuate arsenic compared to clays and other aluminosilicate minerals. Studies (e.g., Lin and Qvarfort, 1996) showed that a sudden change in geochemical condit...

  20. Reaction kinetics of some important site-specific endonucleases.

    PubMed Central

    Hinsch, B; Kula, M R

    1981-01-01

    Reaction kinetics of the site-specific endonucleases BamHI, BgIII, C1aI, EcoRI, HpaII, PstI, SaII, SmaI, and XorII were investigated employing some frequently used substrates. Six of these enzymes could be analyzed under steady-state conditions. Kinetic data were obtained from progress curves applying an integrated Michaelis-Menten equation. KM ranged from 4 x 10(-9) M to 4 x 10(-11) M. Activities also spanned two orders of magnitude. In the case of C1aI the analysis of the pre-steady-state kinetics ("burst reaction") allowed the assessment of several rate constants. The rate-limiting step is the very slow dissociation of the enzyme-product complex (0.22 min(-1)). This complex is formed from the enzyme-bound nicked intermediate at a rate of 1.7 min(-1). The introduction of the first cut is again faster by a factor of about 6. SmaI and XorII resembled C1aI in their kinetics. The burst reaction can be used for the easy and unambiguous determination of molar concentrations of site-specific endonucleases in any preparation, which is free of non-specific DNases. PMID:6269074

  1. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe.

    PubMed

    Shao, Nan; Singh, N Sadananda; Slade, Susan E; Jones, Alexandra M E; Balasubramanian, Mohan K

    2015-01-01

    The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNA(Tyr) and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins.

  2. Towards soft robotic devices for site-specific drug delivery.

    PubMed

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications. PMID:26415110

  3. Recent advances in covalent, site-specific protein immobilization

    PubMed Central

    Meldal, Morten; Schoffelen, Sanne

    2016-01-01

    The properties of biosensors, biomedical implants, and other materials based on immobilized proteins greatly depend on the method employed to couple the protein molecules to their solid support. Covalent, site-specific immobilization strategies are robust and can provide the level of control that is desired in this kind of application. Recent advances include the use of enzymes, such as sortase A, to couple proteins in a site-specific manner to materials such as microbeads, glass, and hydrogels. Also, self-labeling tags such as the SNAP-tag can be employed. Last but not least, chemical approaches based on bioorthogonal reactions, like the azide–alkyne cycloaddition, have proven to be powerful tools. The lack of comparative studies and quantitative analysis of these immobilization methods hampers the selection process of the optimal strategy for a given application. However, besides immobilization efficiency, the freedom in selecting the site of conjugation and the size of the conjugation tag and the researcher’s expertise regarding molecular biology and/or chemical techniques will be determining factors in this regard. PMID:27785356

  4. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe

    PubMed Central

    Shao, Nan; Singh, N. Sadananda; Slade, Susan E.; Jones, Alexandra M. E.; Balasubramanian, Mohan K.

    2015-01-01

    The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins. PMID:26597962

  5. Towards soft robotic devices for site-specific drug delivery.

    PubMed

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications.

  6. Site-specific Probabilistic Seismic Hazard Map of Himachal Pradesh, India. Part I. Site-specific Ground Motion Relations

    NASA Astrophysics Data System (ADS)

    Muthuganeisan, Prabhu; Raghukanth, S. T. G.

    2016-04-01

    This article presents four regional site-specific ground motion relations developed for the state of Himachal Pradesh in northwest Himalaya, situated in a seismically active region. These relations are developed from synthetic free surface ground motion databases obtained from a calibrated stochastic seismological model considering the characteristic properties of this specific region. The adopted methodology incorporates the site effects characterised through active MASW tests conducted in 22 important cities. The estimated ground motion levels from the developed relations are found to be in reasonable agreement with the recorded data.

  7. Generic guidelines versus site-specific assessments: Does marriage make sense?

    SciTech Connect

    Gaudet, C.L.; Keenleyside, K.A.; Smith, S.L.; Kent, R.A.; Wong, M.P.

    1995-12-31

    The maintenance, protection and restoration of a high level of environmental quality requires the availability of practical scientific tools. Environmental quality guidelines (also called criteria) are one such scientific tool that help measure progress towards these goals. These guidelines provide scientific benchmarks that can offer consistency and clarity in defining scientific measures for environmental quality that are easily understood, communicated, and implemented as the basis for management decisions. At the same time, debate exists over the use of generic guidelines versus site-specific risk assessments. It is the contention that generic and site-specific approaches are not mutually exclusive, but complementary decision-support tools and that any apparent controversy stems from an incomplete understanding of the nature and intent of generic environmental quality guidelines or from the use of guidelines in the absence of a coherent framework. The authors advocate an approach that marries the strengths of the generic and site-specific approaches and promotes consistent, scientifically-defensible decisions that support broad societal goals for environmental protection. Using Canadian environmental quality guidelines as an example, they provide an overview of the role of environmental quality guidelines in decision-making, with concrete examples of their implementation in addressing specific environmental quality issues.

  8. Site-specific fatty acid-conjugation to prolong protein half-life in vivo.

    PubMed

    Lim, Sung In; Mizuta, Yukina; Takasu, Akinori; Hahn, Young S; Kim, Yong Hwan; Kwon, Inchan

    2013-09-10

    Therapeutic proteins are indispensable in treating numerous human diseases. However, therapeutic proteins often suffer short serum half-life. In order to extend the serum half-life, a natural albumin ligand (a fatty acid) has been conjugated to small therapeutic peptides resulting in a prolonged serum half-life via binding to patients' serum albumin in vivo. However, fatty acid-conjugation has limited applicability due to lack of site-specificity resulting in the heterogeneity of conjugated proteins and a significant loss in pharmaceutical activity. In order to address these issues, we exploited the site-specific fatty acid-conjugation to a permissive site of a protein, using copper-catalyzed alkyne-azide cycloaddition, by linking a fatty acid derivative to p-ethynylphenylalanine incorporated into a protein using an engineered pair of yeast tRNA/aminoacyl tRNA synthetase. As a proof-of-concept, we show that single palmitic acid conjugated to superfolder green fluorescent protein (sfGFP) in a site-specific manner enhanced a protein's albumin-binding in vitro about 20 times and the serum half-life in vivo 5 times when compared to those of the unmodified sfGFP. Furthermore, the fatty acid conjugation did not cause a significant reduction in the fluorescence of sfGFP. Therefore, these results clearly indicate that the site-specific fatty acid-conjugation is a very promising strategy to prolong protein serum half-life in vivo without compromising its folded structure and activity.

  9. Site-Specific Genome Engineering in Human Pluripotent Stem Cells

    PubMed Central

    Merkert, Sylvia; Martin, Ulrich

    2016-01-01

    The possibility to generate patient-specific induced pluripotent stem cells (iPSCs) offers an unprecedented potential of applications in clinical therapy and medical research. Human iPSCs and their differentiated derivatives are tools for diseases modelling, drug discovery, safety pharmacology, and toxicology. Moreover, they allow for the engineering of bioartificial tissue and are promising candidates for cellular therapies. For many of these applications, the ability to genetically modify pluripotent stem cells (PSCs) is indispensable, but efficient site-specific and safe technologies for genetic engineering of PSCs were developed only recently. By now, customized engineered nucleases provide excellent tools for targeted genome editing, opening new perspectives for biomedical research and cellular therapies. PMID:27347935

  10. Site-specific dual ink dip pen nanolithography

    NASA Astrophysics Data System (ADS)

    Nafday, Omkar A.; Haaheim, Jason R.; Villagran, Fredy; Levesque, Tom

    2009-05-01

    The ability to deposit two different materials with nanoscale precision at user specified locations is a very important attribute of dip pen nanolithography (DPN). However, the potential of DPN goes beyond simple deposition since DPN used in conjunction with lateral force microscopy (LFM) allows site-specific investigations of nanoscale properties. In this work, we use two different inks, 16-Mercaptohexadecanoic acid (MHA) and 1-octadenethiol (ODT) to show sitespecific dual ink DPN enabled exclusively by our proprietary software. A diamond-dot pattern was created by using a layer-to-layer alignment (LLA) algorithm which enables the MHA (diamond) to be written concentric with the ODT (central dot) pattern. This simple demonstration of multi-ink DPN is not specific to alkanethiol ink systems, but is also applicable to other multi-material patterning, interaction and exchange studies.

  11. Site-Specific Genome Engineering in Human Pluripotent Stem Cells.

    PubMed

    Merkert, Sylvia; Martin, Ulrich

    2016-01-01

    The possibility to generate patient-specific induced pluripotent stem cells (iPSCs) offers an unprecedented potential of applications in clinical therapy and medical research. Human iPSCs and their differentiated derivatives are tools for diseases modelling, drug discovery, safety pharmacology, and toxicology. Moreover, they allow for the engineering of bioartificial tissue and are promising candidates for cellular therapies. For many of these applications, the ability to genetically modify pluripotent stem cells (PSCs) is indispensable, but efficient site-specific and safe technologies for genetic engineering of PSCs were developed only recently. By now, customized engineered nucleases provide excellent tools for targeted genome editing, opening new perspectives for biomedical research and cellular therapies. PMID:27347935

  12. Site-specific gene therapy for cardiovascular disease

    PubMed Central

    Fishbein, Ilia; Chorny, Michael; Levy, Robert J

    2010-01-01

    Gene therapy holds considerable promise for the treatment of cardiovascular disease and may provide novel therapeutic solutions for both genetic disorders and acquired pathophysiologies such as arteriosclerosis, heart failure and arrhythmias. Recombinant DNA technology and the sequencing of the human genome have made a plethora of candidate therapeutic genes available for cardiovascular diseases. However, progress in the field of gene therapy for cardiovascular disease has been modest; one of the key reasons for this limited progress is the lack of gene delivery systems for localizing gene therapy to specific sites to optimize transgene expression and efficacy. This review summarizes progress made toward the site-specific delivery of cardiovascular gene therapy and highlights selected promising novel approaches. PMID:20205054

  13. Hydrazide Reactive Peptide Tags for Site-Specific Protein Labeling

    PubMed Central

    Eldridge, Glenn M.; Weiss, Gregory A.

    2011-01-01

    New site-specific protein labeling (SSPL) reactions for targeting specific, short peptides could be useful for the real time detection of proteins inside of living cells. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from phage-displayed libraries using reaction-based selections. Selection conditions included washes of varying pH and treatment with NaCNBH3 in order to specifically select reactive carbonyl containing peptides. Selected peptides were fused to T4 lysozyme or synthesized on filter paper for colorimetric assays of the peptide-hydrazide interaction. A peptide-lysozyme protein fusion demonstrated specific, covalent labeling by the Hydrazide Reactive (HyRe) peptides in crude bacterial cell lysates, sufficient for the specific detection of an over-expressed protein fusion. Chemical synthesis of a short HyRe tag variant and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Rather than isolating reactive carbonyl-containing peptides, we observed reaction with the N–terminal His of HyRe tag 114, amino acid sequence HKSNHSSKNRE, which attacks the hydrazide carbonyl at neutral pH. However, at the pH used during selection wash steps (<6.0), an alternative imine-containing product is formed that can be reduced with sodium cyanoborohydride. MSMS further reveals that this low pH product forms an adduct on Ser6. Further optimization of the novel bimolecular reaction described here could provide a useful tool for in vivo protein labeling and bioconjugate synthesis. The reported selection and screening methods could be widely applicable to the identification of peptides capable of other site-specific protein labeling reactions with bioorthogonal reagents. PMID:21905743

  14. Site-specific DNA Inversion by Serine Recombinases

    PubMed Central

    2015-01-01

    Reversible site-specific DNA inversion reactions are widely distributed in bacteria and their viruses. They control a range of biological reactions that most often involve alterations of molecules on the surface of cells or phage. These programmed DNA rearrangements usually occur at a low frequency, thereby preadapting a small subset of the population to a change in environmental conditions, or in the case of phages, an expanded host range. A dedicated recombinase, sometimes with the aid of additional regulatory or DNA architectural proteins, catalyzes the inversion of DNA. RecA or other components of the general recombination-repair machinery are not involved. This chapter discusses site-specific DNA inversion reactions mediated by the serine recombinase family of enzymes and focuses on the extensively studied serine DNA invertases that are stringently controlled by the Fis-bound enhancer regulatory system. The first section summarizes biological features and general properties of inversion reactions by the Fis/enhancer-dependent serine invertases and the recently described serine DNA invertases in Bacteroides. Mechanistic studies of reactions catalyzed by the Hin and Gin invertases are then discussed in more depth, particularly with regards to recent advances in our understanding of the function of the Fis/enhancer regulatory system, the assembly of the active recombination complex (invertasome) containing the Fis/enhancer, and the process of DNA strand exchange by rotation of synapsed subunit pairs within the invertasome. The role of DNA topological forces that function in concert with the Fis/enhancer controlling element in specifying the overwhelming bias for DNA inversion over deletion and intermolecular recombination is emphasized. PMID:25844275

  15. Geographic origin determination of heroin and cocaine using site-specific isotopic ratio deuterium NMR

    PubMed

    Hays; Remaud; Jamin; Martin

    2000-05-01

    SNIF-NMR (Site-specific natural isotopic fractionation measured by deuterium NMR) was employed on 36 heroin samples from seven different known origins, and two cocaine samples from two different known origins. Heroin has two "synthetic" deuterium labeled sites (the two acetyls from acetic anhydride, each representing three equivalent nuclei) and 15 "natural" deuterium labeled sites (originating from the morphine produced in the opium plant). The "natural" sites have the potential for determining geographic location of the original opium plant, while the "synthetic" sites could assist in giving information about the commercial source of acetic anhydride used to convert morphine to heroin. Cocaine has 15 "natural" deuterium labeled sites. This study shows that SNIF-NMR has some use in determining the geographic origin of heroin and also has good potential for determining the geographical origin of cocaine.

  16. Simultaneous Site-Specific Dual Protein Labeling Using Protein Prenyltransferases.

    PubMed

    Zhang, Yi; Blanden, Melanie J; Sudheer, Ch; Gangopadhyay, Soumyashree A; Rashidian, Mohammad; Hougland, James L; Distefano, Mark D

    2015-12-16

    Site-specific protein labeling is an important technique in protein chemistry and is used for diverse applications ranging from creating protein conjugates to protein immobilization. Enzymatic reactions, including protein prenylation, have been widely exploited as methods to accomplish site-specific labeling. Enzymatic prenylation is catalyzed by prenyltransferases, including protein farnesyltransferase (PFTase) and geranylgeranyltransferase type I (GGTase-I), both of which recognize C-terminal CaaX motifs with different specificities and transfer prenyl groups from isoprenoid diphosphates to their respective target proteins. A number of isoprenoid analogues containing bioorthogonal functional groups have been used to label proteins of interest via PFTase-catalyzed reaction. In this study, we sought to expand the scope of prenyltransferase-mediated protein labeling by exploring the utility of rat GGTase-I (rGGTase-I). First, the isoprenoid specificity of rGGTase-I was evaluated by screening eight different analogues and it was found that those with bulky moieties and longer backbone length were recognized by rGGTase-I more efficiently. Taking advantage of the different substrate specificities of rat PFTase (rPFTase) and rGGTase-I, we then developed a simultaneous dual labeling method to selectively label two different proteins by using isoprenoid analogue and CaaX substrate pairs that were specific to only one of the prenyltransferases. Using two model proteins, green fluorescent protein with a C-terminal CVLL sequence (GFP-CVLL) and red fluorescent protein with a C-terminal CVIA sequence (RFP-CVIA), we demonstrated that when incubated together with both prenyltransferases and the selected isoprenoid analogues, GFP-CVLL was specifically modified with a ketone-functionalized analogue by rGGTase-I and RFP-CVIA was selectively labeled with an alkyne-containing analogue by rPFTase. By switching the ketone-containing analogue to an azide-containing analogue, it was

  17. Inducible site-specific recombination in myelinating cells.

    PubMed

    Doerflinger, Nathalie H; Macklin, Wendy B; Popko, Brian

    2003-01-01

    To explore the function of genes expressed by myelinating cells we have developed a model system that allows for the inducible ablation of predetermined genes in oligodendrocytes and Schwann cells. The Cre/loxP recombination system provides the opportunity to generate tissue-specific somatic mutations in mice. We have used a fusion protein between the Cre recombinase and a mutated ligand-binding domain of the human estrogen receptor (CreER(T)) to obtain inducible, site-specific recombination. CreER(T) expression was placed under the transcriptional control of the regulatory sequences of the myelin proteolipid protein (PLP) gene, which is abundantly expressed in oligodendrocytes and to a lesser extent in Schwann cells. The CreER(T) fusion protein translocated to the nucleus and mediated the recombination of a LacZ reporter transgene in myelinating cells of PLP/CreER(T) mice injected with the synthetic steroid tamoxifen. In untreated animals CreER(T) remained cytoplasmic, and there was no evidence of recombination. The PLP/ CreER(T) animals should be very useful in elucidating and distinguishing a particular gene's function in the formation and maintenance of the myelin sheath and in analyzing mature oligodendrocyte function in pathological conditions. PMID:12481300

  18. Site-specific basal body duplication in Chlamydomonas.

    PubMed

    O'Toole, Eileen T; Dutcher, Susan K

    2014-02-01

    Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine-singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1-1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site-specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation.

  19. Site-specific protein glycosylation analysis with glycan isomer differentiation.

    PubMed

    Hua, Serenus; Nwosu, Charles C; Strum, John S; Seipert, Richard R; An, Hyun Joo; Zivkovic, Angela M; German, J Bruce; Lebrilla, Carlito B

    2012-05-01

    Glycosylation is one of the most common yet diverse post-translational modifications. Information on glycan heterogeneity and glycosite occupancy is increasingly recognized as crucial to understanding glycoprotein structure and function. Yet, no approach currently exists with which to holistically consider both the proteomic and glycomic aspects of a system. Here, we developed a novel method of comprehensive glycosite profiling using nanoflow liquid chromatography/mass spectrometry (nano-LC/MS) that shows glycan isomer-specific differentiation on specific sites. Glycoproteins were digested by controlled non-specific proteolysis in order to produce informative glycopeptides. High-resolution, isomer-sensitive chromatographic separation of the glycopeptides was achieved using microfluidic chip-based capillaries packed with graphitized carbon. Integrated LC/MS/MS not only confirmed glycopeptide composition but also differentiated glycan and peptide isomers and yielded structural information on both the glycan and peptide moieties. Our analysis identified at least 13 distinct glycans (including isomers) corresponding to five compositions at the single N-glycosylation site on bovine ribonuclease B, 59 distinct glycans at five N-glycosylation sites on bovine lactoferrin, 13 distinct glycans at one N-glycosylation site on four subclasses of human immunoglobulin G, and 20 distinct glycans at five O-glycosylation sites on bovine κ-casein. Porous graphitized carbon provided effective separation of glycopeptide isomers. The integration of nano-LC with MS and MS/MS of non-specifically cleaved glycopeptides allows quantitative, isomer-sensitive, and site-specific glycoprotein analysis.

  20. Monomeric site-specific nucleases for genome editing

    PubMed Central

    Kleinstiver, Benjamin P.; Wolfs, Jason M.; Kolaczyk, Tomasz; Roberts, Alanna K.; Hu, Sherry X.; Edgell, David R.

    2012-01-01

    Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genome-editing applications. Fusion of the GIY-YIG nuclease domain to three-member zinc-finger DNA binding domains generated chimeric GIY-zinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5′-CNNNG-3′ cleavage motif. The Tev-ZFEs function to induce recombination in a yeast-based assay with activity on par with a homodimeric Zif268 zinc-finger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5′-CNNNG-3′ motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications. PMID:22566637

  1. Micro-tattoo guided OCT imaging of site specific inflammation

    NASA Astrophysics Data System (ADS)

    Phillips, Kevin G.; Choudhury, Niloy; Samatham, Ravikant V.; Singh, Harvinder; Jacques, Steven L.

    2010-02-01

    Epithelial biologists studying human skin diseases such as cancer formation and psoriasis commonly utilize mouse models to characterize the interplay among cells and intracellular signal transduction pathways that result in programmed changes in gene expression and cellular behaviors. The information obtained from animal models is useful only when phenotypic presentations of disease recapitulate those observed in humans. Excision of tissues followed by histochemical analysis is currently the primary means of establishing the morphological presentation. Non invasive imaging of animal models provides an alternate means to characterize tissue morphology associated with the disease of interest in vivo. While useful, the ability to perform in vivo imaging at different time points in the same tissue location has been a challenge. This information is key to understanding site specific changes as the imaged tissue can now be extracted and analyzed for mRNA expression. We present a method employing a micro-tattoo to guide optical coherence tomography (OCT) imaging of ultraviolet induced inflammation over time in the same tissue locations.

  2. Analysis of Chemokine Receptor Trafficking by Site-Specific Biotinylation.

    PubMed

    Liebick, Marcel; Schläger, Christian; Oppermann, Martin

    2016-01-01

    Chemokine receptors undergo internalization and desensitization in response to ligand activation. Internalized receptors are either preferentially directed towards recycling pathways (e.g. CCR5) or sorted for proteasomal degradation (e.g. CXCR4). Here we describe a method for the analysis of receptor internalization and recycling based on specific Bir A-mediated biotinylation of an acceptor peptide coupled to the receptor, which allows a more detailed analysis of receptor trafficking compared to classical antibody-based detection methods. Studies on constitutive internalization of the chemokine receptors CXCR4 (12.1% ± 0.99% receptor internalization/h) and CCR5 (13.7% ± 0.68%/h) reveals modulation of these processes by inverse (TAK779; 10.9% ± 0.95%/h) or partial agonists (Met-CCL5; 15.6% ± 0.5%/h). These results suggest an actively driven internalization process. We also demonstrate the advantages of specific biotinylation compared to classical antibody detection during agonist-induced receptor internalization, which may be used for immunofluorescence analysis as well. Site-specific biotinylation may be applicable to studies on trafficking of transmembrane proteins, in general.

  3. Site-specific protein labeling with SNAP-tags.

    PubMed

    Cole, Nelson B

    2013-09-24

    Site-specific labeling of cellular proteins with chemical probes is a powerful tool for studying protein function in living cells. A number of small peptide and protein tags have been developed that can be labeled with synthetic probes with high efficiencies and specificities and provide flexibility not available with fluorescent proteins. The SNAP-tag is a modified form of the DNA repair enzyme human O(6)-alkylguanine-DNA-alkyltransferase, and undergoes a self-labeling reaction to form a covalent bond with O(6)-benzylguanine (BG) derivatives. BG can be modified with a wide variety of fluorophores and other reporter compounds, generally without affecting the reaction with the SNAP-tag. In this unit, basic strategies for labeling SNAP-tag fusion proteins, both for live cell imaging and for in vitro analysis, are described. This includes a description of a releasable SNAP-tag probe that allows the user to chemically cleave the fluorophore from the labeled SNAP-tag fusion. In vitro labeling of purified SNAP-tag fusions is briefly described.

  4. Site-specific basal body duplication in Chlamydomonas.

    PubMed

    O'Toole, Eileen T; Dutcher, Susan K

    2014-02-01

    Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine-singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1-1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site-specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation. PMID:24166861

  5. Bone site-specific delivery of siRNA

    PubMed Central

    Liu, Xinli

    2016-01-01

    Abstract Small interfering RNAs (siRNA) have enormous potential as therapeutics to target and treat various bone disorders such as osteoporosis and cancer bone metastases. However, effective and specific delivery of siRNA therapeutics to bone and bone-specific cells in vivo is very challenging. To realize the full therapeutic potential of siRNA in treating bone disorders, a safe and efficient, tissue- and cell-specific delivery system must be developed. This review focuses on recent advances in bone site-specific delivery of siRNA at the tissue or cellular level. Bone-targeted nanoparticulate siRNA carriers and various bone-targeted moieties such as bisphosphonates, oligopeptides (Asp)8 and (AspSerSer)6, and aptamers are highlighted. Incorporation of these bone-seeking targeting moieties into siRNA carriers allows for recognition of different sub-tissue functional domains of bone and also specific cell types residing in bone tissue. It also provides a means for bone-formation surface-, bone-resorption surface-, or osteoblast-specific targeting and transportation of siRNA therapeutics. The discussion mainly focuses on systemic and local bone-specific delivery of siRNA in osteoporosis and bone metastasis preclinical models. PMID:26642236

  6. Analysis of Chemokine Receptor Trafficking by Site-Specific Biotinylation

    PubMed Central

    Liebick, Marcel; Schläger, Christian; Oppermann, Martin

    2016-01-01

    Chemokine receptors undergo internalization and desensitization in response to ligand activation. Internalized receptors are either preferentially directed towards recycling pathways (e.g. CCR5) or sorted for proteasomal degradation (e.g. CXCR4). Here we describe a method for the analysis of receptor internalization and recycling based on specific Bir A-mediated biotinylation of an acceptor peptide coupled to the receptor, which allows a more detailed analysis of receptor trafficking compared to classical antibody-based detection methods. Studies on constitutive internalization of the chemokine receptors CXCR4 (12.1% ± 0.99% receptor internalization/h) and CCR5 (13.7% ± 0.68%/h) reveals modulation of these processes by inverse (TAK779; 10.9% ± 0.95%/h) or partial agonists (Met-CCL5; 15.6% ± 0.5%/h). These results suggest an actively driven internalization process. We also demonstrate the advantages of specific biotinylation compared to classical antibody detection during agonist-induced receptor internalization, which may be used for immunofluorescence analysis as well. Site-specific biotinylation may be applicable to studies on trafficking of transmembrane proteins, in general. PMID:27310579

  7. Site-specific criteria for the completion of landfill aftercare.

    PubMed

    Laner, David; Fellner, Johann; Brunner, Paul H

    2012-09-01

    Municipal solid waste (MSW) landfills need to be managed after closure to assure long-term environmental compatibility. Aftercare can be completed when the authorities consider the landfill not likely to pose a threat to humans and the environment. In this work, a methodology for deriving site-specific aftercare completion criteria is presented and its application is illustrated via a case study. The evaluation method combines models addressing waste emission behavior, long-term barrier performance, and pollutant migration to assess the potential impact of landfill emissions on the environment. Based on the definition of acceptable impact levels at certain points of compliance, scenario- and pollutant-specific aftercare completion criteria are derived. The methodology was applied to a closed MSW landfill in Austria and potential aftercare durations were determined. While landfill gas emissions may become environmentally tolerable within decades at the site, leachate-related aftercare measures were expected to be necessary for centuries (primarily as a result of ammonium). Although the evaluation comes with large uncertainties, it allows for linking aftercare intensity and duration with respect to an environmentally compatible state of the landfill in the absence of aftercare. However, further case studies including regulatory review and acceptance are needed to use the methodology in a decision support tool on aftercare completion.

  8. Site-specific risk assessment in contaminated vegetable gardens.

    PubMed

    Sipter, Emese; Rózsa, Eniko; Gruiz, Katalin; Tátrai, Erzsébet; Morvai, Veronika

    2008-04-01

    A field survey was carried on in Gyöngyösoroszi, Hungary, near to an abandoned lead/zinc mine to analyse the metal contamination of flooded and non-flooded vegetable gardens, and to evaluate the health risks to local population. Contamination levels of arsenic, cadmium, lead, mercury and zinc were measured in soil and homegrown vegetable samples and bioconcentration factors and hazard indices were calculated. The high metal contents of flooded vegetable gardens were caused by floods, the results indicated significant differences between flooded and non-flooded vegetable gardens. The most accumulating vegetable was sorrel, the most mobile elements were cadmium and lead. Arsenic was not available for vegetables. The health risk was calculated for two exposure routes: ingestion of soil and ingestion of vegetables. The site-specific exposure parameters were established after a population based survey and a special equation was created to calculate the health risk due to homegrown vegetable consumption. The highest risk was associated with ingestion of vegetables, the most hazardous element being lead. The hazard index did not exceed the threshold value of one in flooded or non-flooded gardens. The analyses of health risk indicated that despite the high metal concentrations of soil the contamination of vegetable gardens does not pose an unacceptable risk to the inhabitants of the village. PMID:18191173

  9. Development of site-specific water quality criteria for copper

    SciTech Connect

    Giere, M.A.; McIntyre, D.O.; DeGraeve, G.M.

    1995-12-31

    Under its current operating system, the final effluent from a copper mining facility consistently meets its effluent limitation for copper. A change in mining practices to solution mining will result in a decrease in the hardness of the final effluent. The reduced hardness of the effluent will lower the effluent limit for copper to a concentration which cannot be achieved. The water-effect ratio (WER) procedure was selected to develop a site-specific criterion continuous concentration for copper for the effluent and it`s receiving stream. WER procedures followed those described in EPA`s ``Interim Guidance on Determination and Use of Water-Effect Ratios for Metals`` (1994). Three WER determinations were made using simulated downstream water as the site water. 48-hour acute Ceriodaphnia dubia and 96-hour acute fathead minnow toxicity tests were selected as the primary and secondary tests, respectively for use in the WER determinations. The results of the three WER determinations will be presented, as will the process used for predicting future effluent quality and permit compliance.

  10. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  11. Site Specific Cleavage Mediated by MMPs Regulates Function of Agrin

    PubMed Central

    McFarlane, Ainsley; Xie, Irene; Overall, Christopher M.; Stetefeld, Jörg

    2012-01-01

    Background Agrin is the key inducer of postsynaptic differentiations at the neuromuscular junction. The multidomain heparan sulfate proteoglycan is mediating via its N-terminal segment the interaction with laminin, whereas the C-terminal portion is responsible for Dystroglycan binding and clustering of the Acetylcholine receptor. Matrix metalloproteinases (MMP) are known to play essential roles in matrix remodeling, degradation and regulation of extracellular signaling networks. Principal Findings Site-specific processing of Agrin provides key insight into regulatory effects of Matrix metalloproteinases (MMPs). Here, we present a detailed study of agrin processing by different MMPs together with a molecular understanding of binding and cleavage at both terminal fragments. The data suggest for a regulatory effect of MMP cleavage at particularly important functional sites of agrin. Cleave of agrin abolishes the agrin-laminin complex formation and the Acetylcholine receptor clustering at the neuromuscular junction. Conclusion/Significance Agrin is a target of specific MMP processing resulting in agrin subfragments with different regulatory activities. MMP processing is a powerful tool to regulate extracellular signaling networks. PMID:22984437

  12. Site-specific anticancer effects of dietary flavonoid quercetin.

    PubMed

    Sak, Katrin

    2014-01-01

    Food-derived flavonoid quercetin, widely distributed in onions, apples, and tea, is able to inhibit growth of various cancer cells indicating that this compound can be considered as a good candidate for anticancer therapy. Although the exact mechanism of this action is not thoroughly understood, behaving as antioxidant and/or prooxidant as well as modulating different intracellular signalling cascades may all play a certain role. Such inhibitory activity of quercetin has been shown to depend first of all on cell lines and cancer types; however, no comprehensive site-specific analysis of this effect has been published. In this review article, cytotoxicity constants of quercetin measured in various human malignant cell lines of different origin were compiled from literature and a clear cancer selective action was demonstrated. The most sensitive malignant sites for quercetin revealed to be cancers of blood, brain, lung, uterine, and salivary gland as well as melanoma whereas cytotoxic activity was higher in more aggressive cells compared to the slowly growing cells showing that the most harmful cells for the organism are probably targeted. More research is needed to overcome the issues of poor water solubility and relatively low bioavailability of quercetin as the major obstacles limiting its clinical use. PMID:24377461

  13. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  14. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  15. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  16. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  17. 30 CFR 46.11 - Site-specific hazard awareness training.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... STONE, SURFACE CLAY, COLLOIDAL PHOSPHATE, OR SURFACE LIMESTONE MINES. § 46.11 Site-specific hazard... hazard awareness training for each mine. (d) Site-specific hazard awareness training is information...

  18. 75 FR 56526 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION... Environmental Management Site-Specific Advisory Board (EM SSAB), Portsmouth. The Federal Advisory Committee Act... areas of environmental restoration, waste management and related activities. Tentative Agenda...

  19. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    SciTech Connect

    Rohay, Alan C.; Reidel, Steve P.

    2005-02-24

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

  20. Site-specific hydrogen diffusion rates during clinopyroxene dehydration

    NASA Astrophysics Data System (ADS)

    Ferriss, Elizabeth; Plank, Terry; Walker, David

    2016-06-01

    The rate of hydrogen diffusion in clinopyroxene is relevant to interpreting hydrogen ("water") concentrations in xenoliths, phenocrysts, and clinopyroxene-hosted melt inclusions to provide insight into the deep-earth water cycle and volcanic explosivity. Here, we determine bulk and site-specific hydrogen diffusivities in two diopsides and an augite by heating initially homogeneous water-bearing samples in a 1-atm CO/CO2 gas-mixing furnace at 800-1000 °C and oxygen fugacity at the quartz-fayalite-magnetite buffer and observing H-loss profiles. The O-H stretching range between wavenumbers 3000 and 4000 cm-1 in FTIR spectra is resolved into 4-6 peaks, each of which is assumed to represent a distinct defect site for the hydrogen, to determine peak-specific diffusivities using our previously published whole-block method. For the diopside from the Kunlun Mts. in China, Arrhenius relations are reported for peaks at 3645, 3617, 3540, 3443, and 3355 cm-1 based on measurements at 816, 904, and 1000 °C. Bulk and site-specific diffusivities are determined for the same set of peaks at 904 °C for the second diopside (Jaipur). The augite (PMR-53) was a triangular thin slab, and hydrogen diffusivities were determined for bulk hydrogen and peaks at 3620, 3550, 3460, and 3355 cm-1 in the thickness direction at 800 °C. Bulk hydrogen diffusivity in the Jaipur diopside is consistent with previous work, and hydrogen diffusivity in augite PMR-53 is slightly lower than the fast direction diffusivities measured || [100] and [001]* in Jaipur diopside. Both diopsides show 1-2 orders of magnitude differences in the peaks-specific diffusivities, with the fastest diffusivities at 3450 cm-1 and the slowest at 3645 cm-1. However, the hydrogen diffusivities in Jaipur diopside are 2-4 orders of magnitude higher than those in Kunlun diopside for bulk hydrogen and all peaks. Thus, peak-specific differences cannot by themselves adequately explain the 5 orders of magnitude range in hydrogen

  1. Improving Site-Specific Radiological Performance Assessments - 13431

    SciTech Connect

    Tauxe, John; Black, Paul; Catlett, Kate; Lee, Robert; Perona, Ralph; Stockton, Tom; Sully, Mike

    2013-07-01

    An improved approach is presented for conducting complete and defensible radiological site-specific performance assessments (PAs) to support radioactive waste disposal decisions. The basic tenets of PA were initiated some thirty years ago, focusing on geologic disposals and evaluating compliance with regulations. Some of these regulations were inherently probabilistic (i.e., addressing uncertainty in a quantitative fashion), such as the containment requirements of the U.S. Environmental Protection Agency's (EPA's) 40 CFR 191, Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes, Chap. 191.13 [1]. Methods of analysis were developed to meet those requirements, but at their core early PAs used 'conservative' parameter values and modeling approaches. This limited the utility of such PAs to compliance evaluation, and did little to inform decisions about optimizing disposal, closure and long-term monitoring and maintenance, or, in general, maintaining doses 'as low as reasonably achievable' (ALARA). This basic approach to PA development in the United States was employed essentially unchanged through the end of the 20. century, principally by the U.S. Department of Energy (DOE). Performance assessments developed in support of private radioactive waste disposal operations, regulated by the U.S. Nuclear Regulatory Commission (NRC) and its agreement states, were typically not as sophisticated. Discussion of new approaches to PA is timely, since at the time of this writing, the DOE is in the midst of revising its Order 435.1, Radioactive Waste Management [2], and the NRC is revising 10 CFR 61, Licensing Requirements for Land Disposal of Radioactive Waste [3]. Over the previous decade, theoretical developments and improved computational technology have provided the foundation for integrating decision analysis (DA) concepts and objective-focused thinking, plus a Bayesian approach to

  2. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

    PubMed Central

    McClelland, M; Nelson, M; Raschke, E

    1994-01-01

    Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes. PMID:7937074

  3. Tracing Site-Specific Reactions at Mineral/Fluid Interfaces

    NASA Astrophysics Data System (ADS)

    Boily, Jean-François

    2016-04-01

    Mineral surfaces are reactive transformation centres and sinks for gases, solutes and solvents. Under environmental conditions these surfaces are populated by (hydr)oxo functional groups that can undergo protonation, ligand exchange, and form intricate networks of hydrogen bonds. Knowledge of the types, distributions and orientations of these groups is essential for understanding molecular-scale processes taking place at mineral surfaces. This work is focused on the properties of hydroxo groups on important crystallographic planes of synthetic nano-sized iron and aluminum (oxyhydr)oxides exposed to vacuum, water vapor and/or carbon dioxide. Vibration spectroscopic signatures of hydroxo groups on these minerals will be presented alongside predictions from molecular dynamics simulations. This body of work forms the basis for a molecular-scale understanding of reactions taking place at surfaces of geochemically relevant mineral particles. These reactions are not only limited to ion and solvent exchange but are also extended to understand particle-particle interactions in the context of oriented aggregation.

  4. Site-specific retention of colloids at rough rock surfaces.

    PubMed

    Darbha, Gopala Krishna; Fischer, Cornelius; Luetzenkirchen, Johannes; Schäfer, Thorsten

    2012-09-01

    The spatial deposition of polystyrene latex colloids (d = 1 μm) at rough mineral and rock surfaces was investigated quantitatively as a function of Eu(III) concentration. Granodiorite samples from Grimsel test site (GTS), Switzerland, were used as collector surfaces for sorption experiments. At a scan area of 300 × 300 μm(2), the surface roughness (rms roughness, Rq) range was 100-2000 nm, including roughness contribution from asperities of several tens of nanometers in height to the sample topography. Although, an increase in both roughness and [Eu(III)] resulted in enhanced colloid deposition on granodiorite surfaces, surface roughness governs colloid deposition mainly at low Eu(III) concentrations (≤5 × 10(-7) M). Highest deposition efficiency on granodiorite has been found at walls of intergranular pores at surface sections with roughness Rq = 500-2000 nm. An about 2 orders of magnitude lower colloid deposition has been observed at granodiorite sections with low surface roughness (Rq < 500 nm), such as large and smooth feldspar or quartz crystal surface sections as well as intragranular pores. The site-specific deposition of colloids at intergranular pores is induced by small scale protrusions (mean height = 0.5 ± 0.3 μm). These protrusions diminish locally the overall DLVO interaction energy at the interface. The protrusions prevent further rolling over the surface by increasing the hydrodynamic drag required for detachment. Moreover, colloid sorption is favored at surface sections with high density of small protrusions (density (D) = 2.6 ± 0.55 μm(-1), asperity diameter (φ) = 0.6 ± 0.2 μm, height (h) = 0.4 ± 0.1 μm) in contrast to surface sections with larger asperities and lower asperity density (D = 1.2 ± 0.6 μm(-1), φ = 1.4 ± 0.4 μm, h = 0.6 ± 0.2 μm). The study elucidates the importance to include surface roughness parameters into predictive colloid-borne contaminant migration calculations.

  5. Site-specific retention of colloids at rough rock surfaces.

    PubMed

    Darbha, Gopala Krishna; Fischer, Cornelius; Luetzenkirchen, Johannes; Schäfer, Thorsten

    2012-09-01

    The spatial deposition of polystyrene latex colloids (d = 1 μm) at rough mineral and rock surfaces was investigated quantitatively as a function of Eu(III) concentration. Granodiorite samples from Grimsel test site (GTS), Switzerland, were used as collector surfaces for sorption experiments. At a scan area of 300 × 300 μm(2), the surface roughness (rms roughness, Rq) range was 100-2000 nm, including roughness contribution from asperities of several tens of nanometers in height to the sample topography. Although, an increase in both roughness and [Eu(III)] resulted in enhanced colloid deposition on granodiorite surfaces, surface roughness governs colloid deposition mainly at low Eu(III) concentrations (≤5 × 10(-7) M). Highest deposition efficiency on granodiorite has been found at walls of intergranular pores at surface sections with roughness Rq = 500-2000 nm. An about 2 orders of magnitude lower colloid deposition has been observed at granodiorite sections with low surface roughness (Rq < 500 nm), such as large and smooth feldspar or quartz crystal surface sections as well as intragranular pores. The site-specific deposition of colloids at intergranular pores is induced by small scale protrusions (mean height = 0.5 ± 0.3 μm). These protrusions diminish locally the overall DLVO interaction energy at the interface. The protrusions prevent further rolling over the surface by increasing the hydrodynamic drag required for detachment. Moreover, colloid sorption is favored at surface sections with high density of small protrusions (density (D) = 2.6 ± 0.55 μm(-1), asperity diameter (φ) = 0.6 ± 0.2 μm, height (h) = 0.4 ± 0.1 μm) in contrast to surface sections with larger asperities and lower asperity density (D = 1.2 ± 0.6 μm(-1), φ = 1.4 ± 0.4 μm, h = 0.6 ± 0.2 μm). The study elucidates the importance to include surface roughness parameters into predictive colloid-borne contaminant migration calculations. PMID:22861645

  6. Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein

    PubMed Central

    Yang, Sung-Tae; Lim, Sung In; Kiessling, Volker; Kwon, Inchan; Tamm, Lukas K.

    2016-01-01

    Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein’s folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca2+-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches. PMID:27605302

  7. Site-specific stamping of graphene micro-patterns over large areas using flexible stamps.

    PubMed

    Chen, Chun-Hu; Reddy, Kongara M; Padture, Nitin P

    2012-06-15

    Site-specific stamping has the potential of becoming a low-cost, high-throughput method for depositing specific-shaped graphene micro-patterns over large areas on a wide variety of substrates. The use of an approach involving flexible stamps presented here represents an important advance towards reaching that potential. This approach entails lithographic creation (dry etching) of high-quality micro-pillar arrays of highly oriented pyrolytic graphite (HOPG) over large areas. This is followed by embedding the micro-pillar arrays in polydimethylsiloxane (PDMS), and detaching them from the HOPG base. This results in flexible stamps containing embedded HOPG micro-pillar arrays with freshly cleaved stamping surfaces. The flexible HOPG/PDMS stamps are then brought into contact with substrate surfaces to site-specifically stamp graphene or few-layer graphene (FLG) arrays over large areas. The freshly cleaved nature of the micro-pillar surfaces in the flexible stamps, the low elastic modulus of the flexible stamps and the elimination of sidewall deposits on the micro-pillars allow for more uniform stamping, relative to the use of stiff HOPG stamps from earlier studies. This approach has the potential to expand the substrate choice for graphene or FLG stamping to include curved and/or flexible substrates that could have an impact on the burgeoning field of flexible/stretchable electronics. PMID:22595887

  8. Site-specific stamping of graphene micro-patterns over large areas using flexible stamps

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Hu; Reddy, Kongara M.; Padture, Nitin P.

    2012-06-01

    Site-specific stamping has the potential of becoming a low-cost, high-throughput method for depositing specific-shaped graphene micro-patterns over large areas on a wide variety of substrates. The use of an approach involving flexible stamps presented here represents an important advance towards reaching that potential. This approach entails lithographic creation (dry etching) of high-quality micro-pillar arrays of highly oriented pyrolytic graphite (HOPG) over large areas. This is followed by embedding the micro-pillar arrays in polydimethylsiloxane (PDMS), and detaching them from the HOPG base. This results in flexible stamps containing embedded HOPG micro-pillar arrays with freshly cleaved stamping surfaces. The flexible HOPG/PDMS stamps are then brought into contact with substrate surfaces to site-specifically stamp graphene or few-layer graphene (FLG) arrays over large areas. The freshly cleaved nature of the micro-pillar surfaces in the flexible stamps, the low elastic modulus of the flexible stamps and the elimination of sidewall deposits on the micro-pillars allow for more uniform stamping, relative to the use of stiff HOPG stamps from earlier studies. This approach has the potential to expand the substrate choice for graphene or FLG stamping to include curved and/or flexible substrates that could have an impact on the burgeoning field of flexible/stretchable electronics.

  9. Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein.

    PubMed

    Yang, Sung-Tae; Lim, Sung In; Kiessling, Volker; Kwon, Inchan; Tamm, Lukas K

    2016-01-01

    Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein's folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca(2+)-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches. PMID:27605302

  10. Hydrologic and geochemical data collected near Skewed Reservoir, an impoundment for coal-bed natural gas produced water, Powder River Basin, Wyoming

    USGS Publications Warehouse

    Healy, Richard W.; Rice, Cynthia A.; Bartos, Timothy T.

    2012-01-01

    The Powder River Structural Basin is one of the largest producers of coal-bed natural gas (CBNG) in the United States. An important environmental concern in the Basin is the fate of groundwater that is extracted during CBNG production. Most of this produced water is disposed of in unlined surface impoundments. A 6-year study of groundwater flow and subsurface water and soil chemistry was conducted at one such impoundment, Skewed Reservoir. Hydrologic and geochemical data collected as part of that study are contained herein. Data include chemistry of groundwater obtained from a network of 21 monitoring wells and three suction lysimeters and chemical and physical properties of soil cores including chemistry of water/soil extracts, particle-size analyses, mineralogy, cation-exchange capacity, soil-water content, and total carbon and nitrogen content of soils.

  11. Of the necessity of knowledge of the natural pedo-geochemical background content in the evaluation of the contamination of soils by trace elements.

    PubMed

    Baize, D; Sterckeman, T

    2001-01-01

    In order to evaluate the contamination of the Dornach (Switzerland) site within the framework of the CEEM-Soil project, each participating team was allowed to take a maximum of 15 samples. The French team's sampling was organized in such a way as to answer the following questions: (i) what is the natural concentration of the soils at this site (local pedo-geochemical background content)?; (ii) what are the levels of Cd, Cu, Pb and Zn contamination of the soil?; (iii) what is the depth reached by the surface contamination that is derived from atmospheric fallout?; (iv) how is the contamination spread along the longest axis of the area under study? The relationships between total Fe and the trace metals have allowed local variations in the natural pedo-geochemical background content to be detected and thus permitted the anthropogenic contamination to be estimated. There would appear to be a low level of Pb contamination over all the site investigated (an increase of the order of 5-10 mg kg(-1) on the background level), limited to the surface humus-bearing layers. There is also a significant contamination by Cu over all of the site (an increase of the order of 30-40 mg kg(-1)). This contamination has remained in the surface horizons (0-20 cm). Very high Zn and Cd concentrations have been found in the four surface (0-4 cm) and deep horizons (15-70 cm) taken under the forest and very much lower values in the samples taken from cultivated soils. The most likely explanation is an unequal inheritance between the upper part of the site (wooded with thinner very clayey soils) and the lower cultivated part of the site (with thicker less clayey soils developed in a loamy material). For various reasons, it seems unlikely that a contamination of the wooded part should be so much higher than the cultivated part due to the interception of atmospheric dust by the trees. The local pedo-geochemical background Cd and Zn content of the upper wooded part proved to be clearly higher than

  12. Of the necessity of knowledge of the natural pedo-geochemical background content in the evaluation of the contamination of soils by trace elements.

    PubMed

    Baize, D; Sterckeman, T

    2001-01-01

    In order to evaluate the contamination of the Dornach (Switzerland) site within the framework of the CEEM-Soil project, each participating team was allowed to take a maximum of 15 samples. The French team's sampling was organized in such a way as to answer the following questions: (i) what is the natural concentration of the soils at this site (local pedo-geochemical background content)?; (ii) what are the levels of Cd, Cu, Pb and Zn contamination of the soil?; (iii) what is the depth reached by the surface contamination that is derived from atmospheric fallout?; (iv) how is the contamination spread along the longest axis of the area under study? The relationships between total Fe and the trace metals have allowed local variations in the natural pedo-geochemical background content to be detected and thus permitted the anthropogenic contamination to be estimated. There would appear to be a low level of Pb contamination over all the site investigated (an increase of the order of 5-10 mg kg(-1) on the background level), limited to the surface humus-bearing layers. There is also a significant contamination by Cu over all of the site (an increase of the order of 30-40 mg kg(-1)). This contamination has remained in the surface horizons (0-20 cm). Very high Zn and Cd concentrations have been found in the four surface (0-4 cm) and deep horizons (15-70 cm) taken under the forest and very much lower values in the samples taken from cultivated soils. The most likely explanation is an unequal inheritance between the upper part of the site (wooded with thinner very clayey soils) and the lower cultivated part of the site (with thicker less clayey soils developed in a loamy material). For various reasons, it seems unlikely that a contamination of the wooded part should be so much higher than the cultivated part due to the interception of atmospheric dust by the trees. The local pedo-geochemical background Cd and Zn content of the upper wooded part proved to be clearly higher than

  13. MINIMIZING COGNITIVE ERRORS IN SITE-SPECIFIC CAUSAL ASSESSMENT

    EPA Science Inventory

    Interest in causal investigations in aquatic systems has been a natural outgrowth of the increased use of biological monitoring to characterize the condition of resources. Although biological monitoring approaches are critical tools for detecting whether effects are occurring, t...

  14. A geochemical sampling technique for use in areas of active alpine glaciation: an application from the central Alaska Range

    USGS Publications Warehouse

    Stephens, G.C.; Evenson, E.B.; Detra, D.E.

    1990-01-01

    In mountainous regions containing extensive glacier systems there is a lack of suitable material for conventional geochemical sampling. As a result, in most geochemical sampling programs a few stream-sediment samples collected at, or near, the terminus of valley glaciers are used to evaluate the mineral potential of the glaciated area. We have developed and tested a technique which utilizes the medial moraines of valley glaciers for systematic geochemical exploration of the glacial catchment area. Moraine sampling provides geochemical information that is site-specific in that geochemical anomalies can be traced directly up-ice to bedrock sources. Traverses were made across the Trident and Susitna glaciers in the central Alaska Range where fine-grained (clay to sand size) samples were collected from each medial moraine. These samples were prepared and chemically analyzed to determine the concentration of specific elements. Fifty pebbles were collected at each moraine for archival purposes and for subsequent lithologic identification. Additionally, fifty cobbles and fifty boulders were examined and described at each sample site to determine the nature and abundance of lithologies present in the catchment area, the extent and nature of visible mineralization, the presence and intensity of hydrothermal alteration and the existence of veins, dikes and other minor structural features. Results from the central Alaska Range have delineated four distinct multi-element anomalies which are a response to potential mineralization up-ice from the medial moraine traverse. By integrating the lithologic, mineralogical and geochemical data the probable geological setting of the geochemical anomalies is determined. ?? 1990.

  15. In Vitro and In Vivo Evaluation of Cysteine and Site Specific Conjugated Herceptin Antibody-Drug Conjugates

    PubMed Central

    Jackson, Dowdy; Atkinson, John; Guevara, Claudia I.; Zhang, Chunying; Kery, Vladimir; Moon, Sung-Ju; Virata, Cyrus; Yang, Peng; Lowe, Christine; Pinkstaff, Jason; Cho, Ho; Knudsen, Nick; Manibusan, Anthony; Tian, Feng; Sun, Ying; Lu, Yingchun; Sellers, Aaron; Jia, Xiao-Chi; Joseph, Ingrid; Anand, Banmeet; Morrison, Kendall; Pereira, Daniel S.; Stover, David

    2014-01-01

    Antibody drug conjugates (ADCs) are monoclonal antibodies designed to deliver a cytotoxic drug selectively to antigen expressing cells. Several components of an ADC including the selection of the antibody, the linker, the cytotoxic drug payload and the site of attachment used to attach the drug to the antibody are critical to the activity and development of the ADC. The cytotoxic drugs or payloads used to make ADCs are typically conjugated to the antibody through cysteine or lysine residues. This results in ADCs that have a heterogeneous number of drugs per antibody. The number of drugs per antibody commonly referred to as the drug to antibody ratio (DAR), can vary between 0 and 8 drugs for a IgG1 antibody. Antibodies with 0 drugs are ineffective and compete with the ADC for binding to the antigen expressing cells. Antibodies with 8 drugs per antibody have reduced in vivo stability, which may contribute to non target related toxicities. In these studies we incorporated a non-natural amino acid, para acetyl phenylalanine, at two unique sites within an antibody against Her2/neu. We covalently attached a cytotoxic drug to these sites to form an ADC which contains two drugs per antibody. We report the results from the first direct preclinical comparison of a site specific non-natural amino acid anti-Her2 ADC and a cysteine conjugated anti-Her2 ADC. We report that the site specific non-natural amino acid anti-Her2 ADCs have superior in vitro serum stability and preclinical toxicology profile in rats as compared to the cysteine conjugated anti-Her2 ADCs. We also demonstrate that the site specific non-natural amino acid anti-Her2 ADCs maintain their in vitro potency and in vivo efficacy against Her2 expressing human tumor cell lines. Our data suggests that site specific non-natural amino acid ADCs may have a superior therapeutic window than cysteine conjugated ADCs. PMID:24454709

  16. Pre-Existing Carbon Structure and Its Effect on Site-Specific Carbon Isotopes in Small Organic Molecules

    NASA Astrophysics Data System (ADS)

    Piasecki, A.; Eiler, J. M.

    2014-12-01

    The ability to measure site-specific isotopes in organic molecules allows for better understanding of the mechanisms of their biosynthetic and/or catagenic formation and destruction. Here we examine for site-specific isotopic composition of propane from natural and synthetic sources using novel instruments and techniques gas source mass spectrometry 1, and discuss the possible relationship of our findings to recent independent evidence from NMR measurements for the isotopic structures of long-chain alkanes2. A recent NMR study2 demonstrates that n-alkanes can be divided into three groups according to their site-specific carbon isotope structure: long (C16+) even carbon number, long (C17+) odd carbon number , and short (C11-C15). We modeled the isotopic site-specific composition of propane derived from these three distinct groups. If propane is cleaved from such long-chain hydrocarbons without fractionation, the long odd-numbered and the shorter alkanes would produce propane with an average terminal position 6-7‰ lighter than the center position, while the long even-numbered chain compounds would produce propane with a terminal position averaging around 7‰ heavier than the center. If, instead the fractionation associated with cleaving propane from such parent molecules is ~10‰ (as seems likely), then these average terminal — center differences should be decreased by ~5 ‰ (i.e., to -11-12 and +1-2 ‰, respectively). We will compare these predictions with our previous demonstrations of the changes in bulk and site specific compositions in propane due to isotope exchange equilibria, diffusion and conventional models of kerogen 'cracking', and will use these models as a framework for interpreting the observed site-specific isotopic compositions of propane from diverse natural gas deposits. 1. Piasecki, A. et al. Site-Specific Carbon Isotope Measurement of Organics by Gas Source Mass Spectrometry. Mineralogical Magazine 77, (2013). 2. Gilbert, A., Yamada, K

  17. Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

    PubMed Central

    Risso, Valeria A.; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A.; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2015-01-01

    Local protein interactions (“molecular context” effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  18. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

    PubMed

    Risso, Valeria A; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2015-02-01

    Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.

  19. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

    PubMed

    Risso, Valeria A; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2015-02-01

    Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  20. Site specificity of glycation and carboxymethylation of bovine serum albumin by fructose.

    PubMed

    Hinton, D J S; Ames, J M

    2006-06-01

    We report an investigation of the site specificity, extent and nature of modification of bovine serum albumin (BSA) incubated with fructose or glucose at physiological temperature and pH. Sites of early glycation (Heyns rearrangement products (HRP) from fructose; fructoselysine (FL) from glucose) as well as advanced glycation (N(epsilon)-(carboxymethyl)lysine; CML) were analyzed by liquid chromatography-mass spectrometry. The major site of modification by fructose, like glucose, is Lysine-524 and this results in, respectively, 31 and 76% loss of the corresponding unmodified tryptic peptide, Gln525-Lys533. In addition, total lysine, HRP, FL, CML and N(epsilon)-(carboxyethyl)lysine in the incubations, was quantified. Almost all of the loss of lysine in the fructose-modified BSA was attributed to the formation of CML, with the yield of CML being up to 17-fold higher than glucose-modified BSA. A mechanism for the formation of CML from the HRP is proposed. PMID:16583308

  1. Proteomic Approaches for Site-specific O-GlcNAcylation Analysis

    SciTech Connect

    Wang, Sheng; Yang, Feng; Camp, David G.; Rodland, Karin D.; Qian, Weijun; Liu, Tao; Smith, Richard D.

    2014-10-01

    O-GlcNAcylation is a dynamic protein post-translational modification of serine or threonine residues by an O-linked monosaccharide N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation was discovered three decades ago, and it has been shown to contribute to various disease states, such as metabolic diseases, cancer and neurological diseases. Yet it remains technically difficult to characterize comprehensively and quantitatively, due to its exceptionally low abundance and extremely labile nature under conventional tandem mass spectrometry conditions. Herein, we review the recent efforts for tackling these challenges in developing proteomic approaches for site-specific O-GlcNAcylation analysis, such as specific enrichment of O-GlcNAc peptides/proteins, unambiguous site-determination of O-GlcNAc modification, and quantitative analysis of O-GlcNAcylation.

  2. Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquife

    SciTech Connect

    Campbell, K M; K Kukkadapu, R K; Qafoku, N P; Peacock, A D; Lesher, E; Williams, K H; Bargar, J R; Wilkins, M J; Figueroa, L; Ranville, J; Davis, J A; Long, P E

    2012-05-23

    Localized zones or lenses of naturally reduced sediments have the potential to play a significant role in the fate and transport of redox-sensitive metals and metalloids in aquifers. To assess the mineralogy, microbiology and redox processes that occur in these zones, several cores from a region of naturally occurring reducing conditions in a U-contaminated aquifer (Rifle, CO) were examined. Sediment samples from a transect of cores ranging from oxic/suboxic Rifle aquifer sediment to naturally reduced sediment were analyzed for U and Fe content, oxidation state, and mineralogy; reduced S phases; and solid-phase organic C content using a suite of analytical and spectroscopic techniques on bulk sediment and size fractions. Solid-phase U concentrations were higher in the naturally reduced zone, with a high proportion of the U present as U(IV). The sediments were also elevated in reduced S phases and Fe(II), indicating it is very likely that U(VI), Fe(III), and SO4 reduction has occurred or is occurring in the sediment. The microbial community was assessed using lipid- and DNA-based techniques, and statistical redundancy analysis was performed to determine correlations between the microbial community and the geochemistry. Increased concentrations of solid-phase organic C and biomass in the naturally reduced sediment suggests that natural bioreduction is stimulated by a zone of increased organic C concentration associated with fine-grained material and lower permeability to groundwater flow. Characterization of the naturally bioreduced sediment provides an understanding of the natural processes that occur in the sediment under reducing conditions and how they may impact natural attenuation of radionuclides and other redox sensitive materials. Results also suggest the importance of recalcitrant organic C for maintaining reducing conditions and U immobilization.

  3. Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer

    SciTech Connect

    Campbell, Kate M.; Kukkadapu, Ravi K.; Qafoku, Nikolla; Peacock, Aaron D.; Lesher, E.; Williams, Kenneth H.; Bargar, John R.; Wilkins, Michael J.; Figueroa, Linda A.; Ranville, James; Davis, James; Long, Philip E.

    2012-05-23

    Localized zones or lenses of naturally reduced sediments have the potential to play a significant role in the fate and transport of redox-sensitive metals and metalloids in aquifers. To assess the mineralogy, microbiology, and redox processes that occur in these zones, we examined several cores from a region of naturally occurring reducing conditions in a uranium-contaminated aquifer (Rifle, CO). Sediment samples from a transect of cores ranging from oxic/suboxic Rifle aquifer sediment to naturally reduced sediment were analyzed for uranium and iron content, oxidation state, and mineralogy, reduced sulfur phases, and solid phase organic carbon content using a suite of analytical and spectroscopic techniques on bulk sediment and size fractions. Solid-phase uranium concentrations were higher in the naturally reduced zone, with a high proportion of the uranium present as reduced U(IV). The sediments were also elevated in reduced sulfur phases and Fe(II), indicating it is very likely that U(VI), Fe(III), and sulfate reduction occurred or is occurring in the sediment. The microbial community was assessed using lipid- and DNA-based techniques, and statistical redundancy analysis was performed to determine correlations between the microbial community and the geochemistry. Increased concentration of solid phase organic carbon and biomass in the naturally reduced sediment suggests that natural bioreduction is stimulated by a zone of increased organic carbon concentration associated with fine-grained material and lower permeability to groundwater flow. Characterization of the naturally bioreduced sediment provides an understanding of the natural processes that occur in the sediment under reducing conditions and how they may impact natural attenuation of radionuclides and other redox sensitive materials. Results also suggest the importance of recalcitrant organic carbon for maintaining reducing conditions and uranium immobilization.

  4. Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer

    SciTech Connect

    Campbell, K. M.; Kukkadapu, R. K.; Qafoku, N. P.; Peacock, A. D.; Lesher, E.; Williams, K. H.; Bargar, J. R.; Wilkins, M. J.; Figueroa, L.; Ranville, J.; Davis, J. A.; Long, P. E.

    2012-08-01

    Localized zones or lenses of naturally reduced sediments have the potential to play a significant role in the fate and transport of redox-sensitive metals and metalloids in aquifers. To assess the mineralogy, microbiology and redox processes that occur in these zones, several cores from a region of naturally occurring reducing conditions in a U-contaminated aquifer (Rifle, CO) were examined. Sediment samples from a transect of cores ranging from oxic/suboxic Rifle aquifer sediment to naturally reduced sediment were analyzed for U and Fe content, oxidation state, and mineralogy; reduced S phases; and solid-phase organic C content using a suite of analytical and spectroscopic techniques on bulk sediment and size fractions. Solid-phase U concentrations were higher in the naturally reduced zone, with a high proportion of the U present as U(IV). The sediments were also elevated in reduced S phases and Fe(II), indicating it is very likely that U(VI), Fe(III), and SO4 reduction has occurred or is occurring in the sediment. The microbial community was assessed using lipid- and DNA-based techniques, and statistical redundancy analysis was performed to determine correlations between the microbial community and the geochemistry. Increased concentrations of solid-phase organic C and biomass in the naturally reduced sediment suggests that natural bioreduction is stimulated by a zone of increased organic C concentration associated with fine-grained material and lower permeability to groundwater flow. Characterization of the naturally bioreduced sediment provides an understanding of the natural processes that occur in the sediment under reducing conditions and how they may impact natural attenuation of radionuclides and other redox sensitive materials. Results also suggest the importance of recalcitrant organic C for maintaining reducing conditions and U immobilization.

  5. Geological and geochemical criteria for the continental nature of the Mendeleev Rise (the Arctic Ocean) from the data of drilling and dredging of seabed rock material

    NASA Astrophysics Data System (ADS)

    Morozov, Andrey; Petrov, Oleg; Kremenetskiy, Alexander; Kashubin, Sergey; Rekant, Pavel; Gusev, Eugene; Shokalskiy, Sergey; Shevchenko, Sergey; Sergeev, Sergey; Artyushkov, Eugene

    2013-04-01

    The results are presented of geological and geophysical studies on the Mendeleev Rise at 10 test sites at 79°N to 83°N (expedition "Arktika-2012" in August-September 2012). During the expedition, for the first time, three boreholes were drilled in the bedrocks of the Mendeleev Rise basement at a depth of 1700-2600 m, and more than 20 thousand fragments of seabed rock material were dredged. Among them carbonate-bearing rocks including dolomite with relicts of trilobites and ostracoderms (D3-C) constitute up 65 %. Up to 20% are terrigenous rocks with a predominance of quartz sandstones. Magmatic rocks constitute 10-15% of the samples (including 8% of gabbro-dolerite and 2 % of granite) with 5% of metamorphic rocks. The boreholes revealed magmatic mafic rocks of basalt to basaltic andesite to trachyandesite series (SiO2-48-58% K2O+Na2O-3,4-9,2%) including epigenically altered volcanic breccias. All fragments of magmatic mafic rocks have a similar mineral and chemical composition and are grouped with gabbro dolerite (SiO2-49-51%, K2O+Na2O-2,5-3,0%). Preliminary results of mineralogic, geochemical and of isotopic geochemical (ICP-OEC, ICP-MS, RFA, Sm-Nd, Rb-Sr, EPMA and others) analyses suggest the continental nature of the studied rocks and show a distinct difference from rocks of the Gakkel Ridge in the Eurasian part of the ocean, which are of the oceanic origin. U-Pb dating of zircons from the core rocks and seabed rock material (SIMS SHRIMP II) indicate a wide range of their formation age: 2940-995, 639-385 and 303-203 Ma and thus suggest that they belong to volcanogenic terrigeneous carbonate-bearing bed of the ancient platform composing the floor of Amerasian part of the Arctic Ocean.

  6. Geochemical processes and the effects of natural organic solutes on the solubility of selenium in coal-mine backfill samples from the Powder River basin, Wyoming

    USGS Publications Warehouse

    See, R.B.; Reddy, K.J.; Vance, G.F.; Fadlelmawla, A.A.; Blaylock, M.J.

    1995-01-01

    Geochemical processes and the effects of natural organic solutes on the solubility of selenium in coal-mine backfill aquifers were investigated. Backfill and ground-water samples were collected at coal mines in the Powder River Basin, Wyoming. Backfill was generally dominated by aluminum (14,400 to 49,000 mg/kg (milligrams per kilogram)), iron (3,330 to 23,200 mg/kg), and potassium (7,950 to 18,000 mg/kg). Backfill saturated-paste selenium concentrations ranged from 1 to 156 mg/kg (microsiemens per kilogram). Ground-water total selenium concentrations ranged from 3 to 125 mg/L. Dissolved organic carbon in all ground-water samples was dominated by hydrophobic and hydrophilic acids (38 to 84 percent). Selenite sorption/desorption experiments were conducted using background solutions of distilled-deionized water, 0.1 molar calcium chloride, and isolated hydrophobic and hydrophilic acids. Selenite sorption was larger when 0.1 molar calcium chloride was used. The addition of hydrophilic acid decreased selenite sorption more than the addition of hydrophobic acids. Geochemical modelling was used to predict the solid phases controlling dissolved selenium concentrations and to evaluate the effects of dissolved organic carbon on selenium solubility. Results suggested that 55 to 90 percent of selenium in backfill precipitation/dissolution extracts was dominated by magnesium selenate ion pairs. Dissolved organic carbon had little effect on selenium speciation. A redox chamber was constructed to control Eh and pH in water and backfill-core sample suspensions. The response of selenite and selenate in water samples to redox conditions did not follow thermodynamic predictions. Reduction of selenate in water samples did not occur at any of the redox levels tested.

  7. Distribution and geochemical characterization of coalbed gases at excavation fields at natural analogue site area Velenje Basin, Slovenia

    NASA Astrophysics Data System (ADS)

    Kanduč, Tjaša; Žigon, Stojan; Grassa, Fausto; Sedlar, Jerneja; Zadnik, Ivo; Zavšek, Simon

    2016-04-01

    Unconventional gas resources, including coal bed methane and shale gas, are a growing part of the global energy mix, which has changed the economic and strategic picture for gas consuming and producing countries, including the USA, China and Australia that, together are responsible for around half the currently recoverable unconventional gas resources. However, CBM production was often hindered by low permeability and mineralization in cleats and fractures, necessitating the development of cost effective horizontal drilling and completion techniques. Geochemical and isotopic monitoring of coalbed gases at excavation fields in Velenje Basin started in year 2000, with the aim to obtain better insights into the origin of coalbed gases. Results from active excavation fields in the mining areas Pesje and Preloge in the year period 2014-2015 are presented in this study. Composition and isotopic composition of coalbed gases were determined with mass - spectrometric methods. The chemical (methane, carbon dioxide, nitrogen) and isotopic composition of carbon in methane and carbon dioxide in the Velenje Basin vary and depend on the composition of the source of coalbed gas before excavation, advancement of the working face, depth of the longwall face, pre-mining activity and newly mined activity. The basic gas components determined in excavation fields are carbon dioxide and methane. Knowledge of the stable isotope geochemistry of coal bed and shale gas and the related production water is essential to determine not only gas origins but also the dominant methanogenic pathway in the case of microbial gas. Concentrations of methane at active excavation fields are changing from 1.8 to 63.9 %, concentrations of carbon dioxide are changing from 36.1 to 98.2% and CDMI (Carbon Dioxide Methane Index) index from 0.2 to 100 %. Isotopic composition of carbon dioxide is changing from -11.0 to -1.9‰ , isotopic composition of methane from -71.8 to -43.3‰ , isotopic composition of

  8. Site specific passive acoustic detection and densities of humpback whale calls off the coast of California

    NASA Astrophysics Data System (ADS)

    Helble, Tyler Adam

    Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. Automated methods are needed to aid in the analyses of the recorded data. When a mammal vocalizes in the marine environment, the received signal is a filtered version of the original waveform emitted by the marine mammal. The waveform is reduced in amplitude and distorted due to propagation effects that are influenced by the bathymetry and environment. It is important to account for these effects to determine a site-specific probability of detection for marine mammal calls in a given study area. A knowledge of that probability function over a range of environmental and ocean noise conditions allows vocalization statistics from recordings of single, fixed, omnidirectional sensors to be compared across sensors and at the same sensor over time with less bias and uncertainty in the results than direct comparison of the raw statistics. This dissertation focuses on both the development of new tools needed to automatically detect humpback whale vocalizations from single-fixed omnidirectional sensors as well as the determination of the site-specific probability of detection for monitoring sites off the coast of California. Using these tools, detected humpback calls are "calibrated" for environmental properties using the site-specific probability of detection values, and presented as call densities (calls per square kilometer per time). A two-year monitoring effort using these calibrated call densities reveals important biological and ecological information on migrating humpback whales off the coast of California. Call density trends are compared between the monitoring sites and at the same monitoring site over time. Call densities also are compared to several natural and human-influenced variables including season, time of day, lunar illumination, and ocean noise. The results reveal substantial differences in call densities

  9. Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet

    PubMed Central

    Zimmermann, Jörg; Adhikary, Ramkrishna; Dhami, Kirandeep; Ordoukhanian, Phillip; Sun, Zhelin; Xiang, Jie; Romesberg, Floyd E.

    2014-01-01

    We have developed a class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM. To explore the use of these pairs to produce site-specifically labeled DNA, we report the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA via Click chemistry. We find that with the d5SICS scaffold, a propynyl ether linker is accommodated better than its aliphatic analog, but not as well as the protected propargyl amine linker explored previously. We also find that with the dMMO2 and dDMO analogs, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment, and that while aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogs, a variety of them are used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICSCO-dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps “evolution” of nanomaterials. PMID:24026962

  10. Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet.

    PubMed

    Li, Zhengtao; Lavergne, Thomas; Malyshev, Denis A; Zimmermann, Jörg; Adhikary, Ramkrishna; Dhami, Kirandeep; Ordoukhanian, Phillip; Sun, Zhelin; Xiang, Jie; Romesberg, Floyd E

    2013-10-11

    A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials. PMID:24026962

  11. Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet.

    PubMed

    Li, Zhengtao; Lavergne, Thomas; Malyshev, Denis A; Zimmermann, Jörg; Adhikary, Ramkrishna; Dhami, Kirandeep; Ordoukhanian, Phillip; Sun, Zhelin; Xiang, Jie; Romesberg, Floyd E

    2013-10-11

    A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.

  12. Geochemical analysis of atlantic rim water, carbon county, wyoming: New applications for characterizing coalbed natural gas reservoirs

    USGS Publications Warehouse

    McLaughlin, J.F.; Frost, C.D.; Sharma, Shruti

    2011-01-01

    Coalbed natural gas (CBNG) production typically requires the extraction of large volumes of water from target formations, thereby influencing any associated reservoir systems. We describe isotopic tracers that provide immediate data on the presence or absence of biogenic natural gas and the identify methane-containing reservoirs are hydrologically confined. Isotopes of dissolved inorganic carbon and strontium, along with water quality data, were used to characterize the CBNG reservoirs and hydrogeologic systems of Wyoming's Atlantic Rim. Water was analyzed from a stream, springs, and CBNG wells. Strontium isotopic composition and major ion geochemistry identify two groups of surface water samples. Muddy Creek and Mesaverde Group spring samples are Ca-Mg-S04-type water with higher 87Sr/86Sr, reflecting relatively young groundwater recharged from precipitation in the Sierra Madre. Groundwaters emitted from the Lewis Shale springs are Na-HCO3-type waters with lower 87Sr/86Sr, reflecting sulfate reduction and more extensive water-rock interaction. To distinguish coalbed waters, methanogenically enriched ??13CDIC wasused from other natural waters. Enriched ??13CDIC, between -3.6 and +13.3???, identified spring water that likely originates from Mesaverde coalbed reservoirs. Strongly positive ??13CDIC, between +12.6 and +22.8???, identified those coalbed reservoirs that are confined, whereas lower ??13CDIC, between +0.0 and +9.9???, identified wells within unconfined reservoir systems. Copyright ?? 2011. The American Association of Petroleum Geologists. All rights reserved.

  13. Developing a robust geochemical and reactive transport model to evaluate possible sources of arsenic at the CO[subscript 2] sequestration natural analog site in Chimayo, New Mexico

    SciTech Connect

    Viswanathan, Hari; Dai, Zhenxue; Lopano, Christina; Keating, Elizabeth; Hakala, J. Alexandra; Scheckel, Kirk G.; Zheng, Liange; Gutherie, George D.; Pawar, Rajesh

    2012-10-24

    Migration of carbon dioxide (CO{sub 2}) from deep storage formations into shallow drinking water aquifers is a possible system failure related to geologic CO{sub 2} sequestration. A CO{sub 2} leak may cause mineral precipitation/dissolution reactions, changes in aqueous speciation, and alteration of pH and redox conditions leading to potential increases of trace metal concentrations above EPA National Primary Drinking Water Standards. In this study, the Chimayo site (NM) was examined for site-specific impacts of shallow groundwater interacting with CO{sub 2} from deep storage formations. Major ion and trace element chemistry for the site have been previously studied. This work focuses on arsenic (As), which is regulated by the EPA under the Safe Drinking Water Act and for which some wells in the Chimayo area have concentrations higher than the maximum contaminant level (MCL). Statistical analysis of the existing Chimayo groundwater data indicates that As is strongly correlated with trace metals U and Pb indicating that their source may be from the same deep subsurface water. Batch experiments and materials characterization, such as: X-ray diffraction (XRD), scanning electron microscopy (SEM), and synchrotron micro X-ray fluorescence ({mu}-XRF), were used to identify As association with Fe-rich phases, such as clays or oxides, in the Chimayo sediments as the major factor controlling As fate in the subsurface. Batch laboratory experiments with Chimayo sediments and groundwater show that pH decreases as CO{sub 2} is introduced into the system and buffered by calcite. The introduction of CO{sub 2} causes an immediate increase in As solution concentration, which then decreases over time. A geochemical model was developed to simulate these batch experiments and successfully predicted the pH drop once CO{sub 2} was introduced into the experiment. In the model, sorption of As to illite, kaolinite and smectite through surface complexation proved to be the key reactions in

  14. FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they h...

  15. On-the-go nitrogen sensing and fertilizer control for site-specific crop management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In-field site-specific nitrogen (N) management increases crop yield, reduces N application to minimize the risk of nitrate contamination of ground water, and thus reduces farming cost. Real-time N sensing and fertilization is required for efficient N management. An ‘on-the-go’ site-specific N manage...

  16. A cyclopropene-modified nucleotide for site-specific RNA labeling using genetic alphabet expansion transcription.

    PubMed

    Eggert, F; Kath-Schorr, S

    2016-06-01

    Site-specific RNA modification with methyl cyclopropene moieties is performed by T7 in vitro transcription. An existing unnatural base is functionalized with a cyclopropene moiety and used in transcription reactions to produce site-specifically cyclopropene-modified RNA molecules. The posttranscriptional inverse electron demand Diels-Alder cycloaddition reaction with a selected tetrazine-fluorophore conjugate is demonstrated.

  17. A cyclopropene-modified nucleotide for site-specific RNA labeling using genetic alphabet expansion transcription.

    PubMed

    Eggert, F; Kath-Schorr, S

    2016-06-01

    Site-specific RNA modification with methyl cyclopropene moieties is performed by T7 in vitro transcription. An existing unnatural base is functionalized with a cyclopropene moiety and used in transcription reactions to produce site-specifically cyclopropene-modified RNA molecules. The posttranscriptional inverse electron demand Diels-Alder cycloaddition reaction with a selected tetrazine-fluorophore conjugate is demonstrated. PMID:27181840

  18. 78 FR 10612 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road, Santa Fe, NM 87506. Phone (505)...

  19. 76 FR 39080 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... National Laboratory (INL) 101. INL EM Budget. Calcine Path Forward. Advanced Mixed Waste Treatment...

  20. 78 FR 58294 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-23

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... SSAB, Idaho National Laboratory, welcomes the attendance of the public at its advisory...

  1. 77 FR 76475 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-28

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Laboratory/ICP Public Involvement/ Communications Sodium Bearing Waste Treatment Plant Update ICP End...

  2. 75 FR 82004 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public at its...

  3. 75 FR 56527 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act.... Overview Legacy Management--Long-Term Land Use at Idaho National Laboratory. Integrated Waste...

  4. 75 FR 24685 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... to Cleanup Idaho National Laboratory Site Wide Review--CERCLA Long-Term Ecological Program...

  5. 76 FR 68179 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-03

    ... Management Site-Specific Advisory Board, Idaho National Laboratory (76 FR 66917). This document makes a... page at: http://inlcab.energy.gov/ . Correction In the Federal Register of October 28, 2011, in FR Doc... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of...

  6. 78 FR 12747 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-25

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public at its...

  7. 76 FR 25682 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National ] Laboratory. The Federal Advisory Committee Act... National Laboratory, welcomes the attendance of the public at its advisory committee meetings and will...

  8. 75 FR 9590 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-03

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Laboratory, welcomes the attendance of the public at its advisory committee meetings and will make...

  9. 77 FR 38276 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Management Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee... Center Status Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance...

  10. 77 FR 65374 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-26

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... National Laboratory/ICP Public Involvement/ Communications Public Participation: The EM SSAB,...

  11. 77 FR 53192 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-31

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Closeout Process Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance...

  12. 76 FR 66917 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-28

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Environmental Assessment Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the...

  13. 77 FR 10485 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-22

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act...--Future Work Plan Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance...

  14. 75 FR 39008 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Laboratory, welcomes the attendance of the public at its advisory committee meetings and will make...

  15. 76 FR 53888 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-30

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public at its...

  16. 76 FR 10018 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of the public...

  17. 75 FR 346 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-05

    ... Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory. The Federal Advisory Committee Act... Decision. Public Participation: The EM SSAB, Idaho National Laboratory, welcomes the attendance of...

  18. 75 FR 51450 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-20

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... the Board is to make recommendations ] to DOE-EM and site management in the areas of...

  19. 76 FR 17118 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-28

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  20. 75 FR 17701 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-07

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Wednesday,...

  1. 75 FR 6018 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... the Board is to make recommendations to DOE-EM and site management in the areas of...

  2. 76 FR 20651 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ... Environmental Management Site-Specific Advisory Board Chairs (76 FR 17118). This notice announces the... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of cancellation of open meeting. SUMMARY: On March 28, 2011, in FR Doc. 2011-7243, on page 17118, the...

  3. 78 FR 49738 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and...

  4. 76 FR 63613 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-13

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities....

  5. 77 FR 55813 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-11

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  6. 75 FR 8050 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and...

  7. 77 FR 16021 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-19

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  8. 78 FR 26635 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-07

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on May 16, 2013 of the Environmental Management Site-Specific Advisory Board, Paducah (78 FR 25064). This document makes a correction to that notice. FOR...

  9. 78 FR 61348 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-03

    ..., 2013 of the Environmental Management Site-Specific Advisory Board, Portsmouth (78 FR 56871). This... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy. ACTION: Notice of Cancellation of Open Meeting. SUMMARY: On September 16, 2013, in FR Doc. 2013-22453, on page...

  10. 78 FR 64932 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-30

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  11. 76 FR 4645 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities....

  12. 78 FR 59012 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-25

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Wednesday,...

  13. 78 FR 28207 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-14

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and...

  14. Activity of site-specific endonucleases on complexes of plasmid DNA with multiwalled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Veligura, A. A.; Shulitsky, B. G.; Asayonok, A. A.; Vaskovtsev, E. V.

    2016-08-01

    We have synthesized and investigated structural and functional properties of plasmid DNA complexes with multi-walled carbon nanotubes (MWCNTs) for detection of changes in structural state of the plasmid DNA at its recognition by site-specific endonuclease. It has been also established that the site-specific endonuclease is functionally active on the surface of MWCNTs.

  15. 76 FR 38143 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-29

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy, DOE... Site-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  16. 77 FR 26273 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... New Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road, Santa Fe, NM 87506. Phone...

  17. 75 FR 7576 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, March 10, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  18. 75 FR 65466 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, November 10, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  19. 78 FR 63171 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation; Meeting AGENCY: Department of... Management Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  20. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act... 12, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge Turnpike, Oak Ridge,...

  1. 77 FR 29996 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  2. 76 FR 52944 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-24

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, September 14, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  3. 75 FR 57462 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, October 13, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  4. 78 FR 12746 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-25

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  5. 76 FR 78908 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, January 11, 2012; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  6. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, October 12, 2011; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  7. 78 FR 49738 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Center, Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830....

  8. 77 FR 23470 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  9. 76 FR 36101 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, July 13, 2011 at 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  10. 76 FR 9572 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, March 9, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  11. 77 FR 38275 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  12. 76 FR 29732 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, June 8, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  13. 77 FR 45345 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-31

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN 37831. Phone (865) 241-3315; Fax...

  14. 75 FR 27998 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, June 9, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  15. 75 FR 35447 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, July 14, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  16. 78 FR 3890 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-17

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  17. 77 FR 2714 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, February 8, 2012; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  18. 77 FR 64494 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  19. 78 FR 17648 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  20. 78 FR 58292 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  1. 76 FR 1415 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-10

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... January 12, 2011, ] meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Oak... Coordinator, Department of Energy Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN...

  2. 77 FR 9219 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-16

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy, DoE... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P....

  3. 75 FR 24685 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, May 12, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  4. 75 FR 51027 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, September 8, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  5. 77 FR 74836 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  6. 75 FR 71424 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, December 8, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  7. 78 FR 30911 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-23

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  8. 78 FR 23241 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  9. 78 FR 75552 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 ] Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  10. 77 FR 49442 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-16

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Center, Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830....

  11. 76 FR 22388 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-21

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, May 11, 2011; 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  12. 77 FR 58364 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-20

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Office of Science and Technical Information, 1 Science.gov Way, Oak Ridge, Tennessee 37830. FOR...

  13. 76 FR 17637 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-30

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, April 13, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  14. 75 FR 13268 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-19

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Wednesday, April 14, 2010, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak...

  15. 76 FR 28759 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-18

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Register. DATES: Thursday, May 26, 2011, 6 p.m. ADDRESSES: DOE Information Center, 475 Oak Ridge...

  16. 77 FR 18243 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-27

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub... Science.gov Way, Oak Ridge, Tennessee 37830. FOR FURTHER INFORMATION CONTACT: Melyssa P. Noe,...

  17. 75 FR 43518 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-26

    ... Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation AGENCY: Department of Energy... Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub..., Department of Energy Oak Ridge Operations Office, P.O. Box 2001, EM-90, Oak Ridge, TN 37831. Phone (865)...

  18. 75 FR 19630 - Environmental Management Site-Specific Advisory Board Charter Renewal

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-15

    ... Environmental Management Site-Specific Advisory Board Charter Renewal Pursuant to Section 14(a)(2)(A) of the...-Specific Advisory Board will be renewed for a two-year period beginning April 11, 2010. The Board provides... renewal of the Environmental Management Site- Specific Advisory Board has been determined to be...

  19. 40 CFR 170.232 - Knowledge of labeling and site-specific information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Knowledge of labeling and site-specific information. 170.232 Section 170.232 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS WORKER PROTECTION STANDARD Standard for Pesticide Handlers § 170.232 Knowledge of labeling and site-specific...

  20. 76 FR 51362 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

    ... activities. Tentative Agenda 1. Update--Site-Specific Environmental Impact Statement Committee. 2. Update... advance of the meeting at the phone number listed above. Written statements may be filed with the Board... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  1. 77 FR 12044 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-28

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management,...

  2. 76 FR 50204 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-12

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Site-Wide Environmental Impact Statement (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada....

  3. 78 FR 68431 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-14

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and...

  4. 76 FR 55370 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Site-Wide Environmental Impact Statement (EIS) Committee of the Environmental Management Site- Specific Advisory Board (EM SSAB), Nevada....

  5. 75 FR 64718 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-20

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... the areas of environmental restoration, waste management, and related activities. Tentative...

  6. Generalized theory on the mechanism of site-specific DNA-protein interactions

    NASA Astrophysics Data System (ADS)

    Niranjani, G.; Murugan, R.

    2016-05-01

    maximum possible 1Dd length of TFs in a square root manner. Results suggest that 1Dd processes contribute much less to the enhancement of specific binding rate under in vivo conditions for condensed DNA. There exists a critical length of binding stretch of TFs beyond which the probability associated with the random occurrence of similar specific binding sites will be close to zero. TFs in natural systems from prokaryotes to eukaryotes seem to handle sequence-mediated kinetic traps via increasing the length of their recognition stretch or combinatorial binding. TFs overcome the hurdles of roadblocks via switching efficiently between sliding, hopping and intersegmental transfer modes. The site-specific binding rate as well as the maximum possible 1Dd length seem to be directly proportional to the square root of the probability (p R) of finding a nonspecific binding site to be free from dynamic roadblocks. Here p R seems to be a function of the number of nsbs available per DNA binding protein (ϕ) inside the living cell. It seems that p R  >  0.8 when ϕ  >  10 which is true for the Escherichia coli cell system.

  7. Generalized theory on the mechanism of site-specific DNA–protein interactions

    NASA Astrophysics Data System (ADS)

    Niranjani, G.; Murugan, R.

    2016-05-01

    maximum possible 1Dd length of TFs in a square root manner. Results suggest that 1Dd processes contribute much less to the enhancement of specific binding rate under in vivo conditions for condensed DNA. There exists a critical length of binding stretch of TFs beyond which the probability associated with the random occurrence of similar specific binding sites will be close to zero. TFs in natural systems from prokaryotes to eukaryotes seem to handle sequence-mediated kinetic traps via increasing the length of their recognition stretch or combinatorial binding. TFs overcome the hurdles of roadblocks via switching efficiently between sliding, hopping and intersegmental transfer modes. The site-specific binding rate as well as the maximum possible 1Dd length seem to be directly proportional to the square root of the probability (p R) of finding a nonspecific binding site to be free from dynamic roadblocks. Here p R seems to be a function of the number of nsbs available per DNA binding protein (ϕ) inside the living cell. It seems that p R  >  0.8 when ϕ  >  10 which is true for the Escherichia coli cell system.

  8. Linked metatranscriptomic and geochemical data indicate microbial succession in naturally reduced aquifer sediments dominated by H2-oxidizing Comamonadaceae

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Bill, M.; Chakraborty, R.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2015-12-01

    In this study, we sought to better understand what natural organic matter fuels heterotrophic microbial communities in the anoxic subsurface at the Rifle (CO) site and what genes may be diagnostic of that activity. We conducted a 20-day microcosm experiment with naturally reduced zone (NRZ) sediments and collected replicate samples every 5 days for omics (metagenome and metatranscriptome) and biogeochemical measurements (e.g., continuous CO2 production, H2, CH4, acetate, DOC, Fe(II), sulfate, NH4+, spectroscopic analyses of sediment OM). No electron donors were added other than the NRZ sediment, which is enriched in organic matter relative to typical Rifle aquifer material. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with a N2headspace. Biogeochemical measurements indicate that the decomposition of native organic matter occurred in different phases, including depletion of DOC and release of CO2 during the first week of incubation, followed by a pulse of acetogenesis and methanogenesis after 2 weeks (with acetogenesis dominating carbon flux after 2 weeks). While H2 remained below detection levels throughout the study, a peak of [NiFe] uptake hydrogenase, acetyl-CoA synthetase, urease, and nitrate reductase transcripts belonging to the Comamonadaceae family occurred at day 15. Some members of Comamonadaceae are facultative H2-oxidizing chemolithoautotrophs and fix carbon via the acetogenic Wood-Ljungdahl pathway. Comamonadaceae plateaued at 73% of the metagenome at this time and represented 69% of the metatranscriptome, succeeding the S-oxidizing Sulfurimonas genus. Sulfurimonas species were the dominant group at day 0, accounting for 43% of the metagenome and 25% of the metatranscriptome, decreasing to 11% in both the metagenome and metatranscriptome by day 10. Less abundant but still present were transcripts for genes involved in cellulose degradation (glycosyl hydrolases), and glycolysis (phosphofructokinase

  9. Groundwater and Associated Solute Contribution to a Pristine Semi-Arid Estuary Using Resistivity Imaging, Naturally Occurring Radioactive Tracers, and Geochemical Methods.

    NASA Astrophysics Data System (ADS)

    Spalt, N.; Murgulet, D.; Douglas, A. R.

    2015-12-01

    Geophysical, geochemical, and Naturally Occurring Radioactive Tracers (NORTs) were used in a semi-arid National Estuarine Research Reserve to estimate Submarine Groundwater Discharge (SGD) rates and nutrient fluxes. SGD has been identified as an important source of limiting nutrients to coastal ecosystems, and is conceivably even more critical in a dry climate. Groundwater inflows are rarely considered in estuary mass budgets, therefore sampling stations were chosen over the entire bay system to identify spatial differences in SGD and to estimate direct groundwater contributions. This interdisciplinary approach proved necessary to differentiate between the bay recirculation and terrestrial components of SGD. Resistivity measurements using a towed electrode array were used to identify sampling stations at areas favorable to SGD. While NORTs may provide an estimate of basin-wide groundwater input, these sampling stations ascertain the favorable geologic environment for hydraulic interconnectivity between surface water and groundwater in the system. A sampling suite (including metals and nutrients) of surface, bottom, and pore waters during winter and summer months display spatio-temporal changes in nutrient fluxes. This study reinforces the understanding of the necessity to use multiple methods to accurately quantify SGD and associated solute fluxes and advances the knowledge of coastal groundwater interaction in semi-arid environments.

  10. Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

    PubMed Central

    Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

    2014-01-01

    Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

  11. Geochemical survey of Levante Bay, Vulcano Island (Italy), a natural laboratory for the study of ocean acidification.

    PubMed

    Boatta, F; D'Alessandro, W; Gagliano, A L; Liotta, M; Milazzo, M; Rodolfo-Metalpa, R; Hall-Spencer, J M; Parello, F

    2013-08-30

    Shallow submarine gas vents in Levante Bay, Vulcano Island (Italy), emit around 3.6t CO2 per day providing a natural laboratory for the study of biogeochemical processes related to seabed CO2 leaks and ocean acidification. The main physico-chemical parameters (T, pH and Eh) were measured at more than 70 stations with 40 seawater samples were collected for chemical analyses. The main gas vent area had high concentrations of dissolved hydrothermal gases, low pH and negative redox values all of which returned to normal seawater values at distances of about 400m from the main vents. Much of the bay around the vents is corrosive to calcium carbonate; the north shore has a gradient in seawater carbonate chemistry that is well suited to studies of the effects of long-term increases in CO2 levels. This shoreline lacks toxic compounds (such as H2S) and has a gradient in carbonate saturation states.

  12. Geochemical survey of Levante Bay, Vulcano Island (Italy), a natural laboratory for the study of ocean acidification.

    PubMed

    Boatta, F; D'Alessandro, W; Gagliano, A L; Liotta, M; Milazzo, M; Rodolfo-Metalpa, R; Hall-Spencer, J M; Parello, F

    2013-08-30

    Shallow submarine gas vents in Levante Bay, Vulcano Island (Italy), emit around 3.6t CO2 per day providing a natural laboratory for the study of biogeochemical processes related to seabed CO2 leaks and ocean acidification. The main physico-chemical parameters (T, pH and Eh) were measured at more than 70 stations with 40 seawater samples were collected for chemical analyses. The main gas vent area had high concentrations of dissolved hydrothermal gases, low pH and negative redox values all of which returned to normal seawater values at distances of about 400m from the main vents. Much of the bay around the vents is corrosive to calcium carbonate; the north shore has a gradient in seawater carbonate chemistry that is well suited to studies of the effects of long-term increases in CO2 levels. This shoreline lacks toxic compounds (such as H2S) and has a gradient in carbonate saturation states. PMID:23465567

  13. Geochemical behavior of radionuclides in highly altered zircon above the Bangombé natural fission reactor, Gabon

    NASA Astrophysics Data System (ADS)

    Kikuchi, Makiko; Hidaka, Hiroshi; Horie, Kenji

    The isotopic compositions of rare earth elements (REE), Pb and U of highly altered zircons from the clay and black shale layers above the Bangombé natural reactor, Gabon, were determined by a sensitive high resolution ion microprobe (SHRIMP) to discuss the redistribution processes of elements into zircons under the supergene weathering. The clay layer trapped most of the fissiogenic Nd, Sm and Eu derived from the reactor and prevented them migrating into the black shale layer. On the other hand, only the Ce isotopic ratios of the clay and black shale layers have about 2 times larger variations than the other REE. This result suggests that a large chemical fractionation between Ce and other REE above the reactor occurred under the oxidizing condition. The U-Pb data of zircons suggest that the U-Pb system was largely disturbed by migration of chemically fractionated Pb and U from the 2.0 Ga-old uraninite in association with recent weathering.

  14. Geochemical and Isotopic Analysis of Escaped Natural Gases in Hydraulically Fractured and non-Fractured sites in Cumberland Forest, Tennessee

    NASA Astrophysics Data System (ADS)

    Ajayi, M.; Ayers, J. C.; Hornberger, G. M.

    2015-12-01

    Methane (CH4) in the atmosphere accounts for 18% of the climate warming attributed to greenhouse gases. The rapid growth in high volume hydraulic fracturing (HVHF) technologies to procure natural gas raises concern for possible fugitive methane leaks. We measure the flux and carbon isotope composition of methane emitted from the soil into the atmosphere at two geologically similar sites in eastern Tennessee (Morgan Co.), one with HVHF ongoing and the other currently undeveloped. Our objective is to quantify potential non-point source emissions of microbial and thermogenic methane, which are principally distinguished by their δ13C signatures. Using cavity ring down spectroscopy (Picarro G2201-i) we collect rapid (~1 Hz) real-time measurements of methane emissions. The Picarro can measure fluxes of CH4 and CO2 at discrete locations by measuring their concentrations within a static and closed chamber that allows the gases to accumulate over time. Additionally, the mobility of the Picarro instrument permits the continuous collection of data, enabling broad spatial coverage. Applying geostatistical techniques to these data can highlight heterogeneities in the emissions of methane. Trends of where, how much, and what type of methane is escaping from the soil in environments with and without HVHF activities illustrate how to compare and contrast points as well as areas to assess the impact of this extensively implemented method of fossil fuel development.

  15. Progression of natural attenuation processes at a crude-oil spill site . I. Geochemical evolution of the plume

    USGS Publications Warehouse

    Cozzarelli, I.M.; Bekins, B.A.; Baedecker, M.J.; Aiken, G.R.; Eganhouse, R.P.; Tuccillo, M.E.

    2001-01-01

    A 16-year study of a hydrocarbon plume shows that the extent of contaminant migration and compound-specific behavior have changed as redox reactions, most notably iron reduction, have progressed over time. Concentration changes at a small scale, determined from analysis of pore-water samples drained from aquifer cores, are compared with concentration changes at the plume scale, determined from analysis of water samples from an observation well network. The small-scale data show clearly that the hydrocarbon plume is growing slowly as sediment iron oxides are depleted. Contaminants, such as ortho-xylene that appeared not to be moving downgradient from the oil on the basis of observation well data, are migrating in thin layers as the aquifer evolves to methanogenic conditions. However, the plume-scale observation well data show that the downgradient extent of the Fe2+ and BTEX plume did not change between 1992 and 1995. Instead, depletion of the unstable Fe (III) oxides near the subsurface crude-oil source has caused the maximum dissolved iron concentration zone within the plume to spread at a rate of approximately 3 m/year. The zone of maximum concentrations of benzene, toluene, ethylbenzene and xylene (BTEX) has also spread within the anoxic plume. In monitoring the remediation of hydrocarbon-contaminated ground water by natural attenuation, subtle concentration changes in observation well data from the anoxic zone may be diagnostic of depletion of the intrinsic electron-accepting capacity of the aquifer. Recognition of these subtle patterns may allow early prediction of growth of the hydrocarbon plume. Copyright ?? 2001 .

  16. Progression of natural attenuation processes at a crude-oil spill site. I. Geochemical evolution of the plume

    NASA Astrophysics Data System (ADS)

    Cozzarelli, Isabelle M.; Bekins, Barbara A.; Baedecker, Mary Jo; Aiken, George R.; Eganhouse, Robert P.; Tuccillo, Mary Ellen

    2001-12-01

    A 16-year study of a hydrocarbon plume shows that the extent of contaminant migration and compound-specific behavior have changed as redox reactions, most notably iron reduction, have progressed over time. Concentration changes at a small scale, determined from analysis of pore-water samples drained from aquifer cores, are compared with concentration changes at the plume scale, determined from analysis of water samples from an observation well network. The small-scale data show clearly that the hydrocarbon plume is growing slowly as sediment iron oxides are depleted. Contaminants, such as ortho-xylene that appeared not to be moving downgradient from the oil on the basis of observation well data, are migrating in thin layers as the aquifer evolves to methanogenic conditions. However, the plume-scale observation well data show that the downgradient extent of the Fe 2+ and BTEX plume did not change between 1992 and 1995. Instead, depletion of the unstable Fe (III) oxides near the subsurface crude-oil source has caused the maximum dissolved iron concentration zone within the plume to spread at a rate of approximately 3 m/year. The zone of maximum concentrations of benzene, toluene, ethylbenzene and xylene (BTEX) has also spread within the anoxic plume. In monitoring the remediation of hydrocarbon-contaminated ground water by natural attenuation, subtle concentration changes in observation well data from the anoxic zone may be diagnostic of depletion of the intrinsic electron-accepting capacity of the aquifer. Recognition of these subtle patterns may allow early prediction of growth of the hydrocarbon plume.

  17. Geophysical and geochemical nature of relaminated arc-derived lower crust underneath oceanic domain in southern Mongolia

    NASA Astrophysics Data System (ADS)

    Guy, Alexandra; Schulmann, Karel; Janoušek, Vojtech; Štípská, Pavla; Armstrong, Robin; Belousova, Elena; Dolgopolova, Alla; Seltmann, Reimar; Lexa, Ondrej; Jiang, Yingde; Hanžl, Pavel

    2016-04-01

    The Central Asian Orogenic Belt (CAOB) in southern Mongolia consists of E-W trending Neoproterozoic cratons and Silurian-Devonian oceanic tectonic zones. Previous study revealed that the Early Paleozoic accretionary wedge and the oceanic tectonic zone are underlain by a layer giving a homogeneous gravity signal. Forward gravity modelling suggests that this layer is not formed of high-density material typical of lower oceanic crust but is composed of low- to intermediate-density rocks resembling continental crust. The nature of this lower crust is constrained by the whole-rock geochemistry and zircon Hf isotopic signature of abundant Late Carboniferous high-K calc-alkaline and Early Permian A-type granitoids intruding the two Early Paleozoic domains. It is possible to explain the genesis of these granitoids by anatexis of juvenile, metaigneous (tonalitic-gabbroic) rocks of Late Cambrian age, the source of which is presumed to lie in the "Khantaishir" arc (520-495Ma) further north. In order to test this hypothesis, the likely modal composition and density of Khantaishir arc-like protoliths are thermodynamically modelled at granulite- and higher amphibolite-facies conditions. It is shown that the current average density of the lower crust inferred by gravity modelling (2730 ±20kg/m3) matches best metamorphosed leucotonalite to diorite. Based on these results, it is now proposed that Mongolian CAOB has an architecture in which the accretionary wedge and oceanic upper crust is underlain by allochthonous lower crust that originated in a Cambrian arc. A tectonic model explaining relamination of allochthonous felsic to intermediate lower crust beneath mafic upper crust is proposed.

  18. Geophysical and geochemical nature of relaminated arc-derived lower crust underneath oceanic domain in southern Mongolia

    NASA Astrophysics Data System (ADS)

    Guy, Alexandra; Schulmann, Karel; Janoušek, Vojtěch; Å típská, Pavla; Armstrong, Robin; Belousova, Elena; Dolgopolova, Alla; Seltmann, Reimar; Lexa, Ondrej; Jiang, Yingde; Hanžl, Pavel

    2015-05-01

    The Central Asian Orogenic Belt (CAOB) in southern Mongolia consists of E-W trending Neoproterozoic cratons and Silurian-Devonian oceanic tectonic zones. Previous study revealed that the Early Paleozoic accretionary wedge and the oceanic tectonic zone are underlain by a layer giving a homogeneous gravity signal. Forward gravity modelling suggests that this layer is not formed of high-density material typical of lower oceanic crust but is composed of low- to intermediate-density rocks resembling continental crust. The nature of this lower crust is constrained by the whole-rock geochemistry and zircon Hf isotopic signature of abundant Late Carboniferous high-K calc-alkaline and Early Permian A-type granitoids intruding the two Early Paleozoic domains. It is possible to explain the genesis of these granitoids by anatexis of juvenile, metaigneous (tonalitic-gabbroic) rocks of Late Cambrian age, the source of which is presumed to lie in the "Khantaishir" arc (520-495 Ma) further north. In order to test this hypothesis, the likely modal composition and density of Khantaishir arc-like protoliths are thermodynamically modelled at granulite- and higher amphibolite-facies conditions. It is shown that the current average density of the lower crust inferred by gravity modelling (2730 ± 20 kg/m3) matches best metamorphosed leucotonalite to diorite. Based on these results, it is now proposed that Mongolian CAOB has an architecture in which the accretionary wedge and oceanic upper crust is underlain by allochthonous lower crust that originated in a Cambrian arc. A tectonic model explaining relamination of allochthonous felsic to intermediate lower crust beneath mafic upper crust is proposed.

  19. Progression of natural attenuation processes at a crude-oil spill site: I. Geochemical evolution of the plume.

    PubMed

    Cozzarelli, I M; Bekins, B A; Baedecker, M J; Aiken, G R; Eganhouse, R P; Tuccillo, M E

    2001-12-15

    A 16-year study of a hydrocarbon plume shows that the extent of contaminant migration and compound-specific behavior have changed as redox reactions, most notably iron reduction, have progressed over time. Concentration changes at a small scale, determined from analysis of pore-water samples drained from aquifer cores, are compared with concentration changes at the plume scale, determined from analysis of water samples from an observation well network. The small-scale data show clearly that the hydrocarbon plume is growing slowly as sediment iron oxides are depleted. Contaminants, such as ortho-xylene that appeared not to be moving downgradient from the oil on the basis of observation well data, are migrating in thin layers as the aquifer evolves to methanogenic conditions. However, the plume-scale observation well data show that the downgradient extent of the Fe2+ and BTEX plume did not change between 1992 and 1995. Instead, depletion of the unstable Fe (III) oxides near the subsurface crude-oil source has caused the maximum dissolved iron concentration zone within the plume to spread at a rate of approximately 3 m/year. The zone of maximum concentrations of benzene, toluene, ethylbenzene and xylene (BTEX) has also spread within the anoxic plume. In monitoring the remediation of hydrocarbon-contaminated ground water by natural attenuation, subtle concentration changes in observation well data from the anoxic zone may be diagnostic of depletion of the intrinsic electron-accepting capacity of the aquifer. Recognition of these subtle patterns may allow early prediction of growth of the hydrocarbon plume.

  20. Site Specific Emission of Marcellus Shale Development using Fast Mobile Measurements

    NASA Astrophysics Data System (ADS)

    Goetz, J. D.; Floerchinger, C. R.; Fortner, E.; Wormhoudt, J.; Massoli, P.; Herndon, S.; Kolb, C. E.; Knighton, B.; Knipping, E. M.; Shaw, S. L.

    2013-12-01

    The Marcellus Shale is the largest shale gas resource in the United States and is found in parts of Pennsylvania, New York, Ohio, Maryland, and West Virginia. The rapid large-scale development, and lack of measured air emissions make the impact of Marcellus shale development on local and regional air quality and the global climate highly uncertain. Emission sources include transitory emission from well pad development such as well pad preparation, well drilling, hydraulic fracturing, well completions, and trucking. Long-term sources of emission are natural gas infrastructure such as producing wells, pipelines, and compressor stations. During the summer of 2012 the Aerodyne Inc. Mobile Laboratory equipped with a suite of real-time (~ 1 Hz) instrumentation was used to measure source emissions associated with Marcellus Shale development and to characterize regional air quality in the Marcellus basin. The Aerodyne Inc. Mobile Laboratory was equipped to measure Methane, Ethane, N2O (tracer gas), C2H2 (tracer gas), CO2, CO, NOx, SOx, and aerosol number, mass, and composition. Tracer-release methods were employed at selected source locations to estimate emission rates from Marcellus shale operations. Site-specific emissions from transitory and permanent sources were estimated at tracer release locations using regression analysis on single multi-species plumes and by utilizing plume dispersion modeling. Multiple plume intersections per site were averaged to determine an overall emission for each measured species at that site. Tracer release was employed at twelve individual Marcellus sites with the majority of the sites being compressor stations and well pads. Emission plumes associated with natural gas compressor stations commonly exhibited elevated levels of combustion species (i.e. particulate matter, CO, CO2, NOx,) and natural gas constituents. Both emission types were well correlated with tracer gas plumes. Emission plumes associated with well pads exhibited elevated

  1. Site-specific albumination of a therapeutic protein with multi-subunit to prolong activity in vivo

    PubMed Central

    Lim, Sung In; Hahn, Young S.; Kwon, Inchan

    2015-01-01

    Albumin fusion/conjugation (albumination) has been an effective method to prolong in vivo half-life of therapeutic proteins. However, its broader application to proteins with complex folding pathway or multi-subunit is restricted by incorrect folding, poor expression, heterogeneity, and loss of native activity of the proteins linked to albumin. We hypothesized that the site-specific conjugation of albumin to a permissive site of a target protein will expand the utilities of albumin as a therapeutic activity extender to proteins with a complex structure. We show here the genetic incorporation of a non-natural amino acid (NNAA) followed by chemoselective albumin conjugation to prolong therapeutic activity in vivo. Urate oxidase (Uox), a therapeutic enzyme for treatment of hyperuricemia, is a homotetramer with multiple surface lysines, limiting conventional approaches for albumination. Incorporation of p-azido-l-phenylalanine into two predetermined positions of Uox allowed site-specific linkage of dibenzocyclooctyne-derivatized human serum albumin (HSA) through strain-promoted azide-alkyne cycloaddition (SPAAC). The bio-orthogonality of SPAAC resulted in the production of a chemically well-defined conjugate, Uox-HSA, with a retained enzymatic activity. Uox-HSA had a half-life of 8.8 h in mice, while wild-type Uox had a half-life of 1.3 h. The AUC increased 5.5-fold (1657 vs. 303 mU/mL × h). These results clearly demonstrated that site-specific albumination led to the prolonged enzymatic activity of Uox in vivo. Site-specific albumination enabled by NNAA incorporation and orthogonal chemistry demonstrates its promise for the development of long-acting protein therapeutics with high potency and safety. PMID:25862515

  2. Site-specific albumination of a therapeutic protein with multi-subunit to prolong activity in vivo.

    PubMed

    Lim, Sung In; Hahn, Young S; Kwon, Inchan

    2015-06-10

    Albumin fusion/conjugation (albumination) has been an effective method to prolong in vivo half-life of therapeutic proteins. However, its broader application to proteins with complex folding pathway or multi-subunit is restricted by incorrect folding, poor expression, heterogeneity, and loss of native activity of the proteins linked to albumin. We hypothesized that the site-specific conjugation of albumin to a permissive site of a target protein will expand the utilities of albumin as a therapeutic activity extender to proteins with a complex structure. We show here the genetic incorporation of a non-natural amino acid (NNAA) followed by chemoselective albumin conjugation to prolong therapeutic activity in vivo. Urate oxidase (Uox), a therapeutic enzyme for treatment of hyperuricemia, is a homotetramer with multiple surface lysines, limiting conventional approaches for albumination. Incorporation of p-azido-l-phenylalanine into two predetermined positions of Uox allowed site-specific linkage of dibenzocyclooctyne-derivatized human serum albumin (HSA) through strain-promoted azide-alkyne cycloaddition (SPAAC). The bio-orthogonality of SPAAC resulted in the production of a chemically well-defined conjugate, Uox-HSA, with a retained enzymatic activity. Uox-HSA had a half-life of 8.8 h in mice, while wild-type Uox had a half-life of 1.3 h. The AUC increased 5.5-fold (1657 vs. 303 mU/mL x h). These results clearly demonstrated that site-specific albumination led to the prolonged enzymatic activity of Uox in vivo. Site-specific albumination enabled by NNAA incorporation and orthogonal chemistry demonstrates its promise for the development of long-acting protein therapeutics with high potency and safety.

  3. Development of site-specific earthquake response spectra for eastern US sites

    SciTech Connect

    Beavers, J.E.; Brock, W.R.; Hunt, R.J.; Shaffer, K.E.

    1993-08-01

    Site-specific earthquake, uniform-hazard response spectra have been defined for the Department of Energy Oak Ridge, Tennessee, and Portsmouth, Ohio, sites for use in evaluating existing facilities and designing new facilities. The site-specific response spectra were defined from probabilistic and deterministic seismic hazard studies following the requirements in DOE-STD-1024-92, ``Guidelines for Probabilistic Seismic Hazard Curves at DOE Sites.` For these two sites, the results show that site-specific uniform-hazard response spectra are slightly higher in the high-frequency range and considerably lower in the low-frequency range compared with response spectra defined for these sites in the past.

  4. Conversion of the interleukin 1 receptor antagonist into an agonist by site-specific mutagenesis.

    PubMed Central

    Ju, G; Labriola-Tompkins, E; Campen, C A; Benjamin, W R; Karas, J; Plocinski, J; Biondi, D; Kaffka, K L; Kilian, P L; Eisenberg, S P

    1991-01-01

    Interleukin 1 (IL-1) receptor antagonist (IL-1ra) is a naturally occurring protein that binds to the IL-1 receptor present on T cells, fibroblasts, and other cell types and acts to block IL-1-induced responses. IL-1ra is a pure antagonist and has no agonist activity in in vitro or in vivo systems. By site-specific mutagenesis, an analog of IL-1ra was created that contained a substitution of a single amino acid, Lys-145----Asp. This analog, IL-1ra K145D, exhibited partial agonist activity in the D10.G4.1 cell proliferation assay. The newly acquired agonist activity could not be neutralized by antisera to IL-1 alpha or IL-1 beta, but it could be blocked by a monoclonal antibody to the T-cell IL-1 receptor. The analog also showed agonist activity as assayed by increased prostaglandin E2 synthesis from CHO cells expressing recombinant mouse IL-1 receptor. These results with IL-1ra K145D demonstrate the importance of the region surrounding the corresponding Asp-145 residue in IL-1 beta for triggering the biological response to IL-1. Images PMID:1826365

  5. Site-specific cross-linking of proteins through tyrosine hexahistidine tags.

    PubMed

    Stayner, R Scott; Min, Dong-Joon; Kiser, Patrick F; Stewart, Russell J

    2005-01-01

    The genetic addition of hexahistidine (H(6)) tags is widely used to isolate recombinant proteins by immobilized metal-affinity chromatography (IMAC). Addition of a tyrosine residue to H(6) tags enabled proteins to be covalently cross-linked under mild conditions in a manner similar to the natural, site-specific cross-linking of tyrosines into dityrosine. A series of seven hexahistidine tags with tyrosines placed in various positions (H(6)Y tags) were added to the amino terminus of the I28 immunoglobulin domain of the human cardiac titin. The H(6)Y-tagged I28 dimerized in the presence of excess Ni(2+) with a K(D) of 200 microM. Treatment of Ni(2+)-dimerized H(6)Y-I28 with an oxidant, monoperoxyphthalic acid (MMPP) or sodium sulfite, resulted in covalent protein multimerization through chelated Ni(2+)-catalyzed cross-linking of the Y residues engineered into the H(6) tag. The protein oligomerization was observed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). The presence of dityrosine in the cross-linked proteins was confirmed by fluorescence emission at 410 nm. Proteins lacking the Y residue in the H(6) tag treated with the same oxidative conditions did not cross-link or exhibit dityrosine fluorescence, despite the presence of an endogenous Y residue. The method may have potential uses in other protein conjugation applications such as protein labeling and interfacial immobilization of proteins on artificial surfaces. PMID:16287262

  6. Simulation-Based Approach for Site-Specific Optimization of Hydrokinetic Turbine Arrays

    NASA Astrophysics Data System (ADS)

    Sotiropoulos, F.; Chawdhary, S.; Yang, X.; Khosronejad, A.; Angelidis, D.

    2014-12-01

    A simulation-based approach has been developed to enable site-specific optimization of tidal and current turbine arrays in real-life waterways. The computational code is based on the St. Anthony Falls Laboratory Virtual StreamLab (VSL3D), which is able to carry out high-fidelity simulations of turbulent flow and sediment transport processes in rivers and streams taking into account the arbitrary geometrical complexity characterizing natural waterways. The computational framework can be used either in turbine-resolving mode, to take into account all geometrical details of the turbine, or with the turbines parameterized as actuator disks or actuator lines. Locally refined grids are employed to dramatically increase the resolution of the simulation and enable efficient simulations of multi-turbine arrays. Turbine/sediment interactions are simulated using the coupled hydro-morphodynamic module of VSL3D. The predictive capabilities of the resulting computational framework will be demonstrated by applying it to simulate turbulent flow past a tri-frame configuration of hydrokinetic turbines in a rigid-bed turbulent open channel flow as well as turbines mounted on mobile bed open channels to investigate turbine/sediment interactions. The utility of the simulation-based approach for guiding the optimal development of turbine arrays in real-life waterways will also be discussed and demonstrated. This work was supported by NSF grant IIP-1318201. Simulations were carried out at the Minnesota Supercomputing Institute.

  7. Hyaluronan microspheres for sustained gene delivery and site-specific targeting.

    PubMed

    Yun, Yang H; Goetz, Douglas J; Yellen, Paige; Chen, Weiliam

    2004-01-01

    Hyaluronan is a naturally occurring polymer that has enjoyed wide successes in biomedical and cosmetic applications as coatings, matrices, and hydrogels. For controlled delivery applications, formulating native hyaluronan into microspheres could be advantageous but has been difficult to process unless organic solvents are used or hyaluronan has been modified by etherification. Therefore, we present a novel method of preparing hyaluronan microspheres using adipic dihydrazide mediated crosslinking chemistry. To evaluate their potential for medical applications, hyaluronan microspheres are incorporated with DNA for gene delivery or conjugated with an antigen for cell-specific targeting. The results show that our method, originally developed for preparing hyaluronan hydrogels, generates robust microspheres with a size distribution of 5-20mum. The release of the encapsulated plasmid DNA can be sustained for months and is capable of transfection in vitro and in vivo. Hyaluronan microspheres, conjugated with monoclonal antibodies to E- and P-selectin, demonstrate selective binding to cells expressing these receptors. In conclusion, we have developed a novel microsphere preparation using native hyaluronan that delivers DNA at a controlled rate and adaptable for site-specific targeting. PMID:14580918

  8. The role of anthropogenic and natural factors in shaping the geochemical evolution of groundwater in the Subei Lake basin, Ordos energy base, Northwestern China.

    PubMed

    Liu, Fei; Song, Xianfang; Yang, Lihu; Han, Dongmei; Zhang, Yinghua; Ma, Ying; Bu, Hongmei

    2015-12-15

    Groundwater resources are increasingly exploited for industrial and agricultural purposes in many arid regions globally, it is urgent to gain the impact of the enhanced anthropogenic pressure on the groundwater chemistry. The aim of this study was to acquire a comprehensive understanding of the evolution of groundwater chemistry and to identify the impact of natural and anthropogenic factors on the groundwater chemistry in the Subei Lake basin, Northwestern China. A total of 153 groundwater samples were collected and major ions were measured during the three campaigns (August and December 2013, May 2014). At present, the major hydrochemical facies in unconfined groundwater are Ca-Mg-HCO3, Ca-Na-HCO3, Na-Ca-HCO3, Na-HCO3, Ca-Mg-SO4 and Na-SO4-Cl types, while the main hydrochemical facies in confined groundwater are Ca-Mg-HCO3, Ca-Na-HCO3, Na-Ca-HCO3, Ca-HCO3 and Na-HCO3 types. Relatively greater seasonal variation can be observed in the chemical constituents of confined groundwater than that of unconfined groundwater. Rock weathering predominates the evolution of groundwater chemistry in conjunction with the cation exchange, and the dissolution/precipitation of gypsum, halite, feldspar, calcite and dolomite are responsible for the chemical constituents of groundwater. Anthropogenic activities can be classified as: (1) groundwater overexploitation; (2) excessive application of fertilizers in agricultural areas. Due to intensive groundwater pumping, the accelerated groundwater mineralization resulted in the local changes in hydrochemical facies of unconfined groundwater, while the strong mixture, especially a large influx of downward leakage from the unconfined aquifer into the confined aquifer, played a vital role in the fundamental variation of hydrochemical facies in confined aquifer. The nitrate contamination is mainly controlled by the local hydrogeological settings coupled with the traditional flood irrigation. The deeper insight into geochemical evolution of

  9. 78 FR 56871 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda Call to...

  10. A METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

    EPA Science Inventory

    We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific "microequilibrium" constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

  11. 78 FR 10611 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-14

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda Call to...

  12. 75 FR 7577 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-22

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda: Call to...

  13. 76 FR 8359 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-14

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda Call to...

  14. 78 FR 7767 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  15. 77 FR 4799 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  16. 77 FR 20014 - Environmental Management Site-Specific Advisory Board, Paducah, KY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-03

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah, KY AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  17. 78 FR 45518 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  18. 78 FR 32640 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  19. 78 FR 54460 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  20. 76 FR 61350 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of Energy Paducah...

  1. 77 FR 59598 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  2. 77 FR 11516 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-27

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  3. 77 FR 51789 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-27

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Reinhard Knerr, Deputy Designated Federal Officer, Department of...

  4. 78 FR 38969 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  5. 78 FR 25064 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  6. 78 FR 16260 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  7. 78 FR 73519 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE) ACTION: Notice... FURTHER INFORMATION CONTACT: Rachel Blumenfeld, Deputy Designated Federal Officer, Department of...

  8. 78 FR 40130 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-03

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  9. 78 FR 75552 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... and Remediation Committee and Waste Management Committee of the Environmental Management Site-Specific... restoration, waste management, and related activities. Purpose of the Environmental Monitoring and Remediation... environmental remediation activities resulting from historical Los Alamos National Laboratory operations and,...

  10. METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

    EPA Science Inventory

    We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific “microequilibrium” constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

  11. 76 FR 78909 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management, and related activities. Tentative Agenda Call to...

  12. SMART GUIDANCE AND SMARTE - TOOLS FOR DEVELOPING SITE SPECIFIC REDEVELOPMENT PLANS

    EPA Science Inventory

    Site-specific Management Approaches and Redevelopment Tools (SMART) Guidance and its electronic counterpart, SMARTe are being developed jointly with the German Federal Ministry of Education and Research and the Interstate Technology Regulatory Council. These products will assist ...

  13. SUPPORTING THE REDEVELOPMENT OF BROWNFIELD SITES USING SITE-SPECIFIC MANAGEMENT APPROACHES AND REDEVELOPMENT TOOLS (SMART)

    EPA Science Inventory

    The Site-Specific Management Approaches and Redevelopment Tools (SMART) provides potential solutions for facilitating the redevelopment of brownfield sites. The term "brownfield site" refers to previously developed property whose reuse may be complicated by the presence of hazar...

  14. SEDIMENT GEOCHEMICAL MODEL

    EPA Science Inventory

    Until recently, sediment geochemical models (diagenetic models) have been only able to explain sedimentary flux and concentration profiles for a few simplified geochemical cycles (e.g., nitrogen, carbon and sulfur). However with advances in numerical methods, increased accuracy ...

  15. Geologic and geochemical systematics of the occurrence of nonhydrocarbon gases: Towards working models to forecast CO{sub 2}, H{sub 2}S and N{sub 2} in natural gas

    SciTech Connect

    Imbus, S.W.; Bissada, K.K.; Urwongse, T.

    1995-12-31

    Despite recent progress towards understanding the mechanisms responsible for generation of many of the naturally occurring non-hydrocarbon gases, no globally applicable set of geologic or geochemical criteria has been developed to elucidate their origin or forecast their abundance in natural gas systems. The present study attempts to identify empirical relationships between the occurrence of these non-hydrocarbon gases and specific geological conditions including tectonic/structural setting; prevalent lithostratigraphy: present and paleo-geothermal and hydrothermal conditions; source rock type and thermal maturity; reservoir lithology and temperature; etc. The use of geochemical data (molecular and isotopic compositions) to assess the relative importance of the diverse controls (in terms of {open_quotes}basin{close_quotes} vs. {open_quotes}reservoir{close_quotes}, organic vs. inorganic, chemical vs. physicochemical factors) will also be examined in the context of the observations. The incorporation of more detailed geologic observations into this basic framework should provide the basis for working-out the geologic/geochemical systematics. This is a most critical step in developing the ultimate forecasting model.

  16. An Approach to Industrial Stormwater Benchmarks: Establishing and Using Site-Specific Threshold Criteria at Lawrence Livermore National Laboratory

    SciTech Connect

    Campbell, C G; Mathews, S

    2006-09-07

    Current regulatory schemes use generic or industrial sector specific benchmarks to evaluate the quality of industrial stormwater discharges. While benchmarks can be a useful tool for facility stormwater managers in evaluating the quality stormwater runoff, benchmarks typically do not take into account site-specific conditions, such as: soil chemistry, atmospheric deposition, seasonal changes in water source, and upstream land use. Failing to account for these factors may lead to unnecessary costs to trace a source of natural variation, or potentially missing a significant local water quality problem. Site-specific water quality thresholds, established upon the statistical evaluation of historic data take into account these factors, are a better tool for the direct evaluation of runoff quality, and a more cost-effective trigger to investigate anomalous results. Lawrence Livermore National Laboratory (LLNL), a federal facility, established stormwater monitoring programs to comply with the requirements of the industrial stormwater permit and Department of Energy orders, which require the evaluation of the impact of effluent discharges on the environment. LLNL recognized the need to create a tool to evaluate and manage stormwater quality that would allow analysts to identify trends in stormwater quality and recognize anomalous results so that trace-back and corrective actions could be initiated. LLNL created the site-specific water quality threshold tool to better understand the nature of the stormwater influent and effluent, to establish a technical basis for determining when facility operations might be impacting the quality of stormwater discharges, and to provide ''action levels'' to initiate follow-up to analytical results. The threshold criteria were based on a statistical analysis of the historic stormwater monitoring data and a review of relevant water quality objectives.

  17. TAPIR--Finnish national geochemical baseline database.

    PubMed

    Jarva, Jaana; Tarvainen, Timo; Reinikainen, Jussi; Eklund, Mikael

    2010-09-15

    In Finland, a Government Decree on the Assessment of Soil Contamination and Remediation Needs has generated a need for reliable and readily accessible data on geochemical baseline concentrations in Finnish soils. According to the Decree, baseline concentrations, referring both to the natural geological background concentrations and the diffuse anthropogenic input of substances, shall be taken into account in the soil contamination assessment process. This baseline information is provided in a national geochemical baseline database, TAPIR, that is publicly available via the Internet. Geochemical provinces with elevated baseline concentrations were delineated to provide regional geochemical baseline values. The nationwide geochemical datasets were used to divide Finland into geochemical provinces. Several metals (Co, Cr, Cu, Ni, V, and Zn) showed anomalous concentrations in seven regions that were defined as metal provinces. Arsenic did not follow a similar distribution to any other elements, and four arsenic provinces were separately determined. Nationwide geochemical datasets were not available for some other important elements such as Cd and Pb. Although these elements are included in the TAPIR system, their distribution does not necessarily follow the ones pre-defined for metal and arsenic provinces. Regional geochemical baseline values, presented as upper limit of geochemical variation within the region, can be used as trigger values to assess potential soil contamination. Baseline values have also been used to determine upper and lower guideline values that must be taken into account as a tool in basic risk assessment. If regional geochemical baseline values are available, the national guideline values prescribed in the Decree based on ecological risks can be modified accordingly. The national geochemical baseline database provides scientifically sound, easily accessible and generally accepted information on the baseline values, and it can be used in various

  18. TAPIR--Finnish national geochemical baseline database.

    PubMed

    Jarva, Jaana; Tarvainen, Timo; Reinikainen, Jussi; Eklund, Mikael

    2010-09-15

    In Finland, a Government Decree on the Assessment of Soil Contamination and Remediation Needs has generated a need for reliable and readily accessible data on geochemical baseline concentrations in Finnish soils. According to the Decree, baseline concentrations, referring both to the natural geological background concentrations and the diffuse anthropogenic input of substances, shall be taken into account in the soil contamination assessment process. This baseline information is provided in a national geochemical baseline database, TAPIR, that is publicly available via the Internet. Geochemical provinces with elevated baseline concentrations were delineated to provide regional geochemical baseline values. The nationwide geochemical datasets were used to divide Finland into geochemical provinces. Several metals (Co, Cr, Cu, Ni, V, and Zn) showed anomalous concentrations in seven regions that were defined as metal provinces. Arsenic did not follow a similar distribution to any other elements, and four arsenic provinces were separately determined. Nationwide geochemical datasets were not available for some other important elements such as Cd and Pb. Although these elements are included in the TAPIR system, their distribution does not necessarily follow the ones pre-defined for metal and arsenic provinces. Regional geochemical baseline values, presented as upper limit of geochemical variation within the region, can be used as trigger values to assess potential soil contamination. Baseline values have also been used to determine upper and lower guideline values that must be taken into account as a tool in basic risk assessment. If regional geochemical baseline values are available, the national guideline values prescribed in the Decree based on ecological risks can be modified accordingly. The national geochemical baseline database provides scientifically sound, easily accessible and generally accepted information on the baseline values, and it can be used in various

  19. The role of anthropogenic and natural factors in shaping the geochemical evolution of groundwater in the Subei Lake basin, Ordos energy base, Northwestern China.

    PubMed

    Liu, Fei; Song, Xianfang; Yang, Lihu; Han, Dongmei; Zhang, Yinghua; Ma, Ying; Bu, Hongmei

    2015-12-15

    Groundwater resources are increasingly exploited for industrial and agricultural purposes in many arid regions globally, it is urgent to gain the impact of the enhanced anthropogenic pressure on the groundwater chemistry. The aim of this study was to acquire a comprehensive understanding of the evolution of groundwater chemistry and to identify the impact of natural and anthropogenic factors on the groundwater chemistry in the Subei Lake basin, Northwestern China. A total of 153 groundwater samples were collected and major ions were measured during the three campaigns (August and December 2013, May 2014). At present, the major hydrochemical facies in unconfined groundwater are Ca-Mg-HCO3, Ca-Na-HCO3, Na-Ca-HCO3, Na-HCO3, Ca-Mg-SO4 and Na-SO4-Cl types, while the main hydrochemical facies in confined groundwater are Ca-Mg-HCO3, Ca-Na-HCO3, Na-Ca-HCO3, Ca-HCO3 and Na-HCO3 types. Relatively greater seasonal variation can be observed in the chemical constituents of confined groundwater than that of unconfined groundwater. Rock weathering predominates the evolution of groundwater chemistry in conjunction with the cation exchange, and the dissolution/precipitation of gypsum, halite, feldspar, calcite and dolomite are responsible for the chemical constituents of groundwater. Anthropogenic activities can be classified as: (1) groundwater overexploitation; (2) excessive application of fertilizers in agricultural areas. Due to intensive groundwater pumping, the accelerated groundwater mineralization resulted in the local changes in hydrochemical facies of unconfined groundwater, while the strong mixture, especially a large influx of downward leakage from the unconfined aquifer into the confined aquifer, played a vital role in the fundamental variation of hydrochemical facies in confined aquifer. The nitrate contamination is mainly controlled by the local hydrogeological settings coupled with the traditional flood irrigation. The deeper insight into geochemical evolution of

  20. Site-specific water quality guidelines: 1. Derivation approaches based on physicochemical, ecotoxicological and ecological data.

    PubMed

    van Dam, R A; Humphrey, C L; Harford, A J; Sinclair, A; Jones, D R; Davies, S; Storey, A W

    2014-01-01

    Generic water quality guidelines (WQGs) are developed by countries/regions as broad scale tools to assist with the protection of aquatic ecosystems from the impacts of toxicants. However, since generic WQGs cannot adequately account for the many environmental factors that may affect toxicity at a particular site, site-specific WQGs are often needed, especially for high environmental value ecosystems. The Australian and New Zealand Guidelines for Fresh and Marine Water Quality provide comprehensive guidance on methods for refining or deriving WQGs for site-specific purposes. This paper describes three such methods for deriving site-specific WQGs, namely: (1) using local reference water quality data, (2) using biological effects data from laboratory-based toxicity testing, and (3) using biological effects data from field surveys. Two case studies related to the assessment of impacts arising from mining operations in northern Australia are used to illustrate the application of these methods. Finally, the potential of several emerging methods designed to assess thresholds of ecological change from field data for deriving site-specific WQGs is discussed. Ideally, multiple lines of evidence approaches, integrating both laboratory and field data, are recommended for deriving site-specific WQGs. PMID:23846952

  1. Configuration and specifications of an Unmanned Aerial Vehicle (UAV) for early site specific weed management.

    PubMed

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches).

  2. Configuration and specifications of an Unmanned Aerial Vehicle (UAV) for early site specific weed management.

    PubMed

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches). PMID:23483997

  3. Evaluating the results of a site-specific PSHA from the perspective of a risk analyst

    NASA Astrophysics Data System (ADS)

    Klügel, Jens-Uwe

    2016-04-01

    From 1998 till 2015 Swiss Nuclear Power Plants sponsored a set of comprehensive site-specific PSHA-studies (PEGASOS, PEGASOS Refinement Project) to obtain the requested input for their plant specific probabilistic risk assessments following the US SSHAC procedures at their most elaborated level 4. The studies were performed by well-known earth scientists working completely independent from sponsors under participatory review of the Swiss Nuclear Safety Inspectorate. Risk analysts of Swiss Nuclear Power Plants recently have been mandated to implement the final results of the studies in their risk assessment studies. This triggered an in depth assessment of the results focussed on their practical applicability for risk studies. This assessment resulted in some important insights that are of interest for future PSHA studies performed for new nuclear power plants. The assessment included a review of the completeness of results with respect to risk applications as well as plausibility checks of hazard results based on Black Swan Theory and known historical events. The key lessons and recommendations for more detailed project output specifications for future projects are presented in the paper. It was established that future PSHA projects shall provide the joint probability distribution of ground motion hazard and the associated strong motion duration as the output to allow for a technically meaningful risk assessment. The recommendation of WENRA (West European Nuclear Regulators) published in their reference levels to perform natural hazard assessment preferably based on physical grounds (deterministic method) is also rationalized by recommending an holistic approach to hazard analysis comparing PSHA insights with the results of modelling deterministic Seismic Hazard Analysis.

  4. Site-specific updating and aggregation of Bayesian belief network models for multiple experts.

    PubMed

    Stiber, Neil A; Small, Mitchell J; Pantazidou, Marina

    2004-12-01

    A method for combining multiple expert opinions that are encoded in a Bayesian Belief Network (BBN) model is presented and applied to a problem involving the cleanup of hazardous chemicals at a site with contaminated groundwater. The method uses Bayes Rule to update each expert model with the observed evidence, then uses it again to compute posterior probability weights for each model. The weights reflect the consistency of each model with the observed evidence, allowing the aggregate model to be tailored to the particular conditions observed in the site-specific application of the risk model. The Bayesian update is easy to implement, since the likelihood for the set of evidence (observations for selected nodes of the BBN model) is readily computed by sequential execution of the BBN model. The method is demonstrated using a simple pedagogical example and subsequently applied to a groundwater contamination problem using an expert-knowledge BBN model. The BBN model in this application predicts the probability that reductive dechlorination of the contaminant trichlorethene (TCE) is occurring at a site--a critical step in the demonstration of the feasibility of monitored natural attenuation for site cleanup--given information on 14 measurable antecedent and descendant conditions. The predictions for the BBN models for 21 experts are weighted and aggregated using examples of hypothetical and actual site data. The method allows more weight for those expert models that are more reflective of the site conditions, and is shown to yield an aggregate prediction that differs from that of simple model averaging in a potentially significant manner.

  5. Configuration and Specifications of an Unmanned Aerial Vehicle (UAV) for Early Site Specific Weed Management

    PubMed Central

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches). PMID:23483997

  6. Bifunctional chelating agent for the design and development of site specific radiopharmaceuticals and biomolecule conjugation strategy

    DOEpatents

    Katti, Kattesh V.; Prabhu, Kandikere R.; Gali, Hariprasad; Pillarsetty, Nagavara Kishore; Volkert, Wynn A.

    2003-10-21

    There is provided a method of labeling a biomolecule with a transition metal or radiometal in a site specific manner to produce a diagnostic or therapeutic pharmaceutical compound by synthesizing a P.sub.2 N.sub.2 -bifunctional chelating agent intermediate, complexing the intermediate with a radio metal or a transition metal, and covalently linking the resulting metal-complexed bifunctional chelating agent with a biomolecule in a site specific manner. Also provided is a method of synthesizing the --PR.sub.2 containing biomolecules by synthesizing a P.sub.2 N.sub.2 -bifunctional chelating agent intermediate, complexing the intermediate with a radiometal or a transition metal, and covalently linking the resulting radio metal-complexed bifunctional chelating agent with a biomolecule in a site specific manner. There is provided a therapeutic or diagnostic agent comprising a --PR.sub.2 containing biomolecule.

  7. Industrial energy conservation-center-pivot site specific irrigation. Final report, January 1995--December 1996

    SciTech Connect

    McCann, I.R.; King, B.A.; Brady, R.

    1996-12-27

    This project was to aid in the development and commercial transfer of site specific technology to industry and farmers. This report contains the results of data collected during the fall of 1996 on a site near Aberdeen, Idaho. This site was equipped to apply water at variable rates predetermined by a digital control map that resided in a computer controller. The flow rates were then adjusted to maintain desired pressure with an Adjustable Speed Drive. Energy consumption was monitored during implementation of site specific irrigation practices and normal irrigation practices. This final report covers the impact that site specific irrigation has on energy use on a irrigated small grain crop near Aberdeen, Idaho. 3 refs., 20 figs., 1 tab.

  8. Versatile and Efficient Site-Specific Protein Functionalization by Tubulin Tyrosine Ligase.

    PubMed

    Schumacher, Dominik; Helma, Jonas; Mann, Florian A; Pichler, Garwin; Natale, Francesco; Krause, Eberhard; Cardoso, M Cristina; Hackenberger, Christian P R; Leonhardt, Heinrich

    2015-11-01

    A novel chemoenzymatic approach for simple and fast site-specific protein labeling is reported. Recombinant tubulin tyrosine ligase (TTL) was repurposed to attach various unnatural tyrosine derivatives as small bioorthogonal handles to proteins containing a short tubulin-derived recognition sequence (Tub-tag). This novel strategy enables a broad range of high-yielding and fast chemoselective C-terminal protein modifications on isolated proteins or in cell lysates for applications in biochemistry, cell biology, and beyond, as demonstrated by the site-specific labeling of nanobodies, GFP, and ubiquitin. PMID:26404067

  9. Toward site-specific, homogeneous and highly stable fluorescent silver nanoclusters fabrication on triplex DNA scaffolds

    PubMed Central

    Feng, Lingyan; Huang, Zhenzhen; Ren, Jinsong; Qu, Xiaogang

    2012-01-01

    A new strategy to create site-specific, homogeneous, and bright silver nanoclusters (AgNCs) with high-stability was demonstrated by triplex DNA as template. By reasonable design of DNA sequence, homogeneous Ag2 cluster was obtained in the predefined position of CG.C+ site of triplex DNA. This strategy was also explored for controlled alignment of AgNCs on the DNA nanoscaffold. To the best of our knowledge, this was the first example to simultaneously answer the challenges of excellent site-specific nucleation and growth, homogeneity and stability against salt of DNA-templated AgNCs. PMID:22570417

  10. An Efficient Procedure for Marker-Free Mutagenesis of S. coelicolor by Site-Specific Recombination for Secondary Metabolite Overproduction

    PubMed Central

    Dai, Ruixue; Yu, Meiying; Zhao, Guoping; Ding, Xiaoming

    2013-01-01

    Streptomyces bacteria are known for producing important natural compounds by secondary metabolism, especially antibiotics with novel biological activities. Functional studies of antibiotic-biosynthesizing gene clusters are generally through homologous genomic recombination by gene-targeting vectors. Here, we present a rapid and efficient method for construction of gene-targeting vectors. This approach is based on Streptomyces phage φBT1 integrase-mediated multisite in vitro site-specific recombination. Four ‘entry clones’ were assembled into a circular plasmid to generate the destination gene-targeting vector by a one-step reaction. The four ‘entry clones’ contained two clones of the upstream and downstream flanks of the target gene, a selectable marker and an E. coli-Streptomyces shuttle vector. After targeted modification of the genome, the selectable markers were removed by φC31 integrase-mediated in vivo site-specific recombination between pre-placed attB and attP sites. Using this method, part of the calcium-dependent antibiotic (CDA) and actinorhodin (Act) biosynthetic gene clusters were deleted, and the rrdA encoding RrdA, a negative regulator of Red production, was also deleted. The final prodiginine production of the engineered strain was over five times that of the wild-type strain. This straightforward φBT1 and φC31 integrase-based strategy provides an alternative approach for rapid gene-targeting vector construction and marker removal in streptomycetes. PMID:23409083

  11. Theory on the mechanism of site-specific DNA-protein interactions in the presence of traps

    NASA Astrophysics Data System (ADS)

    Niranjani, G.; Murugan, R.

    2016-08-01

    The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA.

  12. Theory on the mechanism of site-specific DNA–protein interactions in the presence of traps

    NASA Astrophysics Data System (ADS)

    Niranjani, G.; Murugan, R.

    2016-08-01

    The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA.

  13. Facile Method for the Site-Specific, Covalent Attachment of full-length IgG onto Nanoparticles

    PubMed Central

    Hui, James Zhe; Al Zaki, Ajlan; Cheng, Zhiliang; Popik, Vladimir; Zhang, Hongtao; Luning Prak, Eline T.

    2014-01-01

    Antibodies, most commonly IgGs, have been widely used as targeting ligands in research and therapeutic applications due to their wide array of targets, high specificity and proven efficacy. Many of these applications require antibodies to be conjugated onto surfaces (e.g. nanoparticles and microplates); however, most conventional bioconjugation techniques exhibit low crosslinking efficiencies, reduced functionality due to non-site-specific labeling and random surface orientation, and/or require protein engineering (e.g. cysteine handles), which can be technically challenging. To overcome these limitations, we have recombinantly expressed Protein Z, which binds the Fc region of IgG, with an UV active non-natural amino acid benzoylphenyalanine (BPA) within its binding domain. Upon exposure to long wavelength UV light, the BPA is activated and forms a covalent link between the Protein Z and the bound Fc region of IgG. This technology was combined with expressed protein ligation (EPL), which allowed for the introduction of a fluorophore and click chemistry-compatible azide group onto the C-terminus of Protein Z during the recombinant protein purification step. This enabled crosslinked-Protein Z-IgG complexes to be efficiently and site-specifically attached to aza-dibenzycyclooctyne-modified nanoparticles, via copper-free click chemistry. PMID:24729432

  14. Theory on the mechanism of site-specific DNA-protein interactions in the presence of traps.

    PubMed

    Niranjani, G; Murugan, R

    2016-01-01

    The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA. PMID:27434174

  15. Integrated decision support, sensor networks and adaptive control for wireless site-specific sprinkler irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  16. Integrated Decision Support, Sensor Networks and Adaptive Control for Wireless Site-specific Sprinkler Irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  17. SITE-SPECIFIC PROTOCOL FOR MEASURING SOIL RADON POTENTIALS FOR FLORIDA HOUSES

    EPA Science Inventory

    The report describes a protocol for site-specific measurement of radon potentials for Florida houses that is consistent with existing residential radon protection maps. The protocol gives further guidance on the possible need for radon-protective house construction features. In a...

  18. 36 CFR 219.33 - Appeals of site-specific decisions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Appeals of site-specific decisions. 219.33 Section 219.33 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE PLANNING National Forest System Land and Resource Management Planning Objections and Appeals §...

  19. 36 CFR 219.33 - Appeals of site-specific decisions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Appeals of site-specific decisions. 219.33 Section 219.33 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE PLANNING National Forest System Land and Resource Management Planning Objections and Appeals §...

  20. 78 FR 20311 - Environmental Management Site-Specific Advisory Board Chairs

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ... Open Webinar. SUMMARY: This notice announces a webinar of the Environmental Management Site-Specific... that public notice of this webinar be announced in the Federal Register. DATES: Thursday, April 25... Update Waste Disposition Strategies EM SSAB Cross-Cutting Issues Public Participation: The webinar...

  1. Site-specific management of soil pH and nutrients in blueberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Site-specific management of soil pH and fertilizers is one of the most promising strategies in precision agriculture and is potentially applicable to many horticultural crops, including blueberry. Unlike most fruit crops, blueberry is adapted to low soil pH conditions in the range of 4-5.5 and has ...

  2. 78 FR 69657 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-20

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  3. 78 FR 22255 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-15

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  4. Stoichiometry of site-specific lysine acetylation in an entire proteome.

    PubMed

    Baeza, Josue; Dowell, James A; Smallegan, Michael J; Fan, Jing; Amador-Noguez, Daniel; Khan, Zia; Denu, John M

    2014-08-01

    Acetylation of lysine ϵ-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.

  5. Site-specific Topguard application based on aerial imagery for effective management of cotton root rot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton root rot is a century-old cotton disease that can be controlled with Topguard Fungicide recently. As this disease tends to occur in the same general areas within fields in recurring years, site-specific application of the fungicide only to the infected areas can be more effective and economic...

  6. CAN SITE-SPECIFIC TRENDS BE EXTRAPOLATED TO A REGION? AN ACIDIFICATION EXAMPLE FOR THE NORTHEAST

    EPA Science Inventory

    In the absence of true regional data on changes in the acid/base status of lakes in the northeastern United States, we explore the possibility of using site-specific trends information from a judgment sample of lakes to assess the efficacy of the Clean Air Act Amendments. A meta-...

  7. Hellsgate Big Game Winter Range Wildlife Mitigation Site Specific Management Plan for the Hellsgate Project.

    SciTech Connect

    Berger, Matthew T.; Judd, Steven L.

    1999-01-01

    This report contains a detailed site-specific management plan for the Hellsgate Winter Range Wildlife Mitigation Project. The report provides background information about the mitigation process, the review process, mitigation acquisitions, Habitat Evaluation Procedures (HEP) and mitigation crediting, current habitat conditions, desired future habitat conditions, restoration/enhancements efforts and maps.

  8. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1.

    PubMed Central

    Sauer, B; Henderson, N

    1988-01-01

    The Cre protein encoded by the coliphage P1 is a 38-kDa protein that efficiently promotes both intra- and intermolecular synapsis and recombination of DNA both in Escherichia coli and in vitro. Recombination occurs at a specific site, called lox, and does not require any other protein factors. The Cre protein is shown here also to be able to cause synapsis of DNA and site-specific recombination in a mammalian cell line. A stable mouse cell line was established that expresses the Cre protein under the control of the Cd2+-inducible metallothionein I gene promoter. DNA recombination was monitored with DNA substrates containing two directly repeated lox sites. One such substrate is a circular plasmid with two directly repeated lox sites (lox2) flanking a marker gene and was introduced into cells by Ca3(PO4)2 transformation. As a second substrate we used a pseudorabies virus (a herpesvirus) containing a lox2 insertion designed to provide a sensitive detection system for recombination. In both cases, site-specific recombination in vivo is dependent on the presence of the Cre protein and occurs specifically at the 34-base-pair lox sites. These results demonstrate the controlled site-specific synapsis of DNA and recombination by a prokaryotic protein in mammalian cells and suggest that Cre-mediated site-specific recombination may be a useful tool for understanding and modulating genome rearrangements in eukaryotes. Images PMID:2839833

  9. 76 FR 70120 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-10

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Taos Highway 68, San Juan Pueblo, New Mexico 87566. FOR FURTHER INFORMATION CONTACT: Menice...

  10. 78 FR 49739 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Pueblo Sur, Taos, New Mexico 87571. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern...

  11. 40 CFR 258.62 - Approval of site-specific flexibility requests in Indian country.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 5 U.S.C. 552(a) and 1 CFR part 51. You may inspect or obtain a copy at the Environmental Protection... other applicable provisions of 40 CFR part 258 remain in effect. ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Approval of site-specific...

  12. 75 FR 35446 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... the areas of environmental restoration, waste management, and related activities. Tentative Agenda 1...

  13. 77 FR 39234 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  14. 76 FR 51361 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-18

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy (DoE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management... the areas of environmental restoration, waste management, and related activities. Tentative Agenda 1...

  15. 75 FR 11872 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-12

    ..., Idaho National Laboratory to be held on March 16, 2010 75 FR 9590. In that notice, the meeting address... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Idaho National Laboratory AGENCY: Department of...

  16. 75 FR 8051 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a combined meeting of the Environmental Management Site... and site management in the areas of environmental restoration, waste management, and...

  17. 75 FR 51026 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  18. 77 FR 2283 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  19. 77 FR 50488 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  20. 78 FR 36543 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-18

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE) ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  1. 75 FR 19379 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-14

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  2. 75 FR 65615 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-26

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  3. 77 FR 63300 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  4. 76 FR 48148 - Environmental Management Site-Specific Advisory Board, Hanford

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-08

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy (DoE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management, and related activities. Tentative Agenda: Annual Tri-Party...

  5. 77 FR 16021 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-19

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  6. 77 FR 37390 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  7. Design, synthesis, and characterization of nucleosomes containing site-specific DNA damage.

    PubMed

    Taylor, John-Stephen

    2015-12-01

    How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.

  8. Using site-specific soil samples as a substitution for improved hydrological and nonpoint source predictions.

    PubMed

    Chen, Lei; Wang, Guobo; Zhong, Yucen; Zhao, Xin; Shen, Zhenyao

    2016-08-01

    Soil databases are one of the most important inputs for watershed models, and the quality of soil properties affects how well a model performs. The objectives of this study were to (1) quantify the sensitivity of model outputs to soil properties and to (2) use site-specific soil properties as a substitution for more accurate hydrological and nonpoint source (H/NPS) predictions. Soil samples were collected from a typical mountainous watershed in China, and the impacts of soil sample parameters on H/NPS predictions were quantified using the Soil and Water Assessment Tool (SWAT). The most sensitive parameters related to predicting flow, sediment, and total phosphorus (TP) mainly were the soil hydrological, the channel erosion processes, and the initial soil chemical environment, respectively. When the site-specific soil properties were used, the uncertainties (coefficient of variation) related to predicting the hydrology, sediment and TP decreased by 75∼80 %, 75∼84 %, and 46∼61 %, respectively. Based on changes in the Nash-Sutcliff coefficient, the model performance improved by 4.9 and 19.45 % for the hydrological and sediment model, accordingly. However, site-specific soil properties did not contribute to better TP predictions because of the high spatial variability of the soil P concentrations across the large watershed. Thus, although site-specific soil samples can be used to obtain more accurate H/NPS predictions, more sampling sites are required to apply this method in large watersheds. PMID:27146539

  9. 77 FR 31837 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION... Energy Paducah Site Office, Post Office Box 1410, MS-103, Paducah, Kentucky 42001, (270)...

  10. 78 FR 63172 - Environmental Management Site-Specific Advisory Board, Paducah; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah; Meeting AGENCY: Department of Energy (DOE... of Energy Paducah Site Office, Post Office Box 1410, MS-103, Paducah, Kentucky 42001, (270)...

  11. Development of Unmanned Aerial Vehicles for Site-Specific Crop Production Management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unmanned Aerial Vehicles (UAV) have been developed and applied to support the practice of precision agriculture. Compared to piloted aircrafts, an Unmanned Aerial Vehicle can focus on much smaller crop fields with much lower flight altitude than regular airplanes to perform site-specific management ...

  12. Use of GIS-based Site-specific Nitrogen Management for Improving Energy Efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To our knowledge, geographical information system (GIS)-based site-specific nitrogen management (SSNM) techniques have not been used to assess agricultural energy costs and efficiency. This chapter uses SSNM case studies for corn (Zea mays L.) grown in Missouri and cotton (Gossypium hirsutum L.) gro...

  13. Use of GIS-based site-specific nitrogen management for improving energy efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrogen (N) is a significant energy component of in support of crop production but it can be highly variable within fields. To our knowledge, no efforts have been made to employ GIS-based site-specific N management (SSNM) to assess and improve energy costs and efficiency. We examine recent SSNM ca...

  14. 40 CFR 60.3019 - What site-specific documentation is required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... procedures. (8) The waste management plan required under §§ 60.3010 through 60.3012. (9) Procedures for... Times for Other Solid Waste Incineration Units That Commenced Construction On or Before December 9, 2004 Model Rule-Operator Training and Qualification § 60.3019 What site-specific documentation is...

  15. 40 CFR 170.232 - Knowledge of labeling and site-specific information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Knowledge of labeling and site... (CONTINUED) PESTICIDE PROGRAMS WORKER PROTECTION STANDARD Standard for Pesticide Handlers § 170.232 Knowledge of labeling and site-specific information. (a) Knowledge of labeling information. (1) The...

  16. Design, development and evaluation of a tree planting-site-specific fumigant applicator

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this research was to use recent advances in the global positioning system (GPS) and computer technology to apply just the right amount of fumigant where it is most needed (i.e., tree-planting-site-specific application) to decrease the incidence of replant disease, and achieve the environ...

  17. 77 FR 24695 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-25

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. . 92... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  18. 75 FR 65466 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-25

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  19. 76 FR 25682 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  20. 78 FR 54461 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  1. 77 FR 39235 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  2. 77 FR 53193 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-31

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... CONTACT: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River...

  3. 76 FR 65706 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-24

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  4. 75 FR 57462 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-21

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. No. 92...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  5. 77 FR 60688 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  6. 77 FR 13104 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  7. 75 FR 82001 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act requires that... Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken, SC 29802; Phone:...

  8. 78 FR 26005 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-03

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  9. 78 FR 65979 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  10. 76 FR 55369 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  11. 76 FR 81487 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-28

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box...

  12. 78 FR 716 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-04

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463..., Office of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  13. 76 FR 11772 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  14. 75 FR 39007 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463...: Gerri Flemming, Office of External Affairs, Department of Energy, Savannah River Operations Office,...

  15. 75 FR 24684 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Savannah River Site AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal Advisory Committee Act (Pub. L. 92-463... of External Affairs, Department of Energy, Savannah River Operations Office, P.O. Box A, Aiken,...

  16. Chemoenzymatic bio-orthogonal chemistry for site-specific double modification of recombinant thrombomodulin.

    PubMed

    Jiang, Rui; Wang, Lin; Weingart, Jacob; Sun, Xue-Long

    2014-01-01

    Best of both worlds: A one-pot strategy for site-specific PEGylation through strain-promoted alkyne-azide cycloaddition (SPAAC) and fluorescent labeling through sortase A-mediated ligation (SML) of recombinant thrombomodulin without prior chemical modification and without diminishing the protein activity has been developed. PMID:24357004

  17. 75 FR 53280 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Pueblo Sur, Taos, New Mexico 87571. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern...

  18. 78 FR 23759 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-22

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Drive, Santa Fe, NM 87501. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  19. 78 FR 38305 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-26

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... 87544. ] FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New Mexico Citizens'...

  20. 77 FR 47047 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463... Road, Pojoaque, NM 87506. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  1. 76 FR 11773 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L. 92-463..., Santa Fe, New Mexico 87507. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New...

  2. 76 FR 11772 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens... Norte, Espanola, New Mexico 87532. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern...

  3. 76 FR 18540 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-04

    ... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens....m.-4 p.m. ADDRESSES: Holiday Inn Express and Suites, 60 Entrada Drive, Los Alamos, New Mexico...

  4. 77 FR 2282 - Environmental Management Site-Specific Advisory Board, Paducah

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on January 19, 2012, of the Environmental Management Site... being cancelled because the board will not have a quorum due to scheduling conflicts by members....

  5. CRISPR Outsourcing: Commissioning IHF for Site-Specific Integration of Foreign DNA at the CRISPR Array.

    PubMed

    Wei, Yunzhou; Terns, Michael P

    2016-06-16

    In this issue of Molecular Cell, Nuñez et al. (2016) report that site-specific integration of foreign DNA into CRISPR loci by the Cas1-Cas2 integrase complex is promoted by a host factor, IHF (integration host factor), that binds and bends CRISPR leader DNA. PMID:27315553

  6. 75 FR 20832 - Environmental Management Site-Specific Advisory Board, Nevada Test Site

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-21

    ...This notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of this meeting be announced in the Federal...

  7. 75 FR 82003 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION... Officer, Department of Energy Portsmouth/Paducah Project Office, Post Office Box 700, Piketon, Ohio...

  8. 75 FR 82004 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  9. 78 FR 53135 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of..., Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator, 232 Energy Way,...

  10. 75 FR 65310 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of..., Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S...

  11. 76 FR 5365 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  12. 77 FR 4027 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice of.... FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy Way, M/S 505, North...

  13. Site-specific mouth rinsing can improve oral odor by altering bacterial counts

    PubMed Central

    Alqumber, Mohammed A.; Arafa, Khaled A.

    2014-01-01

    Objectives: To determine whether site-specific mouth rinsing with oral disinfectants can improve oral odor beyond the traditional panoral mouth disinfection with mouth rinses by targeting specifically oral malodor implicated anaerobic bacteria Methods: Twenty healthy fasting subjects volunteered for a blinded prospective, descriptive correlational crossover cross-section clinical trial conducted during the month of Ramadan between July and August 2013 in Albaha province in Saudi Arabia involving the application of Listerine® Cool Mint® mouth rinse by either the traditional panoral rinsing method, or a site-specific disinfection method targeting the subgingival and supragingival plaque and the posterior third of the tongue dorsum, while avoiding the remaining locations within the oral cavity. The viable anaerobic and aerobic bacterial counts, volatile sulfur compounds (VSCs) levels, organoleptic assessment of oral odor, and the tongue-coating index were compared at baseline, one, 5, and 9 hours after the treatment. Results: The site-specific disinfection method reduced the VSCs and anaerobic bacterial loads while keeping the aerobic bacterial numbers higher than the traditional panoral rinsing method. Conclusion: Site-specific disinfection can more effectively maintain a healthy oral cavity by predominantly disinfecting the niches of anaerobic bacteria within the oral cavity. PMID:25399224

  14. Using site-specific soil samples as a substitution for improved hydrological and nonpoint source predictions.

    PubMed

    Chen, Lei; Wang, Guobo; Zhong, Yucen; Zhao, Xin; Shen, Zhenyao

    2016-08-01

    Soil databases are one of the most important inputs for watershed models, and the quality of soil properties affects how well a model performs. The objectives of this study were to (1) quantify the sensitivity of model outputs to soil properties and to (2) use site-specific soil properties as a substitution for more accurate hydrological and nonpoint source (H/NPS) predictions. Soil samples were collected from a typical mountainous watershed in China, and the impacts of soil sample parameters on H/NPS predictions were quantified using the Soil and Water Assessment Tool (SWAT). The most sensitive parameters related to predicting flow, sediment, and total phosphorus (TP) mainly were the soil hydrological, the channel erosion processes, and the initial soil chemical environment, respectively. When the site-specific soil properties were used, the uncertainties (coefficient of variation) related to predicting the hydrology, sediment and TP decreased by 75∼80 %, 75∼84 %, and 46∼61 %, respectively. Based on changes in the Nash-Sutcliff coefficient, the model performance improved by 4.9 and 19.45 % for the hydrological and sediment model, accordingly. However, site-specific soil properties did not contribute to better TP predictions because of the high spatial variability of the soil P concentrations across the large watershed. Thus, although site-specific soil samples can be used to obtain more accurate H/NPS predictions, more sampling sites are required to apply this method in large watersheds.

  15. 75 FR 3455 - Environmental Management Site-Specific Advisory Board, Oak Ridge Reservation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-21

    ...This notice announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Oak Ridge Reservation. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of this meeting be announced in the Federal...

  16. 77 FR 66962 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-08

    ... Environmental Impact Statement Briefing/Update 3. Nye County Drilling Presentation 4. Industrial Sites-Closing... above. Written statements may be filed with the Board either before or after the meeting. Individuals... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  17. 76 FR 21878 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-19

    .... Greater-Than-Class-C Draft Environmental Impact Statement (EIS) Committee Update. 3. Site-Wide EIS Update... Rupp at least seven days in advance of the meeting at the phone number listed above. Written statements... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  18. 76 FR 29229 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-20

    ... Agenda: 1. Recommendation Development: Greater-Than-Class C Draft Environmental Impact Statement (EIS) 2... number listed above. Written statements may be filed with the Board either before or after the meeting... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  19. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Nevada

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... Impact Statement Public Participation: The EM SSAB, Nevada, welcomes the attendance of the public at its... least seven days in advance of the meeting at the phone number listed above. Written statements may be... Environmental Management Site-Specific Advisory Board, Nevada AGENCY: Department of Energy. ACTION: Notice...

  20. 76 FR 57981 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-19

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  1. 77 FR 29997 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  2. Appreciating "Thirdspace": An Alternative Way of Viewing and Valuing Site-Specific Dance Performance

    ERIC Educational Resources Information Center

    Munjee, Tara

    2014-01-01

    Site-specific dance performance involves the presentation of choreography in connection with a site. The context of the site combined with a viewer's personal history, beliefs, and identity impact the reading and appreciation of the performance. Although both stage and site dance performance valuing elicit multiple interpretations of artistic…

  3. Summary of some feasibility studies for site-specific solar industrial process heat

    SciTech Connect

    1982-01-01

    Some feasibility studies for several different site specific solar industrial process heat applications are summarized. The followng applications are examined. Leather Tanning; Concrete Production: Lumber and Paper Processing; Milk Processing; Molding, Curing or Drying; Automobile Manufacture; and Food Processing and Preparation. For each application, site and process data, system design, and performance and cost estimates are summarized.

  4. 76 FR 36101 - Environmental Management Site-Specific Advisory Board, Northern New Mexico; Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal Advisory Committee Act (Pub. L... Drive, Los Alamos, New Mexico. FOR FURTHER INFORMATION CONTACT: Menice Santistevan, Northern New Mexico... Board: The purpose of the Board is to make recommendations to DOE-EM and site management in the areas...

  5. Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 1: Cysteine Residues and Glycans.

    PubMed

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M

    2016-02-01

    Due to their remarkable selectivity and specificity for cancer biomarkers, immunoconjugates have emerged as extremely promising vectors for the delivery of diagnostic radioisotopes and fluorophores to malignant tissues. Paradoxically, however, these tools for precision medicine are synthesized in a remarkably imprecise way. Indeed, the vast majority of immunoconjugates are created via the random conjugation of bifunctional probes (e.g., DOTA-NCS) to amino acids within the antibody (e.g., lysines). Yet antibodies have multiple copies of these residues throughout their macromolecular structure, making control over the location of the conjugation reaction impossible. This lack of site specificity can lead to the formation of poorly defined, heterogeneous immunoconjugates with suboptimal in vivo behavior. Over the past decade, interest in the synthesis and development of site-specifically labeled immunoconjugates--both antibody-drug conjugates as well as constructs for in vivo imaging--has increased dramatically, and a number of reports have suggested that these better defined, more homogeneous constructs exhibit improved performance in vivo compared to their randomly modified cousins. In this two-part review, we seek to provide an overview of the various methods that have been developed to create site-specifically modified immunoconjugates for positron emission tomography, single photon emission computed tomography, and fluorescence imaging. We will begin with an introduction to the structure of antibodies and antibody fragments. This is followed by the core of the work: sections detailing the four different approaches to site-specific modification strategies based on cysteine residues, glycans, peptide tags, and unnatural amino acids. These discussions will be divided into two installments: cysteine residues and glycans will be detailed in Part 1 of the review, while peptide tags and unnatural amino acids will be addressed in Part 2. Ultimately, we sincerely hope

  6. Fluid-rock interactions in CO2-saturated, granite-hosted geothermal systems: Implications for natural and engineered systems from geochemical experiments and models

    NASA Astrophysics Data System (ADS)

    Lo Ré, Caroline; Kaszuba, John P.; Moore, Joseph N.; McPherson, Brian J.

    2014-09-01

    Hydrothermal experiments were conducted and geochemical models constructed to evaluate the geochemical and mineralogical response of fractured granite and granite + epidote in contact with thermal water, with and without supercritical CO2, at 250 °C and 25-45 MPa. Illite ± smectite ± zeolite(?) precipitate as secondary minerals at the expense of K-feldspar, oligoclase, and epidote. Illite precipitates in experiments reacting granite and granite + epidote with water; metastable smectite forms in the experiments injected with supercritical CO2. Waters are supersaturated with respect to quartz and saturated with respect to chalcedony in CO2-charged experiments, but neither mineral formed. Carbonate formation is predicted for experiments injected with supercritical CO2, but carbonate only formed during cooling and degassing of the granite + epidote + CO2 experiment. Experimental results provide insight into the buffering capacity of granites as well as the drivers of clay formation. Metastable smectite in the experiments is attributed to high water-rock ratios, high silica activities, and high CO2 and magnesium-iron concentrations. Smectite precipitation in supercritical CO2-bearing geothermal systems may affect reservoir permeability. Silicate formation may create or thicken caps within or on the edges of geothermal reservoirs. Carbonate formation, as desired for carbon sequestration projects coinciding with geothermal systems, may require extended periods of time; cooling and degassing of CO2-saturated waters leads to carbonate precipitation, potentially plugging near-surface production pathways.

  7. Site-specific fragmentation caused by core-level photoionization: Effect of chemisorption

    NASA Astrophysics Data System (ADS)

    Nagaoka, Shin-ichi; Mase, Kazuhiko; Nakamura, Arinobu; Nagao, Masashi; Yoshinobu, Jun; Tanaka, Shin-ichiro

    2002-08-01

    We used the energy-selected-photoelectron photoion coincidence (ESPEPICO) method to study site-specific fragmentation caused by C:1s photoionization of 1,1,1-trifluoro-2-propanol-d1 [CF3)CD(OHCH3, TFIP-d1] on a Si(100) surface. High-resolution electron energy loss spectroscopy showed that TFIP-d1 is dissociatively chemisorbed like (CF3)(CH3))CDO-Si(100, and different chemical shifts at the three carbon sites were observed by photoelectron spectroscopy. The site-specific fragmentation evident in the ESPEPICO spectra of the sub-monolayer at room temperature indicates that the TFIP-d1 there has an O-Si bond oriented in the trans position with respect to the C-CF3 bond. Here we discuss the fragmentation processes in light of the results obtained with the ESPEPICO method and the Auger-electron photoion coincidence method.

  8. Recent Developments in the Site-Specific Immobilization of Proteins onto Solid Supports

    SciTech Connect

    Camarero, J A

    2007-02-21

    Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.

  9. Site-specific one-pot dual labeling of DNA by orthogonal cycloaddition chemistry.

    PubMed

    Schoch, Juliane; Staudt, Markus; Samanta, Ayan; Wiessler, Manfred; Jäschke, Andres

    2012-07-18

    Bioorthogonal reactions are of high interest in biosciences as they allow the introduction of fluorescent dyes, affinity tags, or other unnatural moieties into biomolecules. The site-specific attachment of two or more different labels is particularly demanding and typically requires laborious multistep syntheses. Here, we report that the most popular cycloaddition in bioconjugation, the copper-catalyzed azide-alkyne click reaction (CuAAC), is fully orthogonal to the inverse electron-demand Diels-Alder reaction (DAinv). We demonstrate that both bioorthogonal reactions can be conducted concurrently in a one-pot reaction by just mixing all components. Orthogonality has been established even for highly reactive trans-cyclooctene-based dienophiles (with rate constants up to 380 000 M(-1) s(-1)). These properties allow for the convenient site-specific one-step preparation of oligonucleotide FRET probes and related reporters needed in cellular biology and biophysical chemistry.

  10. Generation of site-specific mutations in the rat genome via CRISPR/Cas9.

    PubMed

    Guan, Yuting; Shao, Yanjiao; Li, Dali; Liu, Mingyao

    2014-01-01

    The laboratory rat is a valuable model organism for basic biological studies and drug development. However, due to the lack of genetic tools for site-specific genetic modification in the rat genome, more and more researchers chose the mouse as their favored mammalian models due to the sophisticated embryonic stem cell-based gene-targeting techniques available. Recently, engineered nucleases, including zinc finger nucleases, transcription activator-like effector nucleases, and CRISPR/Cas9 systems, have been adapted to generate knockout rats efficiently. The purpose of this section is to provide detailed procedures for the generation of site-specific mutations in the rat genome through injection of Cas9/sgRNA into one-cell embryos.

  11. A dermal HOX transcriptional program regulates site-specific epidermal fate

    PubMed Central

    Rinn, John L.; Wang, Jordon K.; Allen, Nancy; Brugmann, Samantha A.; Mikels, Amanda J.; Liu, Helen; Ridky, Todd W.; Stadler, H. Scott; Nusse, Roel; Helms, Jill A.; Chang, Howard Y.

    2008-01-01

    Reciprocal epithelial–mesenchymal interactions shape site-specific development of skin. Here we show that site-specific HOX expression in fibroblasts is cell-autonomous and epigenetically maintained. The distal-specific gene HOXA13 is continually required to maintain the distal-specific transcriptional program in adult fibroblasts, including expression of WNT5A, a morphogen required for distal development. The ability of distal fibroblasts to induce epidermal keratin 9, a distal-specific gene, is abrogated by depletion of HOXA13, but rescued by addition of WNT5A. Thus, maintenance of appropriate HOX transcriptional program in adult fibroblasts may serve as a source of positional memory to differentially pattern the epithelia during homeostasis and regeneration. PMID:18245445

  12. Evaluation of a site-specific criterion using outdoor experimental streams

    SciTech Connect

    Hedtke, S.F.; Arthur, J.W.

    1985-02-01

    An overview of a study to evaluate a site-specific water quality criteria for pentachlorophenol (PCP) in outdoor experimental streams is presented. The site-specific criterion was calculated from acute toxicity results for eight resident species and the relationship between acute and chronic toxicity of PCP. The PCP concentration expected to protect aquatic life (30-day average criterion concentration) was less than or equal to 48 micrograms/l. Outdoor experimental streams were subsequently dosed continuously for 84 days at 48, 144, and 432 micrograms PCP/l. Measurements of the biological structure and ecosystem processes within the exposure streams were compared to a control system. Effects on snails were found only at 432 micrograms/l, but effects on fish, periphyton, and system metabolism were found at 432, 144, and 48 micrograms/l. The small differences between the criterion-dosed stream (48 micrograms/l) and the control stream may have been caused by PCP or interstream variation.

  13. Site-specific DNA-affinity chromatography of the lac repressor.

    PubMed Central

    Herrick, G

    1980-01-01

    To test the feasibility of site-specific DNA-affinity chromatography, E. coli lac repressor was bound to an operator-containing DNA column, and in parallel to a non-operator DNA column. Salt gradient elution shows: 1) elution from non-operator DNA was near 250mM KCl or NaCl; interpretation of this result suggests the usefulness of the procedure for studying salt-dependence of DNA-protein affinities; 2) elution from operator-containing DNA was delayed (average elution = 1000mM salt), demonstrating a feasibility of site-specific DNA-affinity chromatography, if one provides a sufficiently favorable ratio of specific to non-specific DNA binding sites; 3) repressor eluted from operator-containing DNA over a very broad salt range, which may represent chromatography-generated repressor heterogeneity. PMID:7001362

  14. Mapping site-specific endonuclease binding to DNA by direct imaging with AFM

    SciTech Connect

    Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J.; Modrich, P.; Isfort, R.J.

    1995-12-31

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  15. Recent Advances in Site Specific Conjugations of Antibody Drug Conjugates (ADCs).

    PubMed

    Gao, Wenlong; Zhang, Jingxin; Xiang, Jun; Zhang, Lei; Wu, Chengbin; Dhal, Pradeep K; Chen, Bo

    2016-01-01

    Antibody-drug conjugates (ADCs) take the advantage of antigen specificity of monoclonal antibodies to deliver highly potent cytotoxic drugs selectively to antigen-expressing tumor cells. The recent approval of Adcetris™ and Kadcyla™ as well as emerging data from numerous ongoing clinical trials underscore the role of ADCs as a new therapeutic option for cancer patients. However, conventional conjugation methods generally result in a heterogeneous mixture of ADCs, which can result in significant therapeutic liabilities and can lead to complicated manufacturing processes. The increased understanding from the clinical investigation of current ADCs and site-specific bioconjugation technologies has enabled scientists to accelerate the discovery and development of the next generation ADCs with defined and homogeneous composition. The present manuscript reviews the recent advances and trends in the research and development of novel ADCs obtained by site-specific conjugation method. PMID:27174056

  16. Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy (AFM)

    NASA Astrophysics Data System (ADS)

    Allison, David P.; Thundat, Thomas G.; Modrich, P.; Isfort, R. J.; Doktycz, Mitchel J.; Kerper, P. S.; Warmack, R. J.

    1995-04-01

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 104, we demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS+) or two (pMP32) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in our preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  17. Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination

    PubMed Central

    Zhang, Lin; Zhao, Guoping; Ding, Xiaoming

    2011-01-01

    We describe a site-specific recombination-based tandem assembly (SSRTA) method for reconstruction of biological parts in synthetic biology. The system was catalyzed by Streptomyces phage φBT1 integrase, which belongs to the large serine recombinase subfamily. This one-step approach was efficient and accurate, and able to join multiple DNA molecules in vitro in a defined order. Thus, it could have applications in constructing metabolic pathways and genetic networks. PMID:22355658

  18. Use of a water effect ratio to develop an estuarine copper site-specific standard

    SciTech Connect

    Brosnan, T.

    1995-12-31

    Development of a copper site-specific standard in New York Harbor involved several steps: (1) EPA`s Indicator Species Procedure was used to develop a Water Effect Ratio (WER), which produces a biologically-based adjustment to the existing criteria. Samples from seven stations were collected during high and low river-flow conditions in 1992--93. Toxicity testing included embryo-larval development tests on two bivalves, an urchin, and a shrimp. A red algae was used for a sexual reproduction test. This testing yielded WER`s of 1.33 2.1 7, with an average of 1.49. When multiplied by the existing EPA criteria of 2.9 ug/L (total recoverable), this yielded a preliminary acute site specific standard of 4.3 ug/L (total recoverable); (2) Further analysis of these data, combined with a literature search of similar data, resulted in a recalculation of the original national acute criteria value, from 2.9 ug/L (total recoverable) to 5.3 ug/L (dissolved). Multiplying the WER by the recalculated national criteria yielded a final acute site, specific criteria of 7.9 ug/L (dissolved); (3) Finally, EPA`s original criteria indicated that achieving the acute criterion would be protective of chronic effects (i.e. the acute:chronic ratio (ACR) was 2). However, EPA, recently decided that an ACR of 2 was no longer valid, and decided to use the freshwater ACR of 2.8. This resulted in a recalculation of the national chronic criteria to 3.75 ug/L (dissolved). Combined with the WER of 1.49, this yielded a final chronic site specific standard of 5.6 ug/L. The new standard eliminated ambient violations in most of the harbor, and removed the need for wasteload allocations at 12 of NYC`s 14 sewage treatment plants.

  19. Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.

    PubMed

    Nishizawa, Tomoyasu; Miura, Takamasa; Harada, Chizuko; Guo, Yong; Narisawa, Kazuhiko; Ohta, Hiroyuki; Takahashi, Hideo; Shirai, Makoto

    2016-01-01

    Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. PMID:27563047

  20. Site-specific functionalization of proteins and their applications to therapeutic antibodies

    PubMed Central

    van Vught, Remko; Pieters, Roland J; Breukink, Eefjan

    2014-01-01

    Protein modifications are often required to study structure and function relationships. Instead of the random labeling of lysine residues, methods have been developed to (sequence) specific label proteins. Next to chemical modifications, tools to integrate new chemical groups for bioorthogonal reactions have been applied. Alternatively, proteins can also be selectively modified by enzymes. Herein we review the methods available for site-specific modification of proteins and their applications for therapeutic antibodies. PMID:24757499

  1. Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4

    PubMed Central

    Miura, Takamasa; Harada, Chizuko; Guo, Yong; Narisawa, Kazuhiko; Ohta, Hiroyuki; Takahashi, Hideo; Shirai, Makoto

    2016-01-01

    Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. PMID:27563047

  2. DAFS study of site-specific local structure of Mn in manganese ferrite films.

    SciTech Connect

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V. G.; X-Ray Science Division; Inst. of Metal Physics; Northeastern Univ.; Nankai Univ.

    2006-01-01

    Manganese ferrite (MnFe{sub 2}O{sub 4}) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency

  3. Determination of a site-specific reference dose for methylmercury for fish-eating populations.

    PubMed

    Shipp, A M; Gentry, P R; Lawrence, G; Van Landingham, C; Covington, T; Clewell, H J; Gribben, K; Crump, K

    2000-11-01

    Environmental risk-management decisions in the U.S. involving potential exposures to methylmercury currently use a reference dose (RfD) developed by the U.S. Environmental Protection Agency (USEPA). This RfD is based on retrospective studies of an acute poisoning incident in Iraq in which grain contaminated with a methylmercury fungicide was inadvertently used in the baking of bread. The exposures, which were relatively high but lasted only a few months, were associated with neurological effects in both adults (primarily paresthesia) and infants (late walking, late talking, etc.). It is generally believed that the developing fetus represents a particularly sensitive subpopulation for the neurological effects of methylmercury. The USEPA derived an RfD of 0.1 microg/kg/day based on benchmark dose (BMD) modeling of the combined neurological endpoints reported for children exposed in utero. This RfD included an uncertainty factor of 10 to consider human pharmacokinetic variability and database limitations (lack of data on multigeneration effects or possible long-term sequelae of perinatal exposure). Alcoa signed an Administrative Order of Consent for the conduct of a remedial investigation/feasibility study (RI/FS) at their Point Comfort Operations and the adjacent Lavaca Bay in Texas to address the effects of historical discharges of mercury-containing wastewater. In cooperation with the Texas Natural Resource Conservation Commission and USEPA Region VI, Alcoa conducted a baseline risk assessment to assess potential risk to human health and the environment. As a part of this assessment. Alcoa pursued the development of a site-specific RfD for methylmercury to specifically address the potential human health effects associated with the ingestion of contaminated finfish and shellfish from Lavaca Bay. Application of the published USEPA RfD to this site is problematic; while the study underlying the RfD represented acute exposure to relatively high concentrations of

  4. Determination of a site-specific reference dose for methylmercury for fish-eating populations.

    PubMed

    Shipp, A M; Gentry, P R; Lawrence, G; Van Landingham, C; Covington, T; Clewell, H J; Gribben, K; Crump, K

    2000-11-01

    Environmental risk-management decisions in the U.S. involving potential exposures to methylmercury currently use a reference dose (RfD) developed by the U.S. Environmental Protection Agency (USEPA). This RfD is based on retrospective studies of an acute poisoning incident in Iraq in which grain contaminated with a methylmercury fungicide was inadvertently used in the baking of bread. The exposures, which were relatively high but lasted only a few months, were associated with neurological effects in both adults (primarily paresthesia) and infants (late walking, late talking, etc.). It is generally believed that the developing fetus represents a particularly sensitive subpopulation for the neurological effects of methylmercury. The USEPA derived an RfD of 0.1 microg/kg/day based on benchmark dose (BMD) modeling of the combined neurological endpoints reported for children exposed in utero. This RfD included an uncertainty factor of 10 to consider human pharmacokinetic variability and database limitations (lack of data on multigeneration effects or possible long-term sequelae of perinatal exposure). Alcoa signed an Administrative Order of Consent for the conduct of a remedial investigation/feasibility study (RI/FS) at their Point Comfort Operations and the adjacent Lavaca Bay in Texas to address the effects of historical discharges of mercury-containing wastewater. In cooperation with the Texas Natural Resource Conservation Commission and USEPA Region VI, Alcoa conducted a baseline risk assessment to assess potential risk to human health and the environment. As a part of this assessment. Alcoa pursued the development of a site-specific RfD for methylmercury to specifically address the potential human health effects associated with the ingestion of contaminated finfish and shellfish from Lavaca Bay. Application of the published USEPA RfD to this site is problematic; while the study underlying the RfD represented acute exposure to relatively high concentrations of

  5. Biologically Derived Nanoparticle Arrays via a Site-Specific Reconstitution of Ferritin and their Electrochemistry

    NASA Technical Reports Server (NTRS)

    Kim, Jae-Woo; Choi, Sang H.; Lillehei, Peter T.; King, Glen C.; Elliott, James R.; Chu, Sang-Hyon; Park, Yeonjoon; Watt, Gerald D.

    2004-01-01

    Nanoparticle arrays biologically derived from an electrochemically-controlled site-specific biomineralization were fabricated on a gold substrate through the immobilization process of biomolecules. The work reported herein includes the immobilization of ferritin with various surface modifications, the electrochemical biomineralization of ferritins with different inorganic cores, the fabrication of self-assembled arrays with the immobilized ferritin, and the electrochemical characterization of various core materials. Protein immobilization on the substrate is achieved by anchoring ferritins with dithiobis-N-succinimidyl propionate (DTSP). A reconstitution process of electrochemical site-specific biomineralization with a protein cage loads ferritins with different core materials such as Pt, Co, Mn, and Ni. The ferritin acts as a nano-scale template, a biocompatible cage, and a separator between the nanoparticles. The nano-sized metalcored ferritins on a gold substrate displayed a good electrochemical activity for the electron transport and storage, which is suitable for bioelectronics applications such as biofuel cell, bionanobattery, biosensors, etc. Keywords: Ferritin, immobilization, site-specific reconstitution, biomineralization, and bioelectronics

  6. Site specific metals criteria as determined by Water Effect Ratio studies

    SciTech Connect

    Castle, C.J.; Neserke, G.

    1994-12-31

    Water Effect Ratios (WER) are being used to implement site-specific water quality criteria to address the variability of physical and chemical characteristics of site water and metals that may influence toxicity. A case in point, Coors Brewing Company in Golden, Colorado, has been granted site-specific criteria for the discharge of copper and zinc based on results of WER studies. Acute bioassays were conducted to determine seasonal WER values for copper, zinc and silver. The tests exposed Ceriodaphnia dubia and Pimephales promelas to graduated levels of metals in Clear Creek site water (below discharge mixing zone), reconstituted laboratory water and effluent. Final WER values, calculated by the ratio of LC50`s determined in site water and laboratory water, were multiplied by the standard metals criteria to develop the site specific values incorporated into the Coors Brewing Company permit to discharge. It is suggested that the high LC50 values for metals in site water is a factor of the effluent`s binding capacity that may reduce the bioavailability of metals in site water.

  7. Site-specific parameter values for the Nuclear Regulatory Commission's food pathway dose model.

    PubMed

    Hamby, D M

    1992-02-01

    Routine operations at the Savannah River Site (SRS) in Western South Carolina result in radionuclide releases to the atmosphere and to the Savannah River. The resulting radiation doses to the off-site maximum individual and the off-site population within 80 km of the SRS are estimated on a yearly basis. These estimates are currently generated using dose models prescribed for the commercial nuclear power industry by the Nuclear Regulatory Commission (NRC). The NRC provides default values for dose-model parameters for facilities without resources to develop site-specific values. A survey of land- and water-use characteristics for the Savannah River area has been conducted to determine site-specific values for water recreation, consumption, and agricultural parameters used in the NRC Regulatory Guide 1.109 (1977) dosimetric models. These site parameters include local characteristics of meat, milk, and vegetable production; recreational and commercial activities on the Savannah River; and meat, milk, vegetable, and seafood consumption rates. This paper describes how parameter data were obtained at the Savannah River Site and the impacts of such data on off-site dose. Dose estimates using site-specific parameter values are compared to estimates using the NRC default values. PMID:1730555

  8. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction

    PubMed Central

    Torres-Kolbus, Jessica; Chou, Chungjung; Deiters, Alexander; Chin, Jason W.

    2013-01-01

    The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNACUA pair in Escherichia coli and mammalian cells. We developed a series of tetrazine-based probes that exhibit `turn-on' fluorescence on their rapid reaction with norbornenes. We demonstrate that the labelling of an encoded norbornene is specific with respect to the entire soluble E. coli proteome and thousands of times faster than established encodable bioorthogonal reactions. We show explicitly the advantages of this approach over state-of-the-art bioorthogonal reactions for protein labelling in vitro and on mammalian cells, and demonstrate the rapid bioorthogonal site-specific labelling of a protein on the mammalian cell surface. PMID:22437715

  9. Comparisons of CAP88PC version 2.0 default parameters to site specific inputs

    SciTech Connect

    Lehto, M. A.; Courtney, J. C.; Charter, N.; Egan, T.

    2000-03-02

    The effects of varying the input for the CAP88PC Version 2.0 program on the total effective dose equivalents (TEDEs) were determined for hypothetical releases from the Hot Fuel Examination Facility (HFEF) located at the Argonne National Laboratory site on the Idaho National Engineering and Environmental Laboratory (INEEL). Values for site specific meteorological conditions and agricultural production parameters were determined for the 80 km radius surrounding the HFEF. Four nuclides, {sup 3}H, {sup 85}Kr, {sup 129}I, and {sup 137}Cs (with its short lived progeny, {sup 137m}Ba) were selected for this study; these are the radioactive materials most likely to be released from HFEF under normal or abnormal operating conditions. Use of site specific meteorological parameters of annual precipitation, average temperature, and the height of the inversion layer decreased the TEDE from {sup 137}Cs-{sup 137m}Ba up to 36%; reductions for other nuclides were less than 3%. Use of the site specific agricultural parameters reduced TEDE values between 7% and 49%, depending on the nuclide. Reductions are associated with decreased committed effective dose equivalents (CEDEs) from the ingestion pathway. This is not surprising since the HFEF is located well within the INEEL exclusion area, and the surrounding area closest to the release point is a high desert with limited agricultural diversity. Livestock and milk production are important in some counties at distances greater than 30 km from the HFEF.

  10. Confident assignment of site-specific glycosylation in complex glycoproteins in a single step.

    PubMed

    Khatri, Kshitij; Staples, Gregory O; Leymarie, Nancy; Leon, Deborah R; Turiák, Lilla; Huang, Yu; Yip, Shun; Hu, Han; Heckendorf, Christian F; Zaia, Joseph

    2014-10-01

    A glycoprotein may contain several sites of glycosylation, each of which is heterogeneous. As a consequence of glycoform diversity and signal suppression from nonglycosylated peptides that ionize more efficiently, typical reversed-phase LC-MS and bottom-up proteomics database searching workflows do not perform well for identification of site-specific glycosylation for complex glycoproteins. We present an LC-MS system for enrichment, separation, and analysis of glycopeptides from complex glycoproteins (>4 N-glycosylation sequons) in a single step. This system uses an online HILIC enrichment trap prior to reversed-phase C18-MS analysis. We demonstrated the effectiveness of the system using a set of glycoproteins including human transferrin (2 sequons), human alpha-1-acid glycoprotein (5 sequons), and influenza A virus hemagglutinin (9 sequons). The online enrichment renders glycopeptides the most abundant ions detected, thereby facilitating the generation of high-quality data-dependent tandem mass spectra. The tandem mass spectra exhibited product ions from both glycan and peptide backbone dissociation for a majority of the glycopeptides tested using collisionally activated dissociation that served to confidently assign site-specific glycosylation. We demonstrated the value of our system to define site-specific glycosylation using a hemagglutinin containing 9 N-glycosylation sequons from a single HILIC-C18-MS acquisition.

  11. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene- Deoxyadenosine Lesions

    PubMed Central

    Wickramaratne, Susith; Seiler, Christopher L.

    2016-01-01

    Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1, N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen, 1,3-butadiene (BD). The resulting oligomers containing site specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis. PMID:26344227

  12. [DEVELOPMENT OF MARKER-FREE TRANSFORMANTS BY SITE-SPECIFIC RECOMBINASES].

    PubMed

    Sekan, A S; Isaenkov, S V; Blume, Ya B

    2015-01-01

    To produce transgenic plants in current biotechnology selectable marker genes are used that lead to the selectivity.of transformants from non-transformed organisms. However, after the transgenic event has been occurred, the presence of these genes in transformed genome in general is uselless. Moreover, the continued presence of this kind of genes in transgenic plants with their further commercialization may raise certain public concern. Therefore, various techniques have been developed in recent years to obtain marker free transgenic plants. In the present review the main strategies for removal of selective marker DNA sequences that are used in genetic engineering are described. The most popular among them is site-specific recombination technology. The particular attention is paid to site-specific recombinase system Cre/loxP. The using of a new approach with site-specific recombinase system Cre/loxP under the control of 35S promoter to generate marker-free genetically modified plants is described. PMID:26841495

  13. Site-specific unfolding thermodynamics of a helix-turn-helix protein.

    PubMed

    Amunson, Krista E; Ackels, Loren; Kubelka, Jan

    2008-07-01

    The thermal unfolding of a 40-residue helix-turn-helix subdomain of the P22 viral coat protein was investigated using circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) with site-specific 13C isotopic labeling. Helix-turn-helix is the simplest alpha-helical structural motif that combines both secondary and tertiary structural elements. The CD of individual helical fragments reveals that the P22 subdomain is stabilized by tertiary interhelical interactions. Overall the temperature-dependent CD and FTIR data can be described by a three-state process with a partially folded intermediate. However, the analysis of the site-specific 13C IR signals reveals distinct unfolding thermodynamics for each of the labeled sites. The thermodynamic parameters of the thermal unfolding of each of the labeled segments were obtained using singular value decomposition in combination with target transformation and global fitting. The P22 subdomain unfolds from the N-terminus toward the helical segments near the turn. Our results show that as few as two 13C labeled residues can be detected in a 40 residue protein and provide local, site-specific structural information about protein unfolding, which is not resolved by standard, nonsite-specific spectroscopic probes.

  14. Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes.

    PubMed

    Govindan, Ganesan; Ramalingam, Sivaprakash

    2016-11-01

    Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc. PMID:26945523

  15. Site-specific immobilization of protein layers on gold surfaces via orthogonal sortases.

    PubMed

    Raeeszadeh-Sarmazdeh, Maryam; Parthasarathy, Ranganath; Boder, Eric T

    2015-04-01

    We report a site-specific, sortase-mediated ligation to immobilize proteins layer-by-layer on a gold surface. Recombinant fluorescent proteins with a Sortase A recognition tag at the C-terminus were immobilized on peptide-modified gold surfaces. We used two sortases with different substrate specificities (Streptococcus pyogenes Sortase A and Staphylococcus aureus Sortase A) to immobilize layers of GFP and mCherry site-specifically on the gold surface. Surfaces were characterized using fluorescence and atomic force microscopy after immobilizing each layer of protein. Fluorescent micrographs showed that both protein immobilization on the modified gold surface and protein oligomerization are sortase-dependent. AFM images showed that either homogenous protein monolayers or layers of protein oligomers can be generated using appropriately tagged substrate proteins. Using Sortase A variants with orthogonal peptide substrate specificities, site-specific immobilization of appropriately tagged GFP onto a layer of immobilized mCherry was achieved without disruption of the underlying protein layer.

  16. Conversion of transuranic waste to low level waste by decontamination: a site specific update

    SciTech Connect

    Allen, R.P.; Hazelton, R.F.

    1985-09-01

    As a followup to an FY-1984 cost/benefit study, a program was conducted in FY-1985 to transfer to the relevant DOE sites the information and technology for the direct conversion of transuranic (TRU) waste to low-level waste (LLW) by decontamination. As part of this work, the economic evaluation of the various TRUW volume reduction and conversion options was updated and expanded to include site-specific factors. The results show, for the assumptions used, that size reduction, size reduction followed by decontamination, or in situ decontamination are cost effective compared with the no-processing option. The technology transfer activities included site presentations and discussions with operations and waste management personnel to identify application opportunities and site-specific considerations and constraints that could affect the implementation of TRU waste conversion principles. These discussions disclosed definite potential for the beneficial application of these principles at most of the sites, but also confirmed the existence of site-specific factors ranging from space limitations to LLW disposal restrictions that could preclude particular applications or diminish expected benefits. 8 refs., 2 figs., 4 tabs.

  17. The concept of electron activity and its relation to redox potentials in aqueous geochemical systems

    USGS Publications Warehouse

    Thorstenson, D.C.

    1984-01-01

    The definition of a formal thermodynamic activity of electrons in redox reactions appears in the literature of the 1920's. The concept of pe as -log (electron activity) was introduced by Jorgensen in 1945 and popularized in the geochemical literature by Sillen, who considered pe and pH as master variables in geochemical reactions. The physical significance of the concept of electron activity was challenged as early as 1928. However, only in the last two decades have sufficient thermodynamic data become available to examine this question quantitatively. The chemical nature of hydrated electrons differs greatly from that of hydrated protons, and thermodynamic data show that hydrated electrons cannot exist at physically meaningful equilibrium concentrations under natural conditions. This has important consequences for the understanding of redox processes in natural waters. These are: (1) the analogy between pe and pH as master variables is generally carried much further than is justified; (2) a thermodynamically meaningful value of redox potential cannot be assigned to disequilibrium systems; (3) the most useful approach to the study of redox characteristics is the analysis and study of multiple redox couples in the system; and (4) for all practical purposes, thermodynamically defined redox potentials do not exist (and thus cannot be measured) in natural waters. The overall implication for natural systems is that, in terms of redox reactions, each case must be considered on an individual and detailed basis. Field studies would appear to be a mandatory part of any site-specific study; conclusions regarding redox processes cannot be based solely on electrode measurements or thermodynamic stability calculations. (USGS)

  18. Site-specific DOTA/europium-labeling of recombinant human relaxin-3 for receptor-ligand interaction studies.

    PubMed

    Zhang, Wei-Jie; Luo, Xiao; Liu, Ya-Li; Shao, Xiao-Xia; Wade, John D; Bathgate, Ross A D; Guo, Zhan-Yun

    2012-08-01

    natural or designed ligands with these receptors. Using this site-specific labeling strategy, other functional probes, such as fluorescent dyes, biotin, or nanoparticles could also be introduced to the A-chain N-terminal of the recombinant human relaxin-3. Additionally, we improved the time-resolved fluorescence assay for the DOTA-bound europium ion which paves the way for the use of DOTA as a lanthanide chelator for protein and peptide labeling in future studies.

  19. Site-Specific Analyses for Demonstrating Compliance with 10 CFR 61 Performance Objectives - 12179

    SciTech Connect

    Grossman, C.J.; Esh, D.W.; Yadav, P.; Carrera, A.G.

    2012-07-01

    The U.S. Nuclear Regulatory Commission (NRC) is proposing to amend its regulations at 10 CFR Part 61 to require low-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance with the performance objectives in Subpart C. The amendments would require licensees to conduct site-specific analyses for protection of the public and inadvertent intruders as well as analyses for long-lived waste. The amendments would ensure protection of public health and safety, while providing flexibility to demonstrate compliance with the performance objectives, for current and potential future waste streams. NRC staff intends to submit proposed rule language and associated regulatory basis to the Commission for its approval in early 2012. The NRC staff also intends to develop associated guidance to accompany any proposed amendments. The guidance is intended to supplement existing low-level radioactive waste guidance on issues pertinent to conducting site-specific analyses to demonstrate compliance with the performance objectives. The guidance will facilitate implementation of the proposed amendments by licensees and assist competent regulatory authorities in reviewing the site-specific analyses. Specifically, the guidance provides staff recommendations on general considerations for the site-specific analyses, modeling issues for assessments to demonstrate compliance with the performance objectives including the performance assessment, intruder assessment, stability assessment, and analyses for long-lived waste. This paper describes the technical basis for changes to the rule language and the proposed guidance associated with implementation of the rule language. The NRC staff, per Commission direction, intends to propose amendments to 10 CFR Part 61 to require licensees to conduct site-specific analyses to demonstrate compliance with performance objectives for the protection of public health and the environment. The amendments would require a

  20. Composition of natural gas and crude oil produced from 10 wells in the Lower Silurian "Clinton" Sandstone, Trumbull County, Ohio: Chapter G.7 in Coal and petroleum resources in the Appalachian basin: distribution, geologic framework, and geochemical character

    USGS Publications Warehouse

    Burruss, Robert A.; Ryder, Robert T.; Ruppert, Leslie F.; Ryder, Robert T.

    2014-01-01

    Natural gases and associated crude oils in the “Clinton” sandstone, Medina Group sandstones, and equivalent Tuscarora Sandstone in the northern Appalachian basin are part of a regional, continuous-type or basin-centered accumulation. The origin of the hydrocarbon charge to regional continuoustype accumulations is poorly understood. We have analyzed the molecular and stable isotopic composition of gases and oils produced from 10 wells in the “Clinton” sandstone in Trumbull County, Ohio, in an initial attempt to identify the characteristics of the accumulated fluids. The analyses show that the fluids have remarkably uniform compositions that are similar to previously published analyses of oils (Cole and others, 1987) and gases (Laughrey and Baldasarre, 1998) in Early Silurian reservoirs elsewhere in Ohio; however, geochemical parameters in the oils and gases suggest that the fluids have experienced higher levels of thermal stress than the present-day burial conditions of the reservoir rocks. The crude oils have an unusual geochemical characteristic: they do not contain detectable levels of sterane and triterpane biomarkers. The origin of these absences is unknown.

  1. Direct site-specific glycoform identification and quantitative comparison of glycoprotein therapeutics: imiglucerase and velaglucerase alfa.

    PubMed

    Ye, Hongping; Hill, John; Gucinski, Ashley C; Boyne, Michael T; Buhse, Lucinda F

    2015-03-01

    Gaucher disease, the most common lysosomal metabolic disorder, can be treated with enzyme replacement therapy (ERT). Recombinant human glucocerebrosidase imiglucerase (Cerezyme(®)), produced in Chinese hamster ovary cells, has been used for ERT of Gaucher disease for 20 years. Another recombinant glucocerebrosidase velaglucerase alfa (VPRIV), expressed in a human fibroblast cell line, was approved by the US Food and Drug Administration in 2010. The amino acid sequence difference at residue 495 of these two products is well documented. The overall N-linked qualitative glycan composition of these two products has also been reported previously. Herein, employing our recently developed approach utilizing isobaric tandem mass tag (TMT) labeling and an LTQ Orbitrap XL electron transfer dissociation (ETD) hybrid mass spectrometer, the site-specific glycoforms of these products were identified with ETD and collision-induced dissociation (CID) spectra. The quantitative comparison of site-specific glycans was achieved utilizing higher-energy collisional dissociation (HCD) spectra with a NanoMate used as both a fraction collector and a sample introduction device. From the trypsin-digested mixture of these two products, over 90 glycopeptides were identified by accurate mass matching. In addition to those previously reported, additional glycopeptides were detected with moderate abundance. The relative amount of each glycoform at a specific glycosylation site was determined based on reporter signal intensities of the TMT labeling reagents. This is the first report of site-specific simultaneous qualitative and quantitative comparison of glycoforms for Cerezyme(®) and VPRIV. The results demonstrate that this method could be utilized for biosimilarity determination and counterfeit identification of glycoproteins. PMID:25501675

  2. Risks of all-cause and site-specific fractures among hospitalized patients with COPD

    PubMed Central

    Liao, Kuang-Ming; Liang, Fu-Wen; Li, Chung-Yi

    2016-01-01

    Abstract Patients with chronic obstructive pulmonary disease (COPD) have a high prevalence of osteoporosis. The clinical sequel of osteoporosis is fracture. Patients with COPD who experience a fracture also have increased morbidity and mortality. Currently, the types of all-cause and site-specific fracture among patients with COPD are unknown. Thus, we elucidated the all-cause and site-specific fractures among patients with COPD. A retrospective, population-based, cohort study was conducted utilizing the Taiwan Longitudinal Health Insurance Database. Patients with COPD were defined as those who were hospitalized with an International Classification of Diseases, Ninth Revision, Clinical Modification code of 490 to 492 or 496 between 2001 and 2011. The index date was set as the date of discharge. The study patients were followed from the index date to the date when they sought care for any type of fracture, date of death, date of health insurance policy termination, or the last day of 2013. The types of fracture analyzed in this study included vertebral, rib, humeral, radial and ulnar/wrist, pelvic, femoral, and tibial and fibular fractures. The cohort consisted of 11,312 patients with COPD. Among these patients, 1944 experienced fractures. The most common site-specific fractures were vertebral, femoral, rib, and forearm fractures (radius, ulna, and wrist) at 32.4%, 31%, 12%, and 11.8%, respectively. The adjusted hazard ratios of fracture were 1.71 [95% confidence interval (95% CI) = 1.56–1.87] for female patient with COPD and 1.50 (95% CI = 1.39–1.52) for patients with osteoporosis after covariate adjustment. Vertebral and hip fractures are common among patients with COPD, especially among males with COPD. Many comorbidities contribute to the high risk of fracture among patients with COPD. PMID:27749576

  3. Empirical modelling of site-specific errors in continuous GPS data

    NASA Astrophysics Data System (ADS)

    Moore, Michael; Watson, Christopher; King, Matt; McClusky, Simon; Tregoning, Paul

    2014-09-01

    Continuous global positioning system (GPS) stations propagate biases and spurious signals into the derived parameter time series when the measurements are subject to site-specific effects, such as multipath. This is a particular problem in the investigation of geophysical and atmospheric phenomena where signals may be small in magnitude. A methodology to remove these erroneous signals from long-term time series will significantly increase the usefulness of the derived time series. This work provides the theoretical basis for use of an empirical site model (ESM) derived from post-fit phase residuals to mitigate unmodelled site-specific errors. Additionally, we also investigate the effectiveness of applying an ESM to a regional GPS network and a short baseline solution. Under most observing scenarios, we show that the ESM approach is predicted to improve the precision and accuracy of the site coordinates. However, it is important to note that we found some scenarios where the ESM can introduce a bias. For instance, when the antenna is mounted close to the ground. In this scenario, for a short baseline, we observed the introduction of a 4-mm bias in height. Use of an ESM for the same short baseline with an uncalibrated radome substantially improves the results by removing a large bias of over 10 mm in height. Similarly, application of an ESM derived from historic data yields similar improvements. This demonstrates that the ESM can be a powerful tool when applied to appropriate site-specific configurations and could potentially be implemented in routine GPS analysis for a broad range of applications.

  4. Site Specific Synthesis and in-situ Immobilization of Fluorescent Silver Nanoclusters on DNA Nanoscaffolds Using Tollens Reaction

    SciTech Connect

    Pal, Suchetan; Varghese, R.; Deng, Z.; Zhao, Z.; Kumar, A.; Yan, Hao; Liu, Yan

    2011-04-06

    DNA strands with specific sequences and covalently attached sugar moieties were used for the site-specific incorporation of the sugar units on a DNA origami scaffold. This approach enabled the subsequent site-specific synthesis and in situ immobilization of fluorescent Ag clusters at predefined positions on the DNA nanoscaffold by treatment with the Tollens reagent.

  5. Development of Combined Site-Specific MESA and LEPA Methods on a Linear Move Sprinkler Irrigation System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A site-specific controller, hardware and software systems were developed with the capability to switch between either mid-elevation spray application (MESA) or low energy precision application (LEPA) methods. These systems were field tested and used to manage site-specific irrigations under a linear...

  6. The species- and site-specific acid-base properties of penicillamine and its homodisulfide

    NASA Astrophysics Data System (ADS)

    Mirzahosseini, Arash; Szilvay, András; Noszál, Béla

    2014-08-01

    Penicillamine, penicillamine disulfide and 4 related compounds were studied by 1H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 14 macroscopic and 28 microscopic protonation constants and the concomitant 7 interactivity parameters. The species- and site-specific basicities are interpreted by means of inductive and shielding effects through various intra- and intermolecular comparisons. The thiolate basicities determined this way are key parameters and exclusive means for the prediction of thiolate oxidizabilities and chelate forming properties in order to understand and influence chelation therapy and oxidative stress at the molecular level.

  7. Use of limited site-specific flood information in estimating flood peaks

    SciTech Connect

    Newton, D.W.; Herrin, J.C.; Roser, S.D.; Kibler, D.F.; Aron, G.; Wall, D.J.

    1984-07-01

    Long-term stream gage records are seldom available at locations where flood-frequency estimates are required. As a result, most estimates are made by transferring information from nearby locations where flood records exist. Occasionally estimates of large past floods (historic flood information) and/or less than 10 years of gage record (short-record flood information) are available at the site. Procedures are developed and evaluated to systematically combine this limited site-specific flood information and regional flow-frequency estimates at ungaged sites or gaged sites with less than 10 years of record to obtain a more accurate flood peak estimate. 29 references, 23 figures, 31 tables.

  8. Environmental restoration and waste management Site-Specific Plan for the Oak Ridge Reservation. FY 1993

    SciTech Connect

    Not Available

    1993-01-15

    The United States Department of Energy (DOE) is committed to achieving and maintaining environmental regulatory compliance while responding to public concerns and emphasizing waste minimization. DOE publishes the Environmental Restoration and Waste Management Five-Year Plan (FYP) annually to document its progress towards these goals. The purpose of this Site-Specific Plan (SSP) is to describe the activities undertaken to implement the FYP goals at the DOE Oak Ridge Field Office (DOE/OR) installations and programs specifically for the Oak Ridge Reservation (ORR) and surrounding areas. This SSP addresses activities and goals to be accomplished during FY93 even through the FYP focuses on FY94.

  9. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions.

    PubMed

    Walkiewicz, Katarzyna W; Girault, Jean-Antoine; Arold, Stefan T

    2015-10-01

    The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein 'nanomachines' to become activated in a site-specific manner.

  10. Site Specific Advisory Board initiative, evaluation survey results supplementary appendix: Summary of individual site results

    SciTech Connect

    1996-08-01

    This Appendix presents results of the Site-Specific Advisory Board (SSAB) Initiative for each of the 11 sites that participated in the survey. These individual results are a supplement to the June 1996 Summary Report which presented overall survey results. Results are presented in 11 sections, arranged alphabetically by site. Each section includes a series of figures and tables that parallel those presented in the Summary Report. To facilitate comparison, figures are presented both for the individual site and for the overall long survey. The sequence of sections is: Fernald, Hanford, Idaho, Los Alamos, Monticello, Nevada, Pantex, Rocky Flats, St. Louis, Sandia, and Savannah River.

  11. Enhanced Aqueous Suzuki–Miyaura Coupling Allows Site-Specific Polypeptide 18F-Labeling

    PubMed Central

    2013-01-01

    The excesses of reagents used in protein chemistry are often incompatible with the reduced or even inverse stoichiometries used for efficient radiolabeling. Analysis and screening of aqueous Pd(0) ligand systems has revealed the importance of a guanidine core and the discovery of 1,1-dimethylguanidine as an enhanced ligand for aqueous Suzuki–Miyaura cross-coupling. This novel Pd catalyst system has now allowed the labeling of small molecules, peptides, and proteins with the fluorine-18 prosthetic [18F]4-fluorophenylboronic acid. These findings now enable site-specific protein 18F-labeling under biologically compatible conditions using a metal-triggered reaction. PMID:23991754

  12. Analysis of site-specific N-glycan remodeling in the endoplasmic reticulum and the Golgi.

    PubMed

    Hang, Ivan; Lin, Chia-wei; Grant, Oliver C; Fleurkens, Susanna; Villiger, Thomas K; Soos, Miroslav; Morbidelli, Massimo; Woods, Robert J; Gauss, Robert; Aebi, Markus

    2015-12-01

    The hallmark of N-linked protein glycosylation is the generation of diverse glycan structures in the secretory pathway. Dynamic, non-template-driven processes of N-glycan remodeling in the endoplasmic reticulum and the Golgi provide the cellular setting for structural diversity. We applied newly developed mass spectrometry-based analytics to quantify site-specific N-glycan remodeling of the model protein Pdi1p expressed in insect cells. Molecular dynamics simulation, mutational analysis, kinetic studies of in vitro processing events and glycan flux analysis supported the defining role of the protein in N-glycan processing. PMID:26240167

  13. Site-specific incorporation of a fluorescent terphenyl unnatural amino acid.

    PubMed

    Lampkowski, Jessica S; Uthappa, Diya M; Young, Douglas D

    2015-11-15

    The site-specific incorporation of unnatural amino acids into proteins has a wide range of biological implications. Of particular interest is the incorporation of fluorescent probes as a mechanism to track protein function, transport, and folding. Thus, the development of a novel system for the incorporation of new fluorescent unnatural amino acids has significant utility. Specifically, we have elucidated an aminoacyl-tRNA synthetase capable of recognizing a terphenyl UAA derivative, and charging a cognate tRNA with this amino acid for protein incorporation. Moreover, we have successfully incorporated this fluorescent UAA into GFP at several key residues, demonstrating a novel means to modulate fluorescence within the protein.

  14. Site-Specific Fragmentation of Polystyrene Molecule Using Size-Selected Ar Gas Cluster Ion Beam

    NASA Astrophysics Data System (ADS)

    Moritani, Kousuke; Mukai, Gen; Hashinokuchi, Michihiro; Mochiji, Kozo

    2009-04-01

    The secondary ion mass spectrum (SIMS) of a polystyrene thin film was investigated using a size-selected Ar gas cluster ion beam (GCIB). The fragmentation in the SIM spectrum varied by kinetic energy per atom (Eatom); the Eatom dependence of the secondary ion intensity of the fragment species of polystyrene can be essentially classified into three types based on the relationship between Eatom and the dissociation energy of a specific bonding site in the molecule. These results indicate that adjusting Eatom of size-selected GCIB may realize site-specific bond breaking within a molecule.

  15. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOEpatents

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  16. Isolation and characterization of site-specific DNA-methyltransferases from Bacillus coagulans K.

    PubMed

    Svadbina, I V; Zelinskaya, N V; Kovalevskaya, N P; Zheleznaya, L A; Matvienko, N I

    2004-03-01

    Two site-specific DNA methyltransferases, M.BcoKIA and M.BcoKIB, were isolated from the thermophilic strain Bacillus coagulans K. Each of the methylases protects the recognition site 5'-CTCTTC-3'/5'-GAAGAG-3' from cleavage with the cognate restriction endonuclease BcoKI. It is shown that M.BcoKIB is an N6-adenine specific methylase and M.BcoKIA is an N4-cytosine specific methylase. According to bisulfite mapping, M.BcoKIA methylates the first cytosine in the sequence 5'-CTCTTC-3'. PMID:15061697

  17. Evaluation of site-specific tactics using bifenazate and Neoseiulus californicus for management of Tetranychus urticae (Acari: Tetranychidae) in strawberries.

    PubMed

    Liu, Ruohan; Nyoike, Teresia W; Liburd, Oscar E

    2016-10-01

    Greenhouse and field experiments were conducted to evaluate the effectiveness of site-specific tactics for management of the twospotted spider mite, Tetranychus urticae Koch, a major pest of greenhouse and field-grown strawberries (Fragaria x ananassa Duchesne). Two site-specific (spot) treatments, the miticide bifenazate (Acramite(®)) and the predatory mite Neoseiulus californicus McGregor, were compared with whole-plot treatments of bifenazate or N. californicus to determine whether T. urticae could be effectively managed in field-grown strawberry using only site-specific tactics. Additionally, the cost of site-specific tactics was compared with whole-plot treatments to determine the economic value of using site-specific management tactics for T. urticae in strawberries. In the greenhouse, all treatments equivalently reduced the number of T. urticae below control. In the field during the 2011-2012 season, more T. urticae eggs and motiles were in the whole-plot treatments of both N. californicus and bifenazate in the mid-season and late season, respectively, compared with the spot treatments. With the exception of site-specific N. californicus during the 2011-2012 field season, there were no differences in marketable yields between plots with site-specific treatments and whole-plot management. An economic analysis demonstrated a significant cost savings (75.3 %) with site-specific treatments of N. californicus compared with whole-plot application of N. californicus. Similarly, a 24.7 % reduction in cost was achieved in using site-specific bifenazate compared with whole-plot application of bifenazate. The findings indicate that site-specific treatments with N. californicus and bifenazate are competitive alternatives to whole-field application for T. urticae management in strawberries. PMID:27502111

  18. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies.

  19. Development of a site-specific marine water quality standard for cyanide

    SciTech Connect

    Arredondo, L.A.; Brix, K.V.; Cardwell, R.D.; Marsden, A.

    1995-12-31

    A study was conducted to develop a site-specific marine standard for cyanide. The generic cyanide standard of 1 {micro}g/L is ``driven`` by toxicity data for eastern rock crab (Cancer irroratus) zoeae. The reported LC50 for C. irroratus is 4.9 {micro}g/L cyanide and is six times more sensitive that any other marine species tested. In order to develop a site-specific standard for Washington state, cyanide toxicity tests were conducted using the first stage zoeae of Cancer magister and Cancer oregonensis, two Cancer resident to Puget Sound, in accordance with standard ASTM test methods. Testing with C. magister and C. oregonensis resulted in Species Mean Acute Values (SMAVS) of 68 and 131 {micro}g/L cyanide based on measured test concentrations. This is considerably higher than that reported for C. irroratus, is more consistent with cyanide toxicity values for other species tested, and results in a water quality criterion of 9.85 {micro}g/L cyanide with inclusion of these values in the data set. This paper presents the test methods used and the potential effects the test results may have on the marine water quality criterion for cyanide.

  20. In vivo site-specific recombination using the beta-rec/six system.

    PubMed

    Servert, Pilar; Díaz, Vicente; Lucas, Daniel; de la Cueva, Teresa; Rodriguez, Maria; García-Castro, Javier; Alonso, Juan; Martínez-A, Carlos; González, Manuel; Bernad, Antonio

    2008-07-01

    The prokaryotic beta serine recombinase (beta-rec) catalyzes site-specific recombination between two directly oriented six sites (93 bp) in mammalian cells, both in episomal and in chromosomally integrated substrates. The beta-rec/six exclusive intramolecular site-specific recombination (SSR) system has been proposed as a suitable approach when several independently controlled recombination events are needed in a single cell. Here we explored the use of the beta-rec/six system for selective induction of genome-targeted modifications. We generated and analyzed mouse transgenic lines (Tgbeta) expressing beta-rec under the control of the Lck promoter. beta-rec activity was demonstrated, and there was no evidence of alterations to thymic or peripheral T cell development. We developed two transgenic mouse lines harboring different target sequences (Tgrec and KOsix) and analyzed the effect of beta-rec expression on these animals. The results indicate that the beta-rec/six SSR system is functional for in vivo gene-targeting applications.

  1. Mapping potential of digitized aerial photographs and space images for site-specific crop management

    NASA Astrophysics Data System (ADS)

    Nielsen, Gerald A.; Long, Daniel S.; Queen, Lloyd P.

    1996-11-01

    In site-specific crop management, treatments (e.g., fertilizer and herbicides) are applied precisely where they are needed. Global positioning system receivers allow accurate navigation of field implements and creation of crop yield maps. Remote sensing products help producers explain the wide range of yields shown on these maps and become the basis for digitized field management maps. Previous sources of remote sensing products for agriculture did not provide services that generated a sustained demand by crop producers, often because data were not delivered quickly enough. Public Access Resource Centers could provide a nearly uninterrupted electronic flow of data from NASA's MODIS and other sensors that could help producers and their advisors monitor crop conditions. This early warning/opportunity system would provide a low-cost way to discover conditions that merit examination on the ground. High-spatial-resolution digital aerial photographs or data from new commercial satellite companies would provide the basis for site-specific treatments. These detailed data are too expensive to acquire often and must be timed so as to represent differences in water supply characteristics and crop yield potentials. Remote sensing products must be linked to specific prescriptions that crop produces use to control operations and improve outcomes.

  2. Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases

    PubMed Central

    Krishnakumar, Radha; Grose, Carissa; Haft, Daniel H.; Zaveri, Jayshree; Alperovich, Nina; Gibson, Daniel G.; Merryman, Chuck; Glass, John I.

    2014-01-01

    Toward achieving rapid and large scale genome modification directly in a target organism, we have developed a new genome engineering strategy that uses a combination of bioinformatics aided design, large synthetic DNA and site-specific recombinases. Using Cre recombinase we swapped a target 126-kb segment of the Escherichia coli genome with a 72-kb synthetic DNA cassette, thereby effectively eliminating over 54 kb of genomic DNA from three non-contiguous regions in a single recombination event. We observed complete replacement of the native sequence with the modified synthetic sequence through the action of the Cre recombinase and no competition from homologous recombination. Because of the versatility and high-efficiency of the Cre-lox system, this method can be used in any organism where this system is functional as well as adapted to use with other highly precise genome engineering systems. Compared to present-day iterative approaches in genome engineering, we anticipate this method will greatly speed up the creation of reduced, modularized and optimized genomes through the integration of deletion analyses data, transcriptomics, synthetic biology and site-specific recombination. PMID:24914053

  3. Effective and site-specific phosphoramidation reaction for universally labeling nucleic acids.

    PubMed

    Su, Yu-Chih; Chen, Hsing-Yin; Ko, Ni Chien; Hwang, Chi-Ching; Wu, Min Hui; Wang, Li-Fang; Wang, Yun-Ming; Chang, Sheng-Nan; Wang, Eng-Chi; Wang, Tzu-Pin

    2014-03-15

    Here we report efficient and selective postsynthesis labeling strategies, based on an advanced phosphoramidation reaction, for nucleic acids of either synthetic or enzyme-catalyzed origin. The reactions provided phosphorimidazolide intermediates of DNA or RNA which, whether reacted in one pot (one-step) or purified (two-step), were directly or indirectly phosphoramidated with label molecules. The acquired fluorophore-labeled nucleic acids, prepared from the phosphoramidation reactions, demonstrated labeling efficacy by their F/N ratio values (number of fluorophores per molecule of nucleic acid) of 0.02-1.2 which are comparable or better than conventional postsynthesis fluorescent labeling methods for DNA and RNA. Yet, PCR and UV melting studies of the one-step phosphoramidation-prepared FITC-labeled DNA indicated that the reaction might facilitate nonspecific hybridization in nucleic acids. Intrinsic hybridization specificity of nucleic acids was, however, conserved in the two-step phosphoramidation reaction. The reaction of site-specific labeling nucleic acids at the 5'-end was supported by fluorescence quenching and UV melting studies of fluorophore-labeled DNA. The two-step phosphoramidation-based, effective, and site-specific labeling method has the potential to expedite critical research including visualization, quantification, structural determination, localization, and distribution of nucleic acids in vivo and in vitro.

  4. New developments for the site-specific attachment of protein to surfaces

    SciTech Connect

    Camarero, J A

    2005-05-12

    Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

  5. Site-specific investigations of aquifer thermal energy storage for space and process cooling

    SciTech Connect

    Brown, D R; Hattrup, M P; Watts, R L

    1991-08-01

    The Pacific Northwest Laboratory (PNL) has completed three preliminary site-specific feasibility studies that investigated using aquifer thermal energy storage (ATES) to reduce space and process cooling costs. Chilled water stored in an ATES system could be used to meet all or part of the process and/or space cooling loads at the three facilities investigated. The work was sponsored by the US Department of Energy's (DOE) Office of Energy Management. The ultimate goal of DOE's Thermal Energy Storage Program is to successfully transfer ATES technology to industrial and commercial sectors. The primary objective of this study was to identify prospective sites and determine the technical and economic feasibility of implementing chill ATES technology. A secondary objective was to identify site-specific factors promoting or inhibiting the application of chill ATES technology so that other potentially attractive sites could be more easily identified and evaluated. A preliminary investigation of the feasibility of commercializing chill ATES in automotive assembly facilities was completed. The results suggested that automotive assembly facilities was completed. The results suggested that automotive assembly facilities represent a good entry market for chill ATES, if the system is cost-effective. As a result, this study was undertaken to identify and evaluate prospective chill ATES applications in the automotive industry. The balance of the report contains two main sections. Section 2.0 describes the site identification process. Site feasibility is addressed in Section 3.0. Overall study conclusions and recommendations are than presented in Section 4.0.

  6. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies. PMID:27432793

  7. Monitoring Protein Misfolding by Site-Specific Labeling of Proteins In Vivo

    PubMed Central

    Hsieh, Tzung-yang; Nillegoda, Nadinath B.; Tyedmers, Jens; Bukau, Bernd; Mogk, Axel; Kramer, Günter

    2014-01-01

    Incorporating fluorescent amino acids by suppression of the TAG amber codon is a useful tool for site-specific labeling of proteins and visualizing their localization in living cells. Here we use a plasmid encoded orthogonal tRNA/aminoacyl-tRNA synthetase pair to site-specifically label firefly luciferase with the environmentally sensitive fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2- aminopropanoic acid (ANAP) and explore the detectability of conformational changes in labeled luciferase in the yeast cytoplasm. We find that ANAP labeling efficiency is greatly increased in [PSI+] cells and show that analysis of the ANAP fluorescence emission by confocal imaging allows for tracking the thermal unfolding and aggregation of luciferase in vivo. Furthermore we demonstrate that flow cytometry can be used to study conformational changes in luciferase and chaperone-mediated refolding in quantitative terms and at the level of single cells. This experimental setup for the first time allows for the direct analysis of the folding state of a protein in living cells and may serve as valuable new tool for examining mechanisms of protein folding, misfolding and aggregation. PMID:24915041

  8. [Case study on health risk assessment based on site-specific conceptual model].

    PubMed

    Zhong, Mao-Sheng; Jiang, Lin; Yao, Jue-Jun; Xia, Tian-Xiang; Zhu, Xiao-Ying; Han, Dan; Zhang, Li-Na

    2013-02-01

    Site investigation was carried out on an area to be redeveloped as a subway station, which is right downstream of the groundwater of a former chemical plant. The results indicate the subsurface soil and groundwater in the area are both polluted heavily by 1,2-dichloroethane, which was caused by the chemical plant upstream with the highest concentration was 104.08 mg.kg-1 for soil sample at 8.6 m below ground and the highest concentration was 18500 microg.L-1 for groundwater. Further, a site-specific contamination conceptual model, giving consideration to the specific structure configuration of the station, was developed, and the corresponding risk calculation equation was derived. The carcinogenic risks calculated with models developed on the generic site conceptual model and derived herein on the site-specific conceptual model were compared. Both models indicate that the carcinogenic risk is significantly higher than the acceptable level which is 1 x 10(-6). The comparison result reveals that the risk calculated with the former models for soil and groundwater are higher than the one calculated with the latter models by 2 times and 1.5 times, respectively. The finding in this paper indicates that the generic risk assessment model may underestimate the risk if specific site conditions and structure configuration are not considered.

  9. Brain site-specific proteome changes in aging-related dementia

    PubMed Central

    Manavalan, Arulmani; Mishra, Manisha; Feng, Lin; Sze, Siu Kwan; Akatsu, Hiroyasu; Heese, Klaus

    2013-01-01

    This study is aimed at gaining insights into the brain site-specific proteomic senescence signature while comparing physiologically aged brains with aging-related dementia brains (for example, Alzheimer's disease (AD)). Our study of proteomic differences within the hippocampus (Hp), parietal cortex (pCx) and cerebellum (Cb) could provide conceptual insights into the molecular mechanisms involved in aging-related neurodegeneration. Using an isobaric tag for relative and absolute quantitation (iTRAQ)-based two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-LC-MS/MS) brain site-specific proteomic strategy, we identified 950 proteins in the Hp, pCx and Cb of AD brains. Of these proteins, 31 were significantly altered. Most of the differentially regulated proteins are involved in molecular transport, nervous system development, synaptic plasticity and apoptosis. Particularly, proteins such as Gelsolin (GSN), Tenascin-R (TNR) and AHNAK could potentially act as novel biomarkers of aging-related neurodegeneration. Importantly, our Ingenuity Pathway Analysis (IPA)-based network analysis further revealed ubiquitin C (UBC) as a pivotal protein to interact with diverse AD-associated pathophysiological molecular factors and suggests the reduced ubiquitin proteasome degradation system (UPS) as one of the causative factors of AD. PMID:24008896

  10. Streptococci Engage TLR13 on Myeloid Cells in a Site-Specific Fashion.

    PubMed

    Kolter, Julia; Feuerstein, Reinhild; Spoeri, Evelyne; Gharun, Kourosh; Elling, Roland; Trieu-Cuot, Patrick; Goldmann, Tobias; Waskow, Claudia; Chen, Zhijian J; Kirschning, Carsten J; Deshmukh, Sachin D; Henneke, Philipp

    2016-03-15

    Streptococci are common human colonizers with a species-specific mucocutaneous distribution. At the same time, they are among the most important and most virulent invasive bacterial pathogens. Thus, site-specific cellular innate immunity, which is predominantly executed by resident and invading myeloid cells, has to be adapted with respect to streptococcal sensing, handling, and response. In this article, we show that TLR13 is the critical mouse macrophage (MΦ) receptor in the response to group B Streptococcus, both in bone marrow-derived MΦs and in mature tissue MΦs, such as those residing in the lamina propria of the colon and the dermis, as well as in microglia. In contrast, TLR13 and its chaperone UNC-93B are dispensable for a potent cytokine response of blood monocytes to group B Streptococcus, although monocytes serve as the key progenitors of intestinal and dermal MΦs. Furthermore, a specific role for TLR13 with respect to MΦ function is supported by the response to staphylococci, where TLR13 and UNC-93B limit the cytokine response in bone marrow-derived MΦs and microglia, but not in dermal MΦs. In summary, TLR13 is a critical and site-specific receptor in the single MΦ response to β-hemolytic streptococci. PMID:26873993

  11. Modelling of Site Specific Effects and the Impact upon Local Tie Residuals

    NASA Astrophysics Data System (ADS)

    Moore, M. J.; Mcclusky, S.

    2012-12-01

    It is well known that site specific effects such as far-field and near-field multipath do not average out over time and that the time varying geometry of GNSS constellations leads to draconitic aliasing of these unmodelled signals into station position time series. Studies have also shown that the structures on which GNSS antennae are mounted introduce near-field multipath effects that can cause position errors reaching magnitudes of 4-5 cm at Polar Regions, and that unmodelled radomes have a significant impact on the Phase Centre Variation (PCV) of Global Positioning System (GPS) antennae, also leading to biases in coordinate time series. In this work we evaluate the efficacy of using empirical site models (ESM) to improve the realisation of the combined multi technique international terrestrial reference frame (ITRF). We use a comparison of local tie residuals, at ITRF, VLBI, SLR and GPS co-location sites, obtained from GPS solutions with and without Empirical Site Models applied. We will show that in order to achieve 1mm local tie residuals between the different space geodetic observation techniques, site specific modelling needs to be taken into consideration.

  12. Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.

    PubMed

    Lund, E D; Wolcott, M C; Hanson, G P

    2001-10-16

    Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

  13. The Potential for Mapping Nematode Distributions for Site-specific Management

    PubMed Central

    Wyse-Pester, Dawn Y.; Wiles, Lori J.; Westra, Philip

    2002-01-01

    The success of site-specific nematode management depends on a grower or advisor being able to afford to make a map of an infestation that is accurate enough for management decisions. The spatial dependence of nematode infestations and correlation of soil attributes with nematode density were assessed to investigate the scale of sampling required to obtain correlated observations of density and the use of soils data to reduce the cost of sampling. Nematodes and soil were sampled on a 76.2 × 76.2-m grid in two irrigated corn (Zea mays) fields for 2 years. Nematodes of each of three species were found in 36% to 77% of the cores from a field. Spatial dependence was detected for 10 of 16 distributions, and 22% to 67% of the variation in density within a field could be attributed to spatial correlation. Density was correlated to distances of 115 to 649 m in the directions of 0, 45, 90, and 135° from the crop row, and distances varied with direction. Correlations between nematode density and soil attributes were inconsistent between species and fields. These results indicate a potential for mapping nematode infestations for site-specific management, but provide no evidence for reducing the cost of sampling by substituting soils data for nematode counts when making a map. PMID:19265913

  14. Precision nitrogen management across site-specific management zones in irrigated maize production systems

    NASA Astrophysics Data System (ADS)

    Inman, Daniel Joseph, II

    In the United States, crop nitrogen-use efficiency (NUE) is very low. Approximately 33% of all N applied towards cereal crop production is captured in the harvested grain. Precision agricultural practices have shown potential for increasing crop NUE. Objectives were: (i) to characterize the within field spatial variability of N uptake across irrigated corn production fields, (ii) to quantify and compare N uptake and grain yield across three site specific management zones (SSMZs), (iii) to compare grain yield response to applied N between management zones, (iv) to examine the relationships between normalized difference vegetation index (NDVI) determined early in the growing season, site-specific management zones, and relative maize yield; (v) to determine if NDVI can be used to estimate relative maize yield; (vi) to determine if site-specific management zones can be used in conjunction with remote sensing to provide yield estimates in irrigated maize, and (vii) to evaluate the effectiveness of using a hand-held active remote sensing instrument to estimate yield potential in irrigated maize. This study was conducted on commercially-operated irrigated production maize fields throughout northeastern Colorado. For objectives i, ii, and iii, fields were classified into high, medium, and low site specific management zones. For objective iv, v, and vi, aerial imagery was acquired at approximately the eight-leaf crop growth stage. Grain was harvested using a commercial-combine outfitted with a yield monitor at the crop's physiological maturity. Objective iv was analyzed using percent areal agreement, kappa statistics, and regression analysis. Objectives v and vi were analyzed using regression analysis with cross-validation and indicator variables. For objective vii, the GreenSeeker(TM) active remote sensing unit was used to measure red and near infrared reflectance of the crop canopy. A response index (RI) was calculated the ratio of the reflectance of an area of interest

  15. INEEL Subregional Conceptual Model Report Volume 2: Summary of Existing Knowledge of Geochemical Influences on the Fate and Transport of Contaminants in the Subsurface at the INEEL

    SciTech Connect

    Paul L. Wichlacz; Robert C. Starr; Brennon Orr

    2003-09-01

    . The documents that appeared to be the most pertinent were selected from further review. These documents are tabulated in the citation list. This report summarizes existing geochemical conceptual models, but does not attempt to generate a new conceptual model or select the ''right'' model. This document is organized as follows. Geochemical models are described in general in Section 2. Geochemical processes that control the transport and fate of contaminants introduced into groundwater are described in Section 3. The natural geochemistry of the Eastern Snake River Plain Aquifer (SRPA) is described in Section 4. The effect of waste disposal on the INEEL subsurface is described in Section 5. The geochemical behavior of the major contaminants is described in Section 6. Section 7 describes the site-specific geochemical models developed for various INEEL facilities.

  16. Site-specific range uncertainties caused by dose calculation algorithms for proton therapy

    NASA Astrophysics Data System (ADS)

    Schuemann, J.; Dowdell, S.; Grassberger, C.; Min, C. H.; Paganetti, H.

    2014-08-01

    The purpose of this study was to assess the possibility of introducing site-specific range margins to replace current generic margins in proton therapy. Further, the goal was to study the potential of reducing margins with current analytical dose calculations methods. For this purpose we investigate the impact of complex patient geometries on the capability of analytical dose calculation algorithms to accurately predict the range of proton fields. Dose distributions predicted by an analytical pencil-beam algorithm were compared with those obtained using Monte Carlo (MC) simulations (TOPAS). A total of 508 passively scattered treatment fields were analyzed for seven disease sites (liver, prostate, breast, medulloblastoma-spine, medulloblastoma-whole brain, lung and head and neck). Voxel-by-voxel comparisons were performed on two-dimensional distal dose surfaces calculated by pencil-beam and MC algorithms to obtain the average range differences and root mean square deviation for each field for the distal position of the 90% dose level (R90) and the 50% dose level (R50). The average dose degradation of the distal falloff region, defined as the distance between the distal position of the 80% and 20% dose levels (R80-R20), was also analyzed. All ranges were calculated in water-equivalent distances. Considering total range uncertainties and uncertainties from dose calculation alone, we were able to deduce site-specific estimations. For liver, prostate and whole brain fields our results demonstrate that a reduction of currently used uncertainty margins is feasible even without introducing MC dose calculations. We recommend range margins of 2.8% + 1.2 mm for liver and prostate treatments and 3.1% + 1.2 mm for whole brain treatments, respectively. On the other hand, current margins seem to be insufficient for some breast, lung and head and neck patients, at least if used generically. If no case specific adjustments are applied, a generic margin of 6.3% + 1.2 mm would be

  17. Development of remote sensing based site specific weed management for Midwest mint production

    NASA Astrophysics Data System (ADS)

    Gumz, Mary Saumur Paulson

    Peppermint and spearmint are high value essential oil crops in Indiana, Michigan, and Wisconsin. Although the mints are profitable alternatives to corn and soybeans, mint production efficiency must improve in order to allow industry survival against foreign produced oils and synthetic flavorings. Weed control is the major input cost in mint production and tools to increase efficiency are necessary. Remote sensing-based site-specific weed management offers potential for decreasing weed control costs through simplified weed detection and control from accurate site specific weed and herbicide application maps. This research showed the practicability of remote sensing for weed detection in the mints. Research was designed to compare spectral response curves of field grown mint and weeds, and to use these data to develop spectral vegetation indices for automated weed detection. Viability of remote sensing in mint production was established using unsupervised classification, supervised classification, handheld spectroradiometer readings and spectral vegetation indices (SVIs). Unsupervised classification of multispectral images of peppermint production fields generated crop health maps with 92 and 67% accuracy in meadow and row peppermint, respectively. Supervised classification of multispectral images identified weed infestations with 97% and 85% accuracy for meadow and row peppermint, respectively. Supervised classification showed that peppermint was spectrally distinct from weeds, but the accuracy of these measures was dependent on extensive ground referencing which is impractical and too costly for on-farm use. Handheld spectroradiometer measurements of peppermint, spearmint, and several weeds and crop and weed mixtures were taken over three years from greenhouse grown plants, replicated field plots, and production peppermint and spearmint fields. Results showed that mints have greater near infrared (NIR) and lower green reflectance and a steeper red edge slope than

  18. Site-specific labeling of proteins via sortase: protocols for the molecular biologist.

    PubMed

    Popp, Maximilian Wei-Lin

    2015-01-01

    Creation of site-specifically labeled protein bioconjugates is an important tool for the molecular biologist and cell biologist. Chemical labeling methods, while versatile with respect to the types of moieties that can be attached, suffer from lack of specificity, often targeting multiple positions within a protein. Here we describe protocols for the chemoenzymatic labeling of proteins at the C-terminus using the bacterial transpeptidase, sortase A. We detail a protocol for the purification of an improved pentamutant variant of the Staphylococcus aureus enzyme (SrtA 5(o)) that exhibits vastly improved kinetics relative to the wild-type enzyme. Importantly, a protocol for the construction of peptide probes compatible with sortase labeling using techniques that can be adapted to any cellular/molecular biology lab with no existing infrastructure for synthetic chemistry is described. Finally, we provide an example of how to optimize the labeling reaction using the improved SrtA 5(o) variant. PMID:25560076

  19. End-to-End Network Simulation Using a Site-Specific Radio Wave Propagation Model

    SciTech Connect

    Djouadi, Seddik M; Kuruganti, Phani Teja; Nutaro, James J

    2013-01-01

    The performance of systems that rely on a wireless network depends on the propagation environment in which that network operates. To predict how these systems and their supporting networks will perform, simulations must take into consideration the propagation environment and how this effects the performance of the wireless network. Network simulators typically use empirical models of the propagation environment. However, these models are not intended for, and cannot be used, to predict a wireless system will perform in a specific location, e.g., in the center of a particular city or the interior of a specific manufacturing facility. In this paper, we demonstrate how a site-specific propagation model and the NS3 simulator can be used to predict the end-to-end performance of a wireless network.

  20. Site-Specific N-Terminal Labeling of Peptides and Proteins using Butelase 1 and Thiodepsipeptide.

    PubMed

    Nguyen, Giang K T; Cao, Yuan; Wang, Wei; Liu, Chuan Fa; Tam, James P

    2015-12-21

    An efficient ligase with exquisite site-specificity is highly desirable for protein modification. Recently, we discovered the fastest known ligase called butelase 1 from Clitoria ternatea for intramolecular cyclization. For intermolecular ligation, butelase 1 requires an excess amount of a substrate to suppress the reverse reaction, a feature similar to other ligases. Herein, we describe the use of thiodepsipeptide substrates with a thiol as a leaving group and an unacceptable nucleophile to render the butelase-mediated ligation reactions irreversible and in high yields. Butelase 1 also accepted depsipeptides as substrates, but unlike a thiodesipeptide, the desipeptide ligation was partially reversible as butelase 1 can tolerate an alcohol group as a poor nucleophile. The thiodesipeptide method was successfully applied in N-terminal labeling of ubiquitin and green fluorescent protein using substrates with or without a biotin group in high yields. PMID:26563575

  1. Induction of site-specific chromosomal translocations in embryonic stem cells by CRISPR/Cas9

    PubMed Central

    Jiang, Junfeng; Zhang, Li; Zhou, Xingliang; Chen, Xi; Huang, Guanyi; Li, Fengsheng; Wang, Ruizhe; Wu, Nancy; Yan, Youzhen; Tong, Chang; Srivastava, Sankalp; Wang, Yue; Liu, Houqi; Ying, Qi-Long

    2016-01-01

    Chromosomal translocation is the most common form of chromosomal abnormality and is often associated with congenital genetic disorders, infertility, and cancers. The lack of cellular and animal models for chromosomal translocations, however, has hampered our ability to understand the underlying disease mechanisms and to develop new therapies. Here, we show that site-specific chromosomal translocations can be generated in mouse embryonic stem cells (mESCs) via CRISPR/Cas9. Mouse ESCs carrying translocated chromosomes can be isolated and expanded to establish stable cell lines. Furthermore, chimeric mice can be generated by injecting these mESCs into host blastocysts. The establishment of ESC-based cellular and animal models of chromosomal translocation by CRISPR/Cas9 provides a powerful platform for understanding the effect of chromosomal translocation and for the development of new therapeutic strategies. PMID:26898344

  2. Efficient Formation of Site-Specific Protein-DNA Hybrids Using Copper-Free Click Chemistry.

    PubMed

    Mukhortava, Ann; Schlierf, Michael

    2016-07-20

    Protein-DNA hybrids have become increasingly popular molecular building blocks in bionanotechnology and single-molecule studies to synergistically combine the programmability of DNA with the chemical diversity of proteins. The growing demand for protein-DNA hybrids requires powerful strategies for their conjugation. Here, we present an efficient two-step method for protein-DNA assembly based on copper-free click chemistry. The method allows site-specificity and high coupling efficiency, while maintaining the conservation of protein activity. We compare our method to a commonly used protocol of direct linkage of maleimide-modified oligos. We demonstrate the significantly higher yield with a protein-DNA conjugate, which is analyzed using single-molecule force spectroscopy. PMID:27322198

  3. WI-38 senescence is associated with global and site-specific hypomethylation

    PubMed Central

    Sidler, Corinne; Woycicki, Rafal; Kovalchuk, Igor; Kovalchuk, Olga

    2014-01-01

    Cellular senescence plays an important role in the age-dependent functional decline of organs and organ systems, as well as in age-related pathologies, such as cancer. Therefore, a better understanding of its underlying molecular mechanisms is crucial in the search for intervening measures. In this study, we considered the role of DNA methylation in senescence. We found that senescence is associated with global DNA hypomethylation, but also involves site-specific DNA hypo- and hypermethylation. In some cases, this differential methylation may affect gene expression and thereby modulate functional processes within cells. However, the majority of the CpG sites that were differentially methylated did not correspond with altered gene expression, suggesting that DNA methylation affects senescence by other means also, such as, for instance, genome stability. PMID:25063771

  4. Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

    DOE PAGESBeta

    Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; et al

    2016-05-23

    New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.« less

  5. A novel suicide substrate for DNA topoisomerases and site-specific recombinases.

    PubMed Central

    Burgin, A B; Huizenga, B N; Nash, H A

    1995-01-01

    DNA topoisomerases and DNA site-specific recombinases are biologically important enzymes involved in a diverse set of cellular processes. We show that replacement of a phosphodiester linkage by a 5'-bridging phosphorothioate linkage creates an efficient suicide substrate for calf thymus topoisomerase I and lambda integrase protein (Int). Although the bridging phosphorothioate linkage is cleaved by these enzymes, the 5'-sulfhydryl which is generated is not competent for subsequent ligation reactions. We use the irreversibility of Int-promoted cleavage to explore conditions and factors that contribute to various steps of lambda integrative recombination. The phosphorothioate substrates offer advantages over conventional suicide substrates, may be potent tools for inhibition of the relevant cellular enzymes and represent a unique tool for the study of many other phosphoryl transfer reactions. Images PMID:7659520

  6. Photo-Activatable Substrates for Site-Specific Differentiation of Stem Cells.

    PubMed

    Han, Kai; Yin, Wei-Na; Fan, Jin-Xuan; Cao, Feng-Yi; Zhang, Xian-Zheng

    2015-10-28

    In this report, a UV sensitive, PEGylated PFSSTKTC (Pro-Phe-Ser-Ser-Thr-Lys-Thr-Cys) peptide was modified on quartz substrate to investigate the spatial controlled differentiation of stem cells. This substrate could restrict the cell adhesion due to the steric hindrance of PEG shell. With UV irradiation, PFSSTKTC became exposed owing to the breakage of o-nitrobenzyl group with the detachment of PEG shell. The irradiation boundary on substrate was stable in the long term. The in vitro osteogenic differentiation results revealed that under the site-specific irradiation, the mesenchymal stem cells (MSCs) could specifically differentiate into osteoblast under the induction of PFSSTKTC peptide. This photoactivatable biomaterial shows great potential for region controllable and precise MSCs differentiation. PMID:26452046

  7. Uncovering Global SUMOylation Signaling Networks in a Site-Specific Manner

    PubMed Central

    Hendriks, Ivo A.; D’Souza, Rochelle C.J.; Yang, Bing; Verlaan-de Vries, Matty; Mann, Matthias; Vertegaal, Alfred C.O.

    2014-01-01

    SUMOylation is a reversible post-translational modification essential for genome stability. Using high-resolution mass spectrometry, we have studied global SUMOylation in human cells and in a site-specific manner, identifying a total of over 4,300 SUMOylation sites in over 1,600 proteins. Moreover, for the first time in excess of 1,000 SUMOylation sites were identified under standard growth conditions. SUMOylation dynamics were quantitatively studied in response to SUMO protease inhibition, proteasome inhibition and heat shock. A considerable amount of SUMOylated lysines have previously been reported to be ubiquitylated, acetylated or methylated, indicating crosstalk between SUMO and other post-translational modifications. We identified 70 phosphorylation and 4 acetylation events in close proximity to SUMOylation sites, and provide evidence for acetylation-dependent SUMOylation of endogenous histone H3. SUMOylation regulates target proteins involved in all nuclear processes including transcription, DNA repair, chromatin remodeling, pre-mRNA splicing and ribosome assembly. PMID:25218447

  8. Targeted site-specific cleavage of HIV-1 viral Rev responsive element by copper aminoglycosides.

    PubMed

    Sreedhara, A; Cowan, J A

    2001-02-01

    Site-specific cleavage of the HIV-1 viral Rev responsive element by copper aminoglycosides is reported under physiological conditions. This bubble and stem-loop RNA structure is efficiently targeted at micromolar concentrations of complex. The specificity of cleavage of structured viral RNA relative to a non-cognate tRNAPhe of well-defined secondary and tertiary structure is demonstrated. Cleavage products from simpler substrates [diribonucleotide (ApA) and 2',3'-cyclic monophosphate ester (cAMP)] were analyzed by 31P NMR and demonstrate a hydrolytic mechanism in the absence of external redox agents. These results demonstrate copper aminoglycosides to be highly efficient chemical nucleases with a targeting capability for viral RNA and suggest a novel methodology to counter RNA viruses.

  9. The species- and site-specific acid-base properties of biological thiols and their homodisulfides.

    PubMed

    Mirzahosseini, Arash; Noszál, Béla

    2014-07-01

    Cysteamine, cysteine, homocysteine, their homodisulfides and 9 related compounds were studied by ¹H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 33 macroscopic and 62 microscopic protonation constants and the concomitant 16 interactivity parameters, providing thus the first complete microspeciation of this vitally important family of biomolecules. The species- and site-specific basicities are interpreted by means of inductive and hydrogen-bonding effects through various intra- and intermolecular comparisons. The pH-dependent distribution of the microspecies is depicted. The thiolate basicities determined this way provide exclusive means for the prediction of thiolate oxidizabilities, a key parameter to understand and influence oxidative stress at the molecular level.

  10. Site-specific phase I, II trials of hyperthermia at Kyoto University.

    PubMed

    Hiraoka, M; Nishimura, Y; Nagata, Y; Mitsumori, M; Okuno, Y; Li, P Y; Abe, M; Takahashi, M; Masunaga, S; Akuta, K

    1994-01-01

    Site-specific phase I, II trials of locoregional hyperthermia undertaken at Kyoto University are briefly reviewed. Thermometry analysis demonstrated the usefulness of RF (radiofrequency) capacitive heating equipment in the treatment of various subsurface or deep-seated tumours including locally advanced breast cancers, soft tissue tumours, lung cancers involving the chest wall, liver tumours, unresectable or recurrent colorectal cancers, and invasive urinary bladder cancers. The difficulty in heating whole tumour volume or hypervascular tumours to therapeutic temperatures was also shown. Non-randomized trials for locally advanced breast cancers, unresectable or recurrent colorectal cancers and invasive urinary bladder cancers demonstrated a higher response rate in thermoradiotherapy than in radiotherapy alone. The complications associated with treatment were not generally serious except for chronic bowel damages in a trial for colorectal cancers. These promising phase I, II trials encourage the future phase III trials.

  11. Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination.

    PubMed Central

    Meyer-Leon, L; Huang, L C; Umlauf, S W; Cox, M M; Inman, R B

    1988-01-01

    Holliday structures are formed and resolved by FLP protein during site-specific recombination. These structures have been isolated and are visualized in both native and partially denatured states by electron microscopy. No single-strand breaks are found within the junction, indicating that the structure results from a reciprocal exchange of strands. These structures have properties consistent with being reaction intermediates. Double-strand cleavage products and "Y structures" are also detected and appear to be by-products of the reaction. The Y structures are three-armed branched molecules with a covalently closed junction located at the FLP recombination target site. Models are discussed, suggesting that both of these novel structures are made by aberrant cleavages during formation and resolution of the Holliday intermediate. Images PMID:3065624

  12. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

    DOE PAGESBeta

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Deerinck, Thomas J.; Yao, Jennifer Z.; Richardson, Douglas; Phipps, William S.; Ye, Anne Z.; Ellisman, Mark H.; et al

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of themore » intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.« less

  13. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

    SciTech Connect

    Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Deerinck, Thomas J.; Yao, Jennifer Z.; Richardson, Douglas; Phipps, William S.; Ye, Anne Z.; Ellisman, Mark H.; Drennan, Catherine L.; Baker, David; Ting, Alice Y.

    2014-10-13

    In this study, chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.

  14. Site-Specific Cassette Exchange Systems in the Aedes aegypti Mosquito and the Plutella xylostella Moth

    PubMed Central

    Haghighat-Khah, Roya Elaine; Scaife, Sarah; Martins, Sara; St John, Oliver; Matzen, Kelly Jean; Morrison, Neil; Alphey, Luke

    2015-01-01

    Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests. PMID:25830287

  15. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhu, Zhikai; Desaire, Heather

    2015-07-01

    Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.

  16. Site-Specific Oligonucleotide Binding Represses Transcription of the Human c-myc Gene in vitro

    NASA Astrophysics Data System (ADS)

    Cooney, Michael; Czernuszewicz, Graznya; Postel, Edith H.; Flint, S. Jane; Hogan, Michael E.

    1988-07-01

    A 27-base-long DNA oligonucleotide was designed that binds to duplex DNA at a single site within the 5' end of the human c-myc gene, 115 base pairs upstream from the transcription origin P1. On the basis of the physical properties of its bound complex, it was concluded that the oligonucleotide forms a colinear triplex with the duplex binding site. By means of an in vitro assay system, it was possible to show a correlation between triplex formation at -115 base pairs and repression of c-myc transcription. The possibility is discussed that triplex formation (site-specific RNA binding to a DNA duplex) could serve as the basis for an alternative program of gene control in vivo.

  17. Site-specific Probabilistic Seismic Hazard Map of Himachal Pradesh, India. Part II. Hazard Estimation

    NASA Astrophysics Data System (ADS)

    Muthuganeisan, Prabhu; Raghukanth, S. T. G.

    2016-08-01

    This article presents site-specific probable seismic hazard of the Himachal Pradesh province, situated in a seismically active region of northwest Himalaya, using the ground motion relations presented in a companion article. Seismic recurrence parameters for all the documented probable sources are established from an updated earthquake catalogue. The contour maps of probable spectral acceleration at 0, 0.2, and 1 s (5% damping) are presented for 475 and 2475 years return periods. Also, the hazard curves and uniform hazard response spectrums are presented for all the important cities in this province. Results indicate that the present codal provision underestimates the seismic hazard at cities of Bilaspur, Shimla, Hamirpur, Chamba, Mandi, and Solan. In addition, regions near Bilaspur and Chamba exhibit higher hazard levels than what is reported in literature.

  18. Thiol-based, site-specific and covalent immobilization of biomolecules for single-molecule experiments.

    PubMed

    Zimmermann, Julia L; Nicolaus, Thomas; Neuert, Gregor; Blank, Kerstin

    2010-06-01

    The success of single-molecule (SM) experiments critically depends on the functional immobilization of the biomolecule(s) to be studied. With the continuing trend of combining SM fluorescence with SM force experiments, methods are required that are suitable for both types of measurements. We describe a general protocol for the site-specific and covalent coupling of any type of biomolecule that can be prepared with a free thiol group. The protocol uses a poly(ethylene glycol) (PEG) spacer, which carries an N-hydroxy succinimide (NHS) group on one end and a maleimide group on the other. After reacting the NHS group with an amino-functionalized surface, the relatively stable but highly reactive maleimide group allows the coupling of the biomolecule. This protocol provides surfaces with low fluorescence background, low nonspecific binding and a large number of reactive sites. Surfaces containing immobilized biomolecules can be obtained within 6 h. PMID:20448543

  19. Site-Specific Gene Expression in Vivo by Direct Gene Transfer into the Arterial Wall

    NASA Astrophysics Data System (ADS)

    Nabel, Elizabeth G.; Plautz, Gregory; Nabel, Gary J.

    1990-09-01

    A recombinant β-galactosidase gene has been expressed in a specific arterial segment in vivo by direct infection with a murine amphotropic retroviral vector or by DNA transfection with the use of liposomes. Several cell types in the vessel wall were transduced, including endothelial and vascular smooth muscle cells. After retroviral infection, a recombinant reporter gene was expressed for at least 5 months, and no helper virus was detected. Recombinant gene expression achieved by direct retroviral infection or liposome-mediated DNA transfection was limited to the site of infection and was absent from liver, lung, kidney, and spleen. These results demonstrate that site-specific gene expression can be achieved by direct gene transfer in vivo and could be applied to the treatment of such human diseases as atherosclerosis or cancer.

  20. The design of a Phase I non site-specific Centralized Interim Storage Facility

    SciTech Connect

    Stringer, J.; Kane, D.

    1997-10-28

    The Department of Energy (DOE), Office of Civilian Radioactive Waste Management (OCRWM) recently completed a Topical Safety Analysis Report (TSAR) for a Phase 1 non site specific Centralized Interim Storage Facility (CISF). The TSAR will be used in licensing the CISF when and if a site is designated. The combined Phase 1 and Phase 2 CISF will provide federal storage capability for 40,000 metric tons of uranium (MTU) Spent Nuclear Fuel (SNF) under the oversight of the DOE. The Phase 1 TSAR was submitted to the NRC on May 1, 1997 and is currently under review having been docketed on June 10, 1997. This paper generally describes the Phase 1 CISF design and its operations as presented in the CISF TSAR.