Science.gov

Sample records for formation sites n44

  1. N44C nebula

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Resembling the hair in Botticelli's famous portrait of the birth of Venus, an image from NASA's Hubble Space Telescope has captured softly glowing filaments streaming from hot young stars in a nearby nebula.

    The image, presented by the Hubble Heritage Project, was taken in 1996 by Hubble's Wide Field and Planetary Camera 2, designed and built by NASA's Jet Propulsion Laboratory, Pasadena, Calif. The image is available online at

    http://heritage.stsci.edu , http://oposite.stsci.edu/pubinfo/pr/2002/12 orhttp://www.jpl.nasa.gov/images/wfpc .

    On the top right of the image is a source of its artistic likeness, a network of nebulous filaments surrounding the Wolf-Rayet star. This type of rare star is characterized by an exceptionally vigorous 'wind' of charged particles. The shock of the wind colliding with the surrounding gas causes the gas to glow.

    The Wolf-Rayet star is part of N44C, a nebula of glowing hydrogen gas surrounding young stars in the Large Magellanic Cloud. Visible from the Southern Hemisphere, the Large Magellanic Cloud is a small companion galaxy to the Milky Way.

    What makes N44C peculiar is the temperature of the star that illuminates it. The most massive stars -- those that are 10 to 50 times more massive than the Sun -- have maximum temperatures of 30,000 to 50,000 degrees Celsius (54,000 to 90,000 degrees Fahrenheit). The temperature of this star is about 75,000 degrees Celsius (135,000 degrees Fahrenheit). This unusually high temperature may be due to a neutron star or black hole that occasionally produces X-rays but is now inactive.

    N44C is part of a larger complex that includes young, hot, massive stars, nebulae, and a 'superbubble' blown out by multiple supernova explosions. Part of the superbubble is seen in red at the very bottom left of the Hubble image.

    The Space Telescope Science Institute is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract with the Goddard

  2. A Novel Acidic Matrix Protein, PfN44, Stabilizes Magnesium Calcite to Inhibit the Crystallization of Aragonite*

    PubMed Central

    Pan, Cong; Fang, Dong; Xu, Guangrui; Liang, Jian; Zhang, Guiyou; Wang, Hongzhong; Xie, Liping; Zhang, Rongqing

    2014-01-01

    Magnesium is widely used to control calcium carbonate deposition in the shell of pearl oysters. Matrix proteins in the shell are responsible for nucleation and growth of calcium carbonate crystals. However, there is no direct evidence supporting a connection between matrix proteins and magnesium. Here, we identified a novel acidic matrix protein named PfN44 that affected aragonite formation in the shell of the pearl oyster Pinctada fucata. Using immunogold labeling assays, we found PfN44 in both the nacreous and prismatic layers. In shell repair, PfN44 was repressed, whereas other matrix proteins were up-regulated. Disturbing the function of PfN44 by RNAi led to the deposition of porous nacreous tablets with overgrowth of crystals in the nacreous layer. By in vitro circular dichroism spectra and fluorescence quenching, we found that PfN44 bound to both calcium and magnesium with a stronger affinity for magnesium. During in vitro calcium carbonate crystallization and calcification of amorphous calcium carbonate, PfN44 regulated the magnesium content of crystalline carbonate polymorphs and stabilized magnesium calcite to inhibit aragonite deposition. Taken together, our results suggested that by stabilizing magnesium calcite to inhibit aragonite deposition, PfN44 participated in P. fucata shell formation. These observations extend our understanding of the connections between matrix proteins and magnesium. PMID:24302723

  3. A novel acidic matrix protein, PfN44, stabilizes magnesium calcite to inhibit the crystallization of aragonite.

    PubMed

    Pan, Cong; Fang, Dong; Xu, Guangrui; Liang, Jian; Zhang, Guiyou; Wang, Hongzhong; Xie, Liping; Zhang, Rongqing

    2014-01-31

    Magnesium is widely used to control calcium carbonate deposition in the shell of pearl oysters. Matrix proteins in the shell are responsible for nucleation and growth of calcium carbonate crystals. However, there is no direct evidence supporting a connection between matrix proteins and magnesium. Here, we identified a novel acidic matrix protein named PfN44 that affected aragonite formation in the shell of the pearl oyster Pinctada fucata. Using immunogold labeling assays, we found PfN44 in both the nacreous and prismatic layers. In shell repair, PfN44 was repressed, whereas other matrix proteins were up-regulated. Disturbing the function of PfN44 by RNAi led to the deposition of porous nacreous tablets with overgrowth of crystals in the nacreous layer. By in vitro circular dichroism spectra and fluorescence quenching, we found that PfN44 bound to both calcium and magnesium with a stronger affinity for magnesium. During in vitro calcium carbonate crystallization and calcification of amorphous calcium carbonate, PfN44 regulated the magnesium content of crystalline carbonate polymorphs and stabilized magnesium calcite to inhibit aragonite deposition. Taken together, our results suggested that by stabilizing magnesium calcite to inhibit aragonite deposition, PfN44 participated in P. fucata shell formation. These observations extend our understanding of the connections between matrix proteins and magnesium.

  4. Site formation processes at Zhoukoudian, China.

    PubMed

    Goldberg, P; Weiner, S; Bar-Yosef, O; Xu, Q; Liu, J

    2001-11-01

    Zhoukoudian is often cited for its human remains and the early evidence of fire. Yet, since its first excavations over 70 years ago, detailed studies of processes responsible for the accumulation of anthropogenic and geogenic sediments in the site have been sparse. This paper provides some details of site formation processes mainly through field observations of the extant section at Locality 1, and the use of soil micromorphology and Fourier Transform Infrared Spectrometry (FTIR) analyses of the sediments. Samples from Layers 10 through 3 show extensive water deposition of fine silt-sized material (reworked loess), including fine-grained organic matter. The dark organic-rich unit in Layer 10--often cited as one of the earliest evidence of fire--is a water-laid accumulation. Much of the fine-grained sediment was derived from outside Locality 1, implying that the site was open to varying extents throughout most of its depositional history. The 4-6 m accumulation of "ashes" in Layer 4 represents subaerial water-laid silt deposits derived from the loess-covered hillslopes surrounding the site. They presumably accumulated in an open depression that formed after the collapse of the brecciated roof deposits represented by Layer 6. Diagenesis is present in many of the Layers, and is exemplified by calcite precipitation and dissolution, and localized apatite (dahllite) replacement of calcite. In Layer 4 diagenesis is more advanced, including calcite/dahllite precipitation, subaerial weathering of the loess and associated precipitation of hematite, alteration of clay and the neoformation of quartz. Many of our conclusions concur with those of Teilhard de Chardin & Young published over 70 years ago.

  5. Globulettes: Formation Sites of Free Floating Planets?

    NASA Astrophysics Data System (ADS)

    Haikala, Lauri

    2017-06-01

    NIR imaging and ALMA arc-second resolution CO, CS and H2CO imaging of two typical Rosette Nebula globulettes is discussed. Velocity structure is observed in the 12CO line whereas the observed CS line widths are are extremely narrow, 0.3kms-1-0.4kms-1, indicating practically no internal motions in the very core. The highest molecular line column densities are detected at the side facing the HII region central cluster. The estimated masses of the globulettes range from 60 to 100 MJupiter (RN88) and 100 to 300MJ (RN122) and thus formation of planetary mass free floating planets is possible.

  6. Orbital resonances and planetary formation sites

    NASA Technical Reports Server (NTRS)

    Torbett, M.; Smoluchowski, R.; Greenberg, R.

    1982-01-01

    A cascaded resonance structure where planetesimal growth was accelerated at 2:1 interior and 1:2 exterior resonances, with an early-formed Jupiter producing runaway growth of planetary embryos, is hypothesized in a solar system formation model. The planetary embryos produce their own resonances, and these in turn lead to additional embryos in a process that successively propagates inwardly and outwardly to generate a resonant configuration of embryos. The early presence of Jupiter would in this way have imposed a harmonic structure on the accumulating planetesimal swarm. The positions of the planetary embryos can be moved into a degree of agreement with most of the present planetary positions which is comparable to that given by the Titius-Bode law, for the case of an accretion disk whose surface density obeys a power law of index -1.2.

  7. View of Yellowknife Bay Formation, with Drilling Sites

    NASA Image and Video Library

    2013-12-09

    This mosaic of images from NASA Curiosity shows geological members of the Yellowknife Bay formation, and the sites where Curiosity drilled into the lowest-lying member, called Sheepbed, at targets John Klein and Cumberland.

  8. Formation of RNA oligomers on montmorillonite: site of catalysis.

    PubMed

    Ertem, G; Ferris, J P

    1998-10-01

    Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

  9. Formation of RNA oligomers on montmorillonite: site of catalysis

    NASA Technical Reports Server (NTRS)

    Ertem, G.; Ferris, J. P.

    1998-01-01

    Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

  10. Formation of RNA oligomers on montmorillonite: site of catalysis

    NASA Technical Reports Server (NTRS)

    Ertem, G.; Ferris, J. P.

    1998-01-01

    Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

  11. Lamellipodial actin mechanically links myosin activity with adhesion site formation

    PubMed Central

    Giannone, Gregory; Dubin-Thaler, Benjamin; Rossier, Olivier; Cai, Yunfei; Chaga, Oleg; Jiang, Guoying; Beaver, William; Döbereiner, Hans-Günther; Freund, Yoav; Borisy, Gary; Sheetz, Michael P.

    2013-01-01

    Summary Cell motility proceeds by cycles of edge protrusion, adhesion and retraction. Whether these functions are coordinated by biochemical or biomechanical processes is unknown. We find that myosin II pulls the rear of the lamellipodial actin network, causing upward bending, edge retraction and initiation of new adhesion sites. The network then separates from the edge and condenses over the myosin. Protrusion resumes as lamellipodial actin regenerates from the front and extends rearward until it reaches newly assembled myosin, initiating the next cycle. Upward bending, observed by evanescence and electron microscopy, results in ruffle formation when adhesion strength is low. Correlative fluorescence and electron microscopy shows that the regenerating lamellipodium forms a cohesive, separable layer of actin above the lamellum. Thus, actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process. PMID:17289574

  12. Cannonballs in the context of gamma ray bursts. Formation sites?

    NASA Astrophysics Data System (ADS)

    Staff, J. E.; Fendt, C.; Ouyed, R.

    2006-05-01

    We investigate possible formation sites of the cannonballs (in the gamma ray bursts context) by calculating their physical parameters, such as density, magnetic field, and temperature close to the origin. Our results favor scenarios where the cannonballs form as instabilities (knots) within magnetized jets from hyperaccreting disks. These instabilities would most likely set in beyond the light cylinder where flow velocity with Lorentz factors as high as 2000 can be achieved. The cannonball model for gamma ray bursts requires that cannonballs form inside core-collapse supernovae. Our findings challenge the cannonball model of gamma ray bursts, unless hyperaccreting disks and the corresponding jets are common occurrences in core-collapse SNe.

  13. Investigation of Gd3N@C2n (40 <= n <= 44) family by Raman and inelastic electron tunneling spectroscopy

    NASA Astrophysics Data System (ADS)

    Burke, Brian; Chan, Jack; Williams, Keith; Ge, Jiechao; Shu, Chunying; Fu, Wujun; Dorn, Harry; Kushmerick, James; Puretzky, Alexander; Geohegan, David

    2010-03-01

    The structure and vibrational spectrum of Gd3N@C80 is studied through Raman and inelastic electron tunneling spectroscopy (IETS) as well as density functional theory (DFT) and universal force field (UFF) calculations. Hindered rotations, shown by both theory and experiment, indicate the formation of a Gd3N-C80 bond which reduces the ideal icosahedral symmetry of the C80 cage. The vibrational modes involving the movement of the encapsulated species are a fingerprint of the interaction between the fullerene cage and the core complex. We present Raman data for the Gd3N@C2n (40 <= n <= 44) family as well as Y3N@C80, Lu3N@C80, and Y3N@C88 for comparison. Conductance measurements have been performed on Gd3N@C80 and reveal a Kondo effect similar to that observed in C60.

  14. Bone formation following implantation of bone biomaterials into extraction sites.

    PubMed

    Molly, Liene; Vandromme, Heleen; Quirynen, Marc; Schepers, Evert; Adams, Jessica L; van Steenberghe, Daniel

    2008-06-01

    Adequate bone volume is imperative for the osseointegration of endosseous implants, but postextraction resorption and remodeling may challenge implant placement. The use of bone biomaterials has been advocated to fill extraction sites and to enhance primary implant stability during osseointegration. The objective of the case series was to evaluate bone formation histologically and biomechanically in extraction sites following implantation of three commercially available bone biomaterials to compare their ability to allow guided bone regeneration. Thirty-six periodontally involved teeth were extracted from eight healthy non-smoking subjects. At least two bone biomaterials, a synthetic sponge based on polylactic-polyglycolic acid technology (FIS), bovine porous bone mineral (BPBM), or a natural coral derivative physically and chemically transformed into a calcium carbonate ceramic (COR), and one non-grafted control were applied to the extraction sockets within each subject and were covered by an expanded polytetrafluoroethylene device. The devices were removed after 2 months, and trephine biopsies were obtained from each site 4 months later. At that time, endosseous implants were placed in 25 of the sites, and healing abutments were placed; measurements were taken 4 to 6 months later with an electronic mobility testing device. The percentage of residual biomaterial was 5.6% +/- 8.9% for FIS (P <0.001), 20.2% +/- 17.0% for BPBM (P <0.05), and 12.0% +/- 16.4% for COR (P <0.001). The amount of residual biomaterial after 6 months showed a significant relationship with the insertion torque measurements during the first third of implant insertion (P <0.05) and with values of the electronic mobility testing device at the abutment connection (P = 0.05). Histologically, new bone apposition was seen on BPBM particles. FIS sites showed similar ingrowth of blood vessels and osteocytes as empty controls. All sites revealed good primary stability at implant insertion and proper

  15. On-site formation of emulsions by controlled air plugs.

    PubMed

    Huang, Xiaowen; Hui, Wenli; Hao, Chonglei; Yue, Wanqing; Yang, Mengsu; Cui, Yali; Wang, Zuankai

    2014-02-26

    Air plugs are usually undesirable in microfluidic systems because of their detrimental effect on the system's stability and integrity. By controlling the wetting properties as well as the topographical geometry of the microchannel, it is reported herein that air plugs can be generated in pre-defined locations to function as a unique valve, allowing for the on-site formation of various emulsions including single-component droplets, composite droplets with droplet-to-droplet concentration gradient, blood droplets, paired droplets, as well as bubble arrays without the need for precious flow control, a difficult task with conventional droplet microfluidics. Moreover, the self-generated air valve can be readily deactivated (turned off) by the introduction of an oil phase, allowing for the on-demand release of as-formed droplets for downstream applications. It is proposed that the simple, yet versatile nature of this technique can act as an important method for droplet microfluidics and, in particular, is ideal for the development of affordable lab-on-a-chip systems without suffering from scalability and manufacturing challenges that typically confound the conventional droplet microfluidics.

  16. Site Saturation Mutagenesis Applications on Candida methylica Formate Dehydrogenase

    PubMed Central

    Özgün, Gülşah P.; Ordu, Emel B.; Tütüncü, H. Esra; Yelboğa, Emrah; Sessions, Richard B.

    2016-01-01

    In NADH regeneration, Candida methylica formate dehydrogenase (cmFDH) is a highly significant enzyme in pharmaceutical industry. In this work, site saturation mutagenesis (SSM) which is a combination of both rational design and directed evolution approaches is applied to alter the coenzyme specificity of NAD+-dependent cmFDH from NAD+ to NADP+ and increase its thermostability. For this aim, two separate libraries are constructed for screening a change in coenzyme specificity and an increase in thermostability. To alter the coenzyme specificity, in the coenzyme binding domain, positions at 195, 196, and 197 are subjected to two rounds of SSM and screening which enabled the identification of two double mutants D195S/Q197T and D195S/Y196L. These mutants increase the overall catalytic efficiency of NAD+ to 5.6 × 104-fold and 5 × 104-fold value, respectively. To increase the thermostability of cmFDH, the conserved residue at position 1 in the catalytic domain of cmFDH is subjected to SSM. The thermodynamic and kinetic results suggest that 8 mutations on the first residue can be tolerated. Among all mutants, M1L has the best residual activity after incubation at 60°C with 17%. These studies emphasize that SSM is an efficient method for creating “smarter libraries” for improving the properties of cmFDH. PMID:27847673

  17. New particle formation events observed at a high altitude site Pico Espejo, Venezuela

    NASA Astrophysics Data System (ADS)

    Nieminen, Tuomo; Kontkanen, Jenni; Krejci, Radovan; Ström, Johan; Tunved, Peter; Hamburger, Thomas; Calderon, Silvia; Hoffman, Pedro

    2013-05-01

    Formation and growth events of nucleation mode particles (10-25 nm in diameter) were analyzed from 27 month period of particle size distribution measurements at the high altitude site Pico Espejo in Venezuela. Particle formation was observed both in air masses connected to boundary layer air and in free tropospheric conditions. The frequency and magnitude of particle formation at this high altitude site was comparable to many observations at lower altitude sites.

  18. EUCAARI ion spectrometer measurements at 12 European sites - analysis of new particle formation events

    NASA Astrophysics Data System (ADS)

    Manninen, H. E.; Nieminen, T.; Asmi, E.; Gagné, S.; Häkkinen, S.; Lehtipalo, K.; Aalto, P.; Vana, M.; Mirme, A.; Mirme, S.; Hõrrak, U.; Plass-Dülmer, C.; Stange, G.; Kiss, G.; Hoffer, A.; Törő, N.; Moerman, M.; Henzing, B.; de Leeuw, G.; Brinkenberg, M.; Kouvarakis, G. N.; Bougiatioti, A.; Mihalopoulos, N.; O'Dowd, C.; Ceburnis, D.; Arneth, A.; Svenningsson, B.; Swietlicki, E.; Tarozzi, L.; Decesari, S.; Facchini, M. C.; Birmili, W.; Sonntag, A.; Wiedensohler, A.; Boulon, J.; Sellegri, K.; Laj, P.; Gysel, M.; Bukowiecki, N.; Weingartner, E.; Wehrle, G.; Laaksonen, A.; Hamed, A.; Joutsensaari, J.; Petäjä, T.; Kerminen, V.-M.; Kulmala, M.

    2010-08-01

    We present comprehensive results on continuous atmospheric cluster and particle measurements in the size range ~1-42 nm within the European Integrated project on Aerosol Cloud Climate and Air Quality interactions (EUCAARI) project. We focused on characterizing the spatial and temporal variation of new particle formation events and relevant particle formation parameters across Europe. Different types of air ion and cluster mobility spectrometers were deployed at 12 field sites across Europe from March 2008 to May 2009. The measurements were conducted in a wide variety of environments, including coastal and continental locations as well as sites at different altitudes (both in the boundary layer and the free troposphere). New particle formation events were detected at all of the 12 field sites during the year-long measurement period. From the data, nucleation and growth rates of newly formed particles were determined for each environment. In a case of parallel ion and neutral cluster measurements, we could also estimate the relative contribution of ion-induced and neutral nucleation to the total particle formation. The formation rates of charged particles at 2 nm accounted for 1-30% of the corresponding total particle formation rates. As a significant new result, we found out that the total particle formation rate varied much more between the different sites than the formation rate of charged particles. This work presents, so far, the most comprehensive effort to experimentally characterize nucleation and growth of atmospheric molecular clusters and nanoparticles at ground-based observation sites on a continental scale.

  19. Effects of Abasic Sites on Triple Helix Formation Characterized by Affinity Cleaving

    DTIC Science & Technology

    1991-06-01

    DNA . The influence of abasic sites in Watson - Crick double helical DNA has been characterized by spectroscopic and calorimetric techniques. (9-12) Two...alter- nate strands of duplex DNA by triple- helix formation (7). the detign ,-f rnmillm ra bases for completion of the triplet code, and the incorporation...prepared in order to compare the relative stabilities of triple helix formation 3 with 30-bp DNA duplexes containing the 15 base pair target sites d

  20. Simultaneous measurements of new particle formation at 1 s time resolution at a street site and a rooftop site

    NASA Astrophysics Data System (ADS)

    Zhu, Yujiao; Yan, Caiqing; Zhang, Renyi; Wang, Zifa; Zheng, Mei; Gao, Huiwang; Gao, Yang; Yao, Xiaohong

    2017-08-01

    This study is the first to use two identical Fast Mobility Particle Sizers for simultaneous measurement of particle number size distributions (PNSDs) at a street site and a rooftop site within 500 m distance in wintertime and springtime to investigate new particle formation (NPF) in Beijing. The collected datasets at 1 s time resolution allow deduction of the freshly emitted traffic particle signal from the measurements at the street site and thereby enable the evaluation of the effects on NPF in an urban atmosphere through a site-by-site comparison. The number concentrations of 8 to 20 nm newly formed particles and the apparent formation rate (FR) in the springtime were smaller at the street site than at the rooftop site. In contrast, NPF was enhanced in the wintertime at the street site with FR increased by a factor of 3 to 5, characterized by a shorter NPF time and higher new particle yields than at the rooftop site. Our results imply that the street canyon likely exerts distinct effects on NPF under warm or cold ambient temperature conditions because of on-road vehicle emissions, i.e., stronger condensation sinks that may be responsible for the reduced NPF in the springtime but efficient nucleation and partitioning of gaseous species that contribute to the enhanced NPF in the wintertime. The occurrence or absence of apparent growth for new particles with mobility diameters larger than 10 nm was also analyzed. The oxidization of biogenic organics in the presence of strong photochemical reactions is suggested to play an important role in growing new particles with diameters larger than 10 nm, but sulfuric acid is unlikely to be the main species for the apparent growth. However, the number of datasets used in this study is relatively small, and larger datasets are essential to draw a general conclusion.

  1. OceanSITES format and Ocean Observatory Output harmonisation: past, present and future

    NASA Astrophysics Data System (ADS)

    Pagnani, Maureen; Galbraith, Nan; Diggs, Stephen; Lankhorst, Matthias; Hidas, Marton; Lampitt, Richard

    2015-04-01

    The Global Ocean Observing System (GOOS) initiative was launched in 1991, and was the first step in creating a global view of ocean observations. In 1999 oceanographers at the OceanObs conference envisioned a 'global system of eulerian observatories' which evolved into the OceanSITES project. OceanSITES has been generously supported by individual oceanographic institutes and agencies across the globe, as well as by the WMO-IOC Joint Technical Commission for Oceanography and Marine Meteorology (under JCOMMOPS). The project is directed by the needs of research scientists, but has a strong data management component, with an international team developing content standards, metadata specifications, and NetCDF templates for many types of in situ oceanographic data. The OceanSITES NetCDF format specification is intended as a robust data exchange and archive format specifically for time-series observatory data from the deep ocean. First released in February 2006, it has evolved to build on and extend internationally recognised standards such as the Climate and Forecast (CF) standard, BODC vocabularies, ISO formats and vocabularies, and in version 1.3, released in 2014, ACDD (Attribute Convention for Dataset Discovery). The success of the OceanSITES format has inspired other observational groups, such as autonomous vehicles and ships of opportunity, to also use the format and today it is fulfilling the original concept of providing a coherent set of data from eurerian observatories. Data in the OceanSITES format is served by 2 Global Data Assembly Centres (GDACs), one at Coriolis, in France, at ftp://ftp.ifremer.fr/ifremer/oceansites/ and one at the US NDBC, at ftp://data.ndbc.noaa.gov/data/oceansites/. These two centres serve over 26,800 OceanSITES format data files from 93 moorings. The use of standardised and controlled features enables the files held at the OceanSITES GDACs to be electronically discoverable and ensures the widest access to the data. The OceanSITES

  2. EUCAARI ion spectrometer measurements at 12 European sites - analysis of new-particle formation events

    NASA Astrophysics Data System (ADS)

    Manninen, H. E.; Nieminen, T.; Asmi, E.; Gagné, S.; Häkkinen, S.; Lehtipalo, K.; Aalto, P.; Vana, M.; Mirme, A.; Mirme, S.; Hõrrak, U.; Plass-Dülmer, C.; Stange, G.; Kiss, G.; Hoffer, A.; TörH{O}, N.; Moerman, M.; Henzing, B.; de Leeuw, G.; Brinkenberg, M.; Kouvarakis, G. N.; Bougiatioti, A.; Mihalopoulos, N.; O'Dowd, C.; Ceburnis, D.; Arneth, A.; Svenningsson, B.; Swietlicki, E.; Tarozzi, L.; Decesari, S.; Facchini, M. C.; Birmili, W.; Sonntag, A.; Wiedensohler, A.; Boulon, J.; Sellegri, K.; Laj, P.; Gysel, M.; Bukowiecki, N.; Weingartner, E.; Wehrle, G.; Laaksonen, A.; Hamed, A.; Joutsensaari, J.; Petäjä, T.; Kerminen, V.-M.; Kulmala, M.

    2010-04-01

    We present comprehensive results on continuous atmospheric cluster and particle measurements in the size range ~1-42 nm within the European Integrated project on Aerosol Cloud Climate and Air Quality interactions (EUCAARI) project. We focused on characterizing the spatial and temporal variation of new-particle formation events and relevant particle formation parameters across Europe. Different types of air ion and cluster mobility spectrometers were deployed at 12 field sites across Europe from March 2008 to May 2009. The measurements were conducted in a wide variety of environments, including coastal and continental locations as well as sites at different altitudes (both in the boundary layer and the free troposphere). New-particle formation events were detected at all of the 12 field sites during the year-long measurement period. From the data, nucleation and growth rates of newly-formed particles were determined for each environment. In a case of parallel ion and neutral cluster measurements, we could also estimate the relative contribution of ion-induced and neutral nucleation to the total particle formation. The formation rates of charged particles at 2 nm accounted for 1-30% of the respective total particle formation rates. As a significant new result, we found out that the total particle formation rate varied much more between the different sites than the formation rate of charged particles. This work presents, so far, the most comprehensive effort to experimentally characterize nucleation and growth of atmospheric molecular clusters and nanoparticles at ground-based observation sites on a continental scale.

  3. Molecular Dynamics Simulations of Solvation and Kink Site Formation at the {001} Barite-Water Interface.

    SciTech Connect

    Stack, Andrew G

    2009-09-01

    Solvation and kink site formation on step edges are known to be controlling parameters in crystal growth and dissolution. However, links from classical crystal growth models to specific reactions at the mineral-water interface have remained elusive. Molecular dynamics is used here to examine the water structure on barium surface sites and kink site formation enthalpies for material adsorbed to and removed from the step parallel to the [120] direction on the {001} barite-water interface. The bariums at the interface are shown to be coordinatively unsaturated with respect to water, and it is suggested that this is due to a steric hindrance from the nature of the interface. Kink site detachment energies that include hydration energies are endothermic for barium and exothermic for sulfate. The implications and problems of using these parameters in a crystal growth model are discussed.

  4. Site and bond selective H- formation in methylated pyrimidine bases driven by potassium molecule collisions

    NASA Astrophysics Data System (ADS)

    Ferreira da Silva, F.; Almeida, D.; Martins, G.; Nunes, Y.; Garcia, G.; Limão-Vieira, P.

    2012-11-01

    In this study we present for the first time site (N1-H / N3-H) and bond (N-H / C-H) selectivity of H- formation in 1-methylthymine, 3-methyluracil and deuterated thymine (C positions) triggered by potassium molecule collisions. By comparing the H loss of these molecules with H loss in thymine and uracil and setting the energy one can predict site and bond selectivity in these set of molecules.

  5. New investigations at Kalambo Falls, Zambia: Luminescence chronology, site formation, and archaeological significance.

    PubMed

    Duller, Geoff A T; Tooth, Stephen; Barham, Lawrence; Tsukamoto, Sumiko

    2015-08-01

    Fluvial deposits can provide excellent archives of early hominin activity but may be complex to interpret, especially without extensive geochronology. The Stone Age site of Kalambo Falls, northern Zambia, has yielded a rich artefact record from dominantly fluvial deposits, but its significance has been restricted by uncertainties over site formation processes and a limited chronology. Our new investigations in the centre of the Kalambo Basin have used luminescence to provide a chronology and have provided key insights into the geomorphological and sedimentological processes involved in site formation. Excavations reveal a complex assemblage of channel and floodplain deposits. Single grain quartz optically stimulated luminescence (OSL) measurements provide the most accurate age estimates for the youngest sediments, but in older deposits the OSL signal from some grains is saturated. A different luminescence signal from quartz, thermally transferred OSL (TT-OSL), can date these older deposits. OSL and TT-OSL results are combined to provide a chronology for the site. Ages indicate four phases of punctuated deposition by the dominantly laterally migrating and vertically aggrading Kalambo River (∼500-300 ka, ∼300-50 ka, ∼50-30 ka, ∼1.5-0.49 ka), followed by deep incision and renewed lateral migration at a lower topographic level. A conceptual model for site formation provides the basis for improved interpretation of the generation, preservation, and visibility of the Kalambo archaeological record. This model highlights the important role of intrinsic meander dynamics in site formation and does not necessarily require complex interpretations that invoke periodic blocking of the Kalambo River, as has previously been suggested. The oldest luminescence ages place the Mode 2/3 transition between ∼500 and 300 ka, consistent with other African and Asian sites where a similar transition can be found. The study approach adopted here can potentially be applied to other

  6. Salivary glands act as mucosal inductive sites via the formation of ectopic germinal centers after site-restricted MCMV infection

    PubMed Central

    Grewal, Jasvir S.; Pilgrim, Mark J.; Grewal, Suman; Kasman, Laura; Werner, Phillip; Bruorton, Mary E.; London, Steven D.; London, Lucille

    2011-01-01

    We investigated the hypothesis that salivary gland inoculation stimulates formation of ectopic germinal centers (GCs), transforming the gland into a mucosal inductive site. Intraglandular infection of mice with murine cytomegalovirus (MCMV; control: UV-inactivated MCMV) induces salivary gland ectopic follicles comprising cognate interactions between CD4+ and B220+ lymphocytes, IgM+ and isotype-switched IgG+ and IgA+ B cells, antigen presenting cells, and follicular dendritic cells. B cells coexpressed the GC markers GCT (57%) and GL7 (52%), and bound the lectin peanut agglutinin. Lymphoid follicles were characterized by a 2- to 3-fold increase in mRNA for CXCL13 (lymphoid neogenesis), syndecan-1 (plasma cells), Blimp-1 (plasma cell development/differentiation), and a 2- to 6-fold increase for activation-induced cytidine deaminase, PAX5, and the nonexcised rearranged DNA of an IgA class-switch event, supporting somatic hypermutation and class-switch recombination within the salivary follicles. Intraglandular inoculation also provided protection against a systemic MCMV challenge, as evidenced by decreased viral titers (105 plaque-forming units to undetectable), and restoration of normal salivary flow rates from a 6-fold decrease. Therefore, these features suggest that the salivary gland participates in oral mucosal immunity via generation of ectopic GCs, which function as ectopic mucosal inductive sites.—Grewal, J. S., Pilgrim, M. J., Grewal, S., Kasman, L., Werner, P., Bruorton, M. E., London, S. D., London, L. Salivary glands act as mucosal inductive sites via the formation of ectopic germinal centers after site-restricted MCMV infection. PMID:21307334

  7. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    NASA Astrophysics Data System (ADS)

    Ma, Kun; Cui, Qinghua; Liu, Guiying; Wu, Fei; Xu, Shujuan; Shao, Yong

    2011-07-01

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  8. Hydraulic testing of Salado Formation evaporites at the Waste Isolation Pilot Plant site: Second interpretive report

    SciTech Connect

    Beauheim, R.L.; Roberts, R.M.; Dale, T.F.; Fort, M.D.; Stensrud, W.A.

    1993-12-01

    Pressure-pulse, constant-pressure flow, and pressure-buildup tests have been performed in bedded evaporites of the Salado Formation at the Waste Isolation Pilot Plant (WIPP) site to evaluate the hydraulic properties controlling brine flow through the Salado. Transmissivities have been interpreted from six sequences of tests conducted on five stratigraphic intervals within 15 m of the WIPP underground excavations.

  9. Insertion site and sealing technique affect residual hearing and tissue formation after cochlear implantation.

    PubMed

    Burghard, Alice; Lenarz, Thomas; Kral, Andrej; Paasche, Gerrit

    2014-06-01

    Tissue formation around the electrode array of a cochlear implant has been suggested to influence preservation of residual hearing as well as electrical hearing performance of implanted subjects. Further, inhomogeneity in the electrical properties of the scala tympani shape the electrical field and affect current spread. Intracochlear trauma due to electrode insertion and the insertion site itself are commonly seen as triggers for the tissue formation. The present study investigates whether the insertion site, round window membrane (RWM) vs. cochleostomy (CS), or the sealing material, no seal vs. muscle graft vs. carboxylate cement, have an influence on the amount of fibrous tissue and/or new bone formation after CI implantation in the guinea pig. Hearing thresholds were determined by auditory brainstem response (ABR) measurements prior to implantation and after 28 days. The amount of tissue formation was quantified by evaluation of microscopic images obtained by a grinding/polishing procedure to keep the CI in place during histological processing. An insertion via the round window membrane resulted after 28 days in less tissue formation in the no seal and muscle seal condition compared to the cochleostomy approach. Between these two sealing techniques there was no difference. Sealing the cochlea with carboxylate cement resulted always in a strong new bone formation and almost total loss of residual hearing. The amount of tissue formation and the hearing loss correlated at 1-8 kHz. Consequently, the use of carboxylate cement as a sealing material in cochlear implantation should be avoided even in animal studies, whereas sealing the insertion site with a muscle graft did not induce an additional tissue growth compared to omitting a seal. For hearing preservation the round window approach should be used.

  10. Mineral abundances at the final four curiosity study sites and implications for their formation

    NASA Astrophysics Data System (ADS)

    Poulet, F.; Carter, J.; Bishop, J. L.; Loizeau, D.; Murchie, S. M.

    2014-03-01

    A component of the landing site selection process for the Mars Science Laboratory (MSL) involved the presence of phyllosilicates as the main astrobiological targets. Gale crater was selected as the MSL landing site from among 4 down selected study sites (Gale, Eberswalde and Holden craters, Mawrth Vallis) that addressed the primary scientific goal of assessing the past habitability of Mars. A key constraint on the formation process of these phyllosilicate-bearing deposits is in the precise mineralogical composition. We present a reassessment of the mineralogy of the sites combined with a determination of the modal mineralogy of the major phyllosilicate-bearing deposits of the four final study sites from the modeling of near-infrared spectra using a radiative transfer model. The largest abundance of phyllosilicates (30-70%) is found in Mawrth Vallis, the lowest one in Eberswalde (<25%). Except for Mawrth Vallis, the anhydrous phases (plagioclase, pyroxenes and martian dust) are the dominant phases, suggesting formation conditions with a lower alteration grade and/or a post-formation mixing with anhydrous phases. The composition of Holden layered deposits (mixture of saponite and micas with a total abundance in the range of 25-45%) suggests transport and deposition of altered basalts of the Noachian crust without major chemical transformation. For Eberswalde, the modal mineralogy is also consistent with detrital clays, but the presence of opaline silica indicates that an authigenic formation occurred during the deposition. The overall composition including approximately 20-30% smectite detected by MSL in the rocks of Yellow-knife Bay area interpreted to be material deposited on the floor of Gale crater by channels (http://www.nasa.gov/mission_pages/msl/news/msl20130312.html).

  11. Authigenic Carbonate Formation on the Peru Margin; New Insights from IODP Site 1230

    NASA Astrophysics Data System (ADS)

    Abdullajintakam, S.; Naehr, T. H.

    2015-12-01

    Fluid seepage of reduced organic compounds such as methane impacts the geology and biology of the seabed by inducing complex, microbially mediated biogeochemical processes. Authigenic carbonates serve as one of the few permanent records of these of dynamic biogeochemical interactions that involve methanogenesis, methanotrophy, sulfate reduction and carbonate precipitation. Meister et al. (2007) investigated deep-sea dolomite formation at Sites 1227-1229 on the Peru margin, where dolomite precipitation occurs in association with organic carbon-rich continental margin sediments. Geochemical and petrographic studies indicated episodic dolomite precipitation at a dynamic sulfate methane transition zone (SMTZ). Variations in δ13C values of these dolomites between +15‰ and -15‰ were attributed to non-steady state conditions as a result of the upward and downward migration of the SMTZ. Our study aims to better understand the biogeochemical processes associated with authigenic carbonate precipitation in this dynamic deep-sea setting. We focused our efforts on IODP Site 1230, which is a gas-hydrate-bearing site that shows sulphate consumption within the uppermost 10 m below the seafloor as well as high methane production. Using a multi proxy approach, we combined X-ray diffraction, stable isotope geochemistry, and trace metal analysis of authigenic carbonates to elucidate conditions for authigenic carbonate formation. Results from Site 1230 are compared to Sites 1227 and 1229, which lacks gas hydrates and is characterized by high pore water sulfate and low methane concentrations. This study contributes to a more comprehensive understanding of authigenic carbonate formation and associated biogeochemical processes in continental margin sediments. Meister, P., Mckenzie, J. A., Vasconcelos, C., Bernasconi, S., Frank, M., Gutjhar, M. and SCHRAG, D. P. (2007), Dolomite formation in the dynamic deep biosphere: results from the Peru Margin. Sedimentology, 54: 1007-1032.

  12. Cytosine containing dipyrimidine sites can be hotspots of cyclobutane pyrimidine dimer formation after UVB exposure.

    PubMed

    Bastien, Nathalie; Therrien, Jean-Philippe; Drouin, Régen

    2013-08-01

    Exposure to the UV component of sunlight is the principal factor leading to skin cancer development. Cyclobutane pyrimidine dimers (CPD) are considered to be the most important pre-mutagenic type of DNA damage involved in skin carcinogenesis. To better understand the biological mechanisms of UV carcinogenesis, it is critical to understand the CPD distribution between the four types of dipyrimidine sites. Most of our knowledge regarding CPD distribution comes from in vitro studies or from investigations using UVC, even though we are not naturally exposed to these UV wavelengths. We exposed normal human fibroblasts and purified DNA to UVB. Using ligation-mediated PCR, we quantified the CPD formation at 952 dipyrimidine sites among the PGK1 (phosphoglycerate kinase 1), JUN, HRAS, KRAS, NRAS and TP53 genes. In cellulo, we found a CPD distribution of 27 : 27 : 25 : 21 for TT : CC : TC : CT. This distribution is similar to that observed in vitro. In the analysed genes, we observed some extremely frequently damaged dipyrimidine sites and many of these occurred at potentially frequently mutated sites, i.e. at dipyrimidine sites containing cytosine. Also, most of the frequently damaged dipyrimidine sites in cellulo that are not frequently damaged in vitro are found on TP53 and NRAS. This indicates that many of the frequently damaged dipyrimidine sites in cellulo are on genes frequently mutated in skin cancer. All these results support the view that CPD are the main UVB-induced mutagenic photoproducts and provide evidence of the importance of CPD formation at sites containing cytosine.

  13. A novel mechanism for Prp5 function in prespliceosome formation and proofreading the branch site sequence

    PubMed Central

    Liang, Wen-Wei; Cheng, Soo-Chen

    2015-01-01

    The DEAD-box RNA helicase Prp5 is required for the formation of the prespliceosome through an ATP-dependent function to remodel U2 small nuclear ribonucleoprotein particles (snRNPs) and an ATP-independent function of unknown mechanism. Prp5 has also been implicated in proofreading the branch site sequence, but the molecular mechanism has not been well characterized. Using actin precursor mRNA (pre-mRNA) carrying branch site mutations, we identified a Prp5-containing prespliceosome with Prp5 directly bound to U2 small nuclear RNA (snRNA). Prp5 is in contact with U2 in regions on and near the branchpoint-interacting stem–loop (BSL), suggesting that Prp5 may function in stabilizing the BSL. Regardless of its ATPase activity, Prp5 mutants that suppress branch site mutations associate with the spliceosome less tightly and allow more tri-snRNP binding for the reaction to proceed. Our results suggest a novel mechanism for how Prp5 functions in prespliceosome formation and proofreading of the branch site sequence. Prp5 binds to the spliceosome in association with U2 by interacting with the BSL and is released upon the base-pairing of U2 with the branch site to allow the recruitment of the tri-snRNP. Mutations impairing U2–branch site base-pairing retard Prp5 release and impede tri-snRNP association. Prp5 mutations that destabilize the Prp5–U2 interaction suppress branch site mutations by allowing progression of the pathway. PMID:25561497

  14. Site formation and chronology of the new Paleolithic site Sima de Las Palomas de Teba, southern Spain

    NASA Astrophysics Data System (ADS)

    Kehl, Martin; Burow, Christoph; Cantalejo, Pedro; Domínguez-Bella, Salvador; Durán, Juan José; Henselowsky, Felix; Klasen, Nicole; Linstädter, Jörg; Medianero, Javier; Pastoors, Andreas; Ramos, José; Reicherter, Klaus; Schmidt, Christoph; Weniger, Gerd-Christian

    2016-03-01

    The newly identified Paleolithic site Sima de Las Palomas de Teba hosts an almost seven-m-thick sediment profile investigated here to elucidate the rock shelter's chronostratigraphy and formation processes. At its base, the sediment sequence contains rich archeological deposits recording intensive occupation by Neanderthals. Luminescence provides a terminus ante quem of 39.4 ± 2.6 ka or 44.9 ± 4.1 ka (OSL) and 51.4 ± 8.4 ka (TL). This occupation ended with a rockfall event followed by accumulation of archeologically sterile sediments. These were covered by sediments containing few Middle Paleolithic artifacts, which either indicate ephemeral occupation by Neanderthals or reworking as suggested by micromorphological features. Above this unit, scattered lithic artifacts of undiagnostic character may represent undefined Paleolithic occupations. Sediment burial ages between about 23.0 ± 1.5 ka (OSL) and 40.5 ± 3.4 ka (pIRIR) provide an Upper Paleolithic chronology for sediments deposited above the rockfall. Finally, a dung-bearing Holocene layer in the uppermost part of the sequence contains a fragment of a human mandible dated to 4032 ± 39 14C yr BP. Overall, the sequence represents an important new site for studying the end of Neanderthal occupation in southern Spain.

  15. Inhibition by alcohols of the localization of radioactive nitrosonornicotine in sites of tumor formation

    SciTech Connect

    Waddell, W.J.; Marlowe, C.

    1983-06-01

    Oral administration of ethanol, n-butanol, or t-butanol to mice 20 minutes before injection of carbon-14-labeled nitrosonornicotine inhibited the localization of radioactivity in bronchial and salivary duct epithelium and in the liver. Localization of radioactivity in the nasal epithelium and esophagus was not significantly reduced. These alcohols therefore may selectively inhibit tumor formation in three of the five sites where this carcinogen typically acts.

  16. Osterix regulates tooth root formation in a site-specific manner.

    PubMed

    Kim, T H; Bae, C H; Lee, J C; Kim, J E; Yang, X; de Crombrugghe, B; Cho, E S

    2015-03-01

    Bone and dentin share similar biochemical compositions and physiological properties. Dentin, a major tooth component, is formed by odontoblasts; in contrast, bone is produced by osteoblasts. Osterix (Osx), a zinc finger-containing transcription factor, has been identified as an essential regulator of osteoblast differentiation and bone formation. However, it has been difficult to establish whether Osx functions in odontoblast differentiation and dentin formation. To understand the role of Osx in dentin formation, we analyzed mice in which Osx was subjected to tissue-specific ablation under the control of either the Col1a1 or the OC promoter. Two independent Osx conditional knockout mice exhibited similar molar abnormalities. Although no phenotype was found in the crowns of these teeth, both mutant lines exhibited short molar roots due to impaired root elongation. Furthermore, the interradicular dentin in these mice showed severe hypoplastic features, which were likely caused by disruptions in odontoblast differentiation and dentin formation. These phenotypes were closely related to the temporospatial expression pattern of Osx during tooth development. These findings indicate that Osx is required for root formation by regulating odontoblast differentiation, maturation, and root elongation. Cumulatively, our data strongly indicate that Osx is a site-specific regulator in tooth root formation.

  17. Localized arteriole formation directly adjacent to the site of VEGF-induced angiogenesis in muscle.

    PubMed

    Springer, Matthew L; Ozawa, Clare R; Banfi, Andrea; Kraft, Peggy E; Ip, Tze-Kin; Brazelton, Timothy R; Blau, Helen M

    2003-04-01

    We have shown previously that implantation of myoblasts constitutively expressing the VEGF-A gene into nonischemic mouse skeletal muscle leads to overgrowth of capillary-like blood vessels and hemangioma formation. These aberrant effects occurred directly at the implantation site. We show here that these regions result from angiogenic capillary growth and involve a change in capillary growth pattern and that smooth muscle-coated vessels similar to arterioles form directly adjacent to the implantation site. Myoblasts genetically engineered to produce VEGF were implanted into mouse leg muscles. Implantation sites were surrounded by a zone of dense capillary-sized vessels, around which was a second zone of muscle containing larger, smooth-muscle-covered vessels but few capillaries, and an outer zone of muscle exhibiting normal capillary density. The lack of capillaries in the middle region suggests that the preexisting capillaries adjacent to the implantation site underwent enlargement and/or fusion and recruited a smooth muscle coat. Capillaries at the implantation site were frequently wrapped around VEGF-producing muscle fibers and were continuous with the circulation and were not observed to include bone-marrow-derived endothelial cells. In contrast with the distant arteriogenesis resulting from VEGF delivery described in previous studies, we report here that highly localized arterioles also form adjacent to the site of delivery.

  18. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

    SciTech Connect

    Lin, Xueju; Kennedy, David W.; Fredrickson, Jim K.; Bjornstad, Bruce N.; Konopka, Allan

    2011-11-29

    Microbial diversity in subsurface sediments at the Hanford Site 300 Area near Richland, Washington State (USA) was investigated by analyzing samples recovered from depths of 9 to 52 m. Approximately 8000 near full-length 16S rRNA gene sequences were analyzed across geological strata that include a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (Operational Taxonomic Units at the 97% identity level), respectively. Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (Chao1 estimator) was highest (>700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic interface, richness was about 325 and declined to less than 50 in the deeper reduced zones. The deeper Ringold strata were characterized by a preponderance (ca. 90%) of Proteobacteria. The Bacterial community in the oxic sediments contained not only members of 9 well-recognized phyla but also an unusually high proportion of 3 candidate divisions (GAL15, NC10, and SPAM). Additionally, novel phylogenetic orders were identified within the Delta-proteobacteria, a clade rich in microbes that carry out redox transformations of metals that are important contaminants on the Hanford Site.

  19. Temporal analysis of recruitment of mammalian ATG proteins to the autophagosome formation site.

    PubMed

    Koyama-Honda, Ikuko; Itakura, Eisuke; Fujiwara, Takahiro K; Mizushima, Noboru

    2013-10-01

    Autophagosome formation is governed by sequential functions of autophagy-related (ATG) proteins. Although their genetic hierarchy in terms of localization to the autophagosome formation site has been determined, their temporal relationships remain largely unknown. In this study, we comprehensively analyzed the recruitment of mammalian ATG proteins to the autophagosome formation site by live-cell imaging, and determined their temporal relationships. Although ULK1 and ATG5 are separated in the genetic hierarchy, they synchronously accumulate at pre-existing VMP1-positive punctate structures, followed by recruitment of ATG14, ZFYVE1, and WIPI1. Only a small number of ATG9 vesicles appear to be associated with these structures. Finally, LC3 and SQSTM1/p62 accumulate synchronously, while the other ATG proteins dissociate from the autophagic structures. These results suggest that autophagosome formation takes place on the VMP1-containing domain of the endoplasmic reticulum or a closely related structure, where ULK1 and ATG5 complexes are synchronously recruited.

  20. Secondary new particle formation in Northern Finland Pallas site between the years 2000 and 2010

    NASA Astrophysics Data System (ADS)

    Asmi, E.; Kivekäs, N.; Kerminen, V.-M.; Komppula, M.; Hyvärinen, A.-P.; Hatakka, J.; Viisanen, Y.; Lihavainen, H.

    2011-09-01

    Secondary new particle formation affects atmospheric aerosol and cloud droplet numbers and thereby, the aerosol effects on climate. In this paper, the frequency of nucleation events and the associated particle formation and growth rates, along with their seasonal variation, was analysed based on over ten years of aerosol measurements conducted at the Pallas GAW station in northern Finland. The long-term measurements also allowed a detailed examination of factors possibly favouring or suppressing particle formation. Effects of meteorological parameters and air mass properties as well as vapour sources and sinks for particle formation frequency and event parameters were inspected. In addition, the potential of secondary particle formation to increase the concentration of cloud condensation nuclei (CCN) sized particles was examined. Findings from these long-term measurements confirmed previous observations: event frequency peaked in spring and the highest growth rates were observed in summer, affiliated with increased biogenic activity. Events were almost exclusively observed in marine air masses on sunny cloud-free days. A low vapour sink by the background particle population as well as an elevated sulphuric acid concentration were found to favour particle formation. These were also conditions taking place most likely in marine air masses. Inter-annual trend showed a minimum in event frequency in 2003, when also the smallest annual median of growth rate was observed. This gives further evidence of the importance and sensitivity of particle formation for the condensing vapour concentrations at Pallas site. The particle formation was observed to increase CCN80 (>80 nm particle number) concentrations especially in summer and autumn seasons when the growth rates were the highest. When the growing mode exceeded the selected 80 nm limit, on average in those cases, 211 ± 114 % increase of CCN80 concentrations was observed.

  1. Secondary new particle formation in Northern Finland Pallas site between the years 2000 and 2010

    NASA Astrophysics Data System (ADS)

    Asmi, E.; Kivekäs, N.; Kerminen, V.-M.; Komppula, M.; Hyvärinen, A.-P.; Hatakka, J.; Viisanen, Y.; Lihavainen, H.

    2011-12-01

    Secondary new particle formation affects atmospheric aerosol and cloud droplet numbers and thereby, the aerosol effects on climate. In this paper, the frequency of nucleation events and the associated particle formation and growth rates, along with their seasonal variation, was analysed based on over ten years of aerosol measurements conducted at the Pallas GAW station in northern Finland. The long-term measurements also allowed a detailed examination of factors possibly favouring or suppressing particle formation. Effects of meteorological parameters and air mass properties as well as vapour sources and sinks for particle formation frequency and event parameters were inspected. In addition, the potential of secondary particle formation to increase the concentration of cloud condensation nuclei (CCN) sized particles was examined. Findings from these long-term measurements confirmed previous observations: event frequency peaked in spring and the highest growth rates were observed in summer, affiliated with increased biogenic activity. Events were almost exclusively observed in marine air masses on sunny cloud-free days. A low vapour sink by the background particle population as well as an elevated sulphuric acid concentration were found to favour particle formation. These were also conditions taking place most likely in marine air masses. Inter-annual trend showed a minimum in event frequency in 2003, when also the smallest annual median of growth rate was observed. This gives further evidence of the importance and sensitivity of particle formation for the condensing vapour concentrations at Pallas site. The particle formation was observed to increase CCN80 (>80 nm particle number) concentrations especially in summer and autumn seasons when the growth rates were the highest. When the growing mode exceeded the selected 80 nm limit, on average in those cases, 211 ± 114% increase of CCN80 concentrations was observed.

  2. Characteristics of formation and growth of atmospheric nanoparticles observed at four regional background sites in Korea

    NASA Astrophysics Data System (ADS)

    Kim, Yumi; Kim, Sang-Woo; Yoon, Soon-Chang; Park, Jin-Soo; Lim, Jae-Hyun; Hong, Jihyung; Lim, Han-Cheol; Ryu, Jegyu; Lee, Chul-Kyu; Heo, Bok-Haeng

    2016-02-01

    Measurements of the number concentration and size distribution of atmospheric nanoparticles were conducted at four sites on the west coast of the Korean Peninsula by using identical scanning mobility particle sizers (SMPSs) in October 2012. The new particle formation and subsequent growth (NPF) of atmospheric nanoparticles, which were identified by the cyclostationary empirical orthogonal function (CSEOF) analysis technique, was observed on 11 out of 21 days at the Baengnyeong-do Comprehensive Monitoring Observatory (BCMO); and on 10 out of 21 days at the Korea Global Atmosphere Watch Center (KGAWC) from October 9 to 29, 2012. We also observed NPF events for 9 out of 21 days at both the Gosan Climate Observatory (GCO) and the Jeju Comprehensive Monitoring Observatory (JCMO). During the study period, NPF was simultaneously observed for five days at all four sites, which indicates that the NPF event had a spatial extent of at least 540 km. A cold, dry and cloud-free continental air mass originated from northern China, formed favorable environmental conditions (e.g., increasing solar insolation at the surface) on simultaneous NPF at the four sites. These synoptic weather patterns were closely associated with an extraordinary typhoon passing over the south of Japan. The mean values of particle formation rates at BCMO (1.26 cm- 3 s- 1) and KGAWC (1.49 cm- 3 s- 1) were relatively higher than those at GCO (0.39 cm- 3 s- 1) and JCMO (0.74 cm- 3 s- 1), however, the growth rate showed a similar level among four sites. An increase in the spatial homogeneity and inter-site correlation of atmospheric particles among the four sites was apparent for small particles (diameter < 30 nm) on simultaneous NPF event days.

  3. Geoarchaeological investigation at Al-Khiday (central Sudan): late Quaternary palaeoenvironment and site formation

    NASA Astrophysics Data System (ADS)

    Zerboni, Andrea; Usai, Donatella; Salvatori, Sandro

    2010-05-01

    The micromorphological investigation on several pluristratified archaeological sites in central Sudan (Al-Khiday, left bank of the White Nile, Khartoum region, Sudan) permitted to elucidate depositional and post-depositional processes playing a role in the formation and preservation of the archaeological record. At Al-Khiday sites are located at the top of small mounds, representing the remains of Pleistocene sandy fluvial bars, and were attended since the beginning of the Holocene. The first occupation of the area corresponds to a pre-Mesolithic cemetery; than Mesolithic groups lived upon the mounds and their occupation is testified by several archaeological features: pits filled by ash and bones and living floors. Preserved Neolithic features are scarce and limited to few graves (V millennium BC). After this phase, a long gap in human attendance is registered, during which wind continued to dismantling the mounds and the sites; at ca. 2000 years BP Meroitic/Post-Meroitic groups built their tombs at the top of the archaeological sequences and altered most of the stratigraphic record. Thanks to micromorphology, it was possible to distinguish between archaeological strata still in situ and those disturbed by natural and anthropic processes; furthermore, this approach allowed to interpret the significance of several archaeological features (living floors, fireplaces, and garbage pits). In this case micromorphology of archaeological deposits was a key tool to reconstruct the depositional and post-depositional processes that contributed to the formation and preservation of the archaeological record.

  4. Tracing the sites of obscured star formation in the Antennae galaxies with Herschel-PACS

    NASA Astrophysics Data System (ADS)

    Klaas, U.; Nielbock, M.; Haas, M.; Krause, O.; Schreiber, J.

    2010-07-01

    Aims: FIR imaging of interacting galaxies allows locating even hidden sites of star formation and measuring of the relative strength of nuclear and extra-nuclear star formation. We want to resolve the star-forming sites in the nearby system of the Antennae. Methods: Thanks to the unprecedented sharpness and depth of the PACS camera onboard ESA's Herschel Space Observatory, it is possible for the first time to achieve a complete assessment of individual star-forming knots in the FIR with scan maps at 70, 100, and 160 μm. We used clump extraction photometry and SED diagnostics to derive the properties related to star-forming activity. Results: The PACS 70, 100, and 160 μm maps trace the knotty structure of the most recent star formation along an arc between the two nuclei in the overlap area. The resolution of the starburst knots and additional multi-wavelength data allow their individual star formation history and state to be analysed. In particular, the brightest knot in the mid-infrared (K1), east of the southern nucleus, exhibits the highest activity by far in terms of dust heating and star formation rate, efficiency, and density. With only 2 kpc in diameter, this area has a 10-1000 μm luminosity, which is as high as that of our Milky Way. It shows the highest deficiency in radio emission in the radio-to-FIR luminosity ratio and a lack of X-ray emission, classifying it as a very young complex. The brightest 100 and 160 μm emission region (K2), which is close to the collision front and consists of 3 knots, also shows a high star formation density and efficiency and lack of X-ray emission in its most obscured part, but an excess in the radio-to-FIR luminosity ratio. This suggests a young stage, too, but different conditions in its interstellar medium. Our results provide important checkpoints for numerical simulations of interacting galaxies when modelling the star formation and stellar feedback. Herschel is an ESA space observatory with science instruments

  5. Isomer ratio measurements for the reaction 29Si( 18O, p2n) 44m, 44gSc

    NASA Astrophysics Data System (ADS)

    Groening, H.; Aleklett, K.; Moody, K. J.; McGaughey, P. L.; Loveland, W.; Seaborg, G. T.

    1982-11-01

    Isomer ratios for the reaction 29Si( 18O, p2n) 44gSc, 44gSc have been deduced from activity measurements for projectile energies between 30 and 99 MeV. Statistical model calculations show that the isomer ratio dependence on projectile energy up to about 80 MeV can be adequately described by assuming a fixed ratio of quadrupole to dipole γ-ray strengths. Such a ratio of E2/E1 strengths agrees with corresponding values deduced from the literature. The values of the γ-ray strength ratios needed to fit the experimental isomer ratios are extremely sensitive to the relative amounts of quadrupole γ-ray admixture and to the presence of discrete levels other than those which conform to the yrast line.

  6. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

    SciTech Connect

    Lin, Xueju; Kennedy, David W.; Fredrickson, Jim K.; Bjornstad, Bruce N.; Konopka, Allan

    2012-02-01

    The microbial diversity in subsurface sediments at the Hanford Site's 300 Area in southeastern Washington State was investigated by analyzing 21 samples recovered from depths that ranged from 9 to 52 m. Approximately 8000 non-chimeric Bacterial and Archaeal 16S rRNA gene sequences were analyzed across geological strata that contain a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (Operational Taxonomic Units, defined at the 97% identity level). Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (based upon Chao1 estimator) was highest (>700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic transition zone, richness was about 325 and declined to less than 50 in the deeper reduced zones. The Bacterial community in the oxic Hanford and Ringold Formations contained members of 9 major well-recognized phyla as well 30 as unusually high proportions of 3 candidate divisions (GAL15, NC10, and SPAM). The deeper Ringold strata were characterized by low OTU richness and a very high preponderance (ca. 90%) of Proteobacteria. The study has greatly expanded the intralineage phylogenetic diversity within some major divisions. These subsurface sediments have been shown to contain a large number of phylogenetically novel microbes, with substantial heterogeneities between sediment samples from the same geological formation.

  7. VOC emissions, evolutions and contributions to SOA formation at a receptor site in eastern China

    NASA Astrophysics Data System (ADS)

    Yuan, B.; Hu, W. W.; Shao, M.; Wang, M.; Chen, W. T.; Lu, S. H.; Zeng, L. M.; Hu, M.

    2013-09-01

    Volatile organic compounds (VOCs) were measured by two online instruments (GC-FID/MS and PTR-MS) at a receptor site on Changdao Island (37.99° N, 120.70° E) in eastern China. Reaction with OH radical dominated chemical losses of most VOC species during the Changdao campaign. A photochemical-age-based parameterization method is used to calculate VOC emission ratios and to quantify the evolution of ambient VOCs. The calculated emission ratios of most hydrocarbons agree well with those obtained from emission inventory data, but determined emission ratios of oxygenated VOCs (OVOCs) are significantly higher than those from emission inventory data. The photochemical-age-based parameterization method is also used to investigate primary emissions and secondary formation of organic aerosol. The primary emission ratio of organic aerosol (OA) to CO is determined to be 14.9 μg m-3 ppm-1, and secondary organic aeorosols (SOA) are produced at an enhancement ratio of 18.8 μg m-3 ppm-1 to CO after 50 h of photochemical processing in the atmosphere. SOA formation is significantly higher than the level determined from VOC oxidation under both high-NOx (2.0 μg m-3 ppm-1 CO) and low-NOx conditions (6.5 μg m-3 ppm-1 CO). Polycyclic aromatic hydrocarbons (PAHs) and higher alkanes (> C10) account for as high as 17.4% of SOA formation, which suggests semi-volatile organic compounds (SVOCs) may be a large contributor to SOA formation during the Changdao campaign. The SOA formation potential of primary VOC emissions determined from field campaigns in Beijing and Pearl River Delta (PRD) is lower than the measured SOA levels reported in the two regions, indicating SOA formation is also beyond explainable by VOC oxidation in the two city clusters.

  8. Hydraulic Testing of Salado Formation Evaporites at the Waste Isolation Pilot Plant Site: Final Report

    SciTech Connect

    Beauheim, Richard L.; Domski, Paul S.; Roberts, Randall M.

    1999-07-01

    This report presents interpretations of hydraulic tests conducted in bedded evaporates of the Salado Formation from May 1992 through May 1995 at the Waste Isolation Pilot Plant (WIPP) site in southeastern New Mexico. The WIPP is a US Department of Energy research and development facility designed to demonstrate safe disposal of transuranic wastes from the nation's defense programs. The WIPP disposal horizon is located in the lower portion of the Permian Salado Formation. The hydraulic tests discussed in this report were performed in the WIPP underground facility by INTERA inc. (now Duke Engineering and Services, Inc.), Austin, Texas, following the Field Operations Plan and Addendum prepared by Saulnier (1988, 1991 ) under the technical direction of Sandia National Laboratories, Albuquerque, New Mexico.

  9. SITES OF FORMATION OF IMMUNE GLOBULINS AND OF A COMPONENT OF C'3

    PubMed Central

    Hochwald, G. M.; Thorbecke, G. J.; Asofsky, R.

    1961-01-01

    The development of a new method for the determination of the sites of serum protein formation has been described. The method involves the incorporation of C14-labeled amino acids by tissues cultured in vitro, and subsequent autoradiography of immunoelectrophoretic patterns prepared from a mixture of culture fluids and carrier serum with an antiserum against the carrier serum. This technique has been used to demonstrate formation of γ-globulin, of β2-macroglobulin, and of a component of C'3 by mouse spleen tissue, and of various other serum proteins by liver tissue. The specificity and sensitivity of this method have been discussed, and some of its advantages and pitfalls were mentioned. In addition, a rabbit antimouse serum was prepared, and the immunoelectrophoretic patterns obtained with mouse serum were compared with those described in the literature. PMID:19867195

  10. Posssibles sites for the formation of the planet at the γ-Cephei system

    NASA Astrophysics Data System (ADS)

    Aparecido de Moraes, Ricardo; Vieira Neto, Ernesto

    2015-08-01

    In the past years more and more extra-solar planets were discovered in binary star systems. All the planets discovered orbit the more massive star, and the companion star acts as a disturber body, these type of orbits are called S-type orbit, if the planet orbits the two stars the orbit is call P-type. It is not easy to study the formation of a planetary system around a single star, therefore it is a greater challenge to study the formation of a planetary system in a binary star system due to the gravitational effects of the secondary star, which is very close to the host star. In this work we will try to find the possibles sites for formation of the planetary system around the binary star system γ-Cephei adding the effects of the secondary star using fully hydrodynamical simulations to reproduce the formation of the planet, far from its real position, and its migration to near of its present position. We also analyze the eccentricity of the planet to see if our results are consistent with what is observed.

  11. Rapid On-Site Formation of a Free-Standing Flexible Optical Link for Sensing Applications

    PubMed Central

    Barrios, Carlos Angulo

    2016-01-01

    An optical link, based on a conventional Scotch tape waveguide, for sensing applications requiring rapid on-site assembly is proposed and demonstrated. The flexible waveguide contains an integrated aluminum one-dimensional grating coupler that, when stuck on the radiative surface of a light emitting device, allows light to be coupled in and transmitted through the tape, whose tip end is, in turn, adhered onto the photosensitive surface of a photodetector. The (de)coupling approaches exhibit high alignment tolerances that permit the formation of a free-standing flexible optical connection between surface-normal optoelectronic devices without the need of specialized equipment. As the first demonstration of a sensing application, the proposed optical link is easily configured as a cost-effective intensity-based refractometric sensor for liquid detection, which can be applicable to on-site quality and process control of, for example, beverages. PMID:27782049

  12. [Recruitment of osteogenic cells to bone formation sites during development and fracture repair - German Version].

    PubMed

    Böhm, A-M; Dirckx, N; Maes, C

    2016-04-01

    Recruitment of osteoblast lineage cells to their bone-forming locations is essential for skeletal development and fracture healing. In developing bones, osteoprogenitor cells invade the cartilage mold to establish the primary ossification center. Similarly, osteogenic cells infiltrate and populate the callus tissue that is formed following an injury. Proper bone development and successful fracture repair must, therefore, rely on controlled temporal and spatial navigation cues guiding the cells to the sites where new bone formation is needed. Some cellular mechanisms and molecular pathways involved have been elucidated.

  13. BOREAS TE-20 Soils Data Over the NSA-MSA and Tower Sites in Raster Format

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Veldhuis, Hugo; Knapp, David; Veldhuis, Hugo

    2000-01-01

    The BOREAS TE-20 team collected several data sets for use in developing and testing models of forest ecosystem dynamics. This data set was gridded from vector layers of soil maps that were received from Dr. Hugo Veldhuis, who did the original mapping in the field during 1994. The vector layers were gridded into raster files that cover the NSA-MSA and tower sites. The data are stored in binary, image format files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Center (DAAC).

  14. Assessment of the potential for karst in the Rustler Formation at the WIPP site.

    SciTech Connect

    Lorenz, John Clay

    2006-01-01

    This report is an independent assessment of the potential for karst dissolution in evaporitic strata of the Rustler Formation at the Waste Isolation Pilot Plant (WIPP) site. Review of the available data suggests that the Rustler strata thicken and thin across the area in depositional patterns related to lateral variations in sedimentary accommodation space and normal facies changes. Most of the evidence that has been offered for the presence of karst in the subsurface has been used out of context, and the different pieces are not mutually supporting. Outside of Nash Draw, definitive evidence for the development of karst in the Rustler Formation near the WIPP site is limited to the horizon of the Magenta Member in drillhole WIPP-33. Most of the other evidence cited by the proponents of karst is more easily interpreted as primary sedimentary structures and the localized dissolution of evaporitic strata adjacent to the Magenta and Culebra water-bearing units. Some of the cited evidence is invalid, an inherited baggage from studies made prior to the widespread knowledge of modern evaporite depositional environments and prior to the existence of definitive exposures of the Rustler Formation in the WIPP shafts. Some of the evidence is spurious, has been taken out of context, or is misquoted. Lateral lithologic variations from halite to mudstone within the Rustler Formation under the WIPP site have been taken as evidence for the dissolution of halite such as that seen in Nash Draw, but are more rationally explained as sedimentary facies changes. Extrapolation of the known karst features in Nash Draw eastward to the WIPP site, where conditions are and have been significantly different for half a million years, is unwarranted. The volumes of insoluble material that would remain after dissolution of halite would be significantly less than the observed bed thicknesses, thus dissolution is an unlikely explanation for the lateral variations from halite to mudstone and siltstone

  15. Inhibition of thrombin formation by active site mutated (S360A) activated protein C.

    PubMed

    Nicolaes, Gerry A F; Bock, Paul E; Segers, Kenneth; Wildhagen, Karin C A A; Dahlbäck, Björn; Rosing, Jan

    2010-07-23

    Activated protein C (APC) down-regulates thrombin formation through proteolytic inactivation of factor Va (FVa) by cleavage at Arg(506) and Arg(306) and of factor VIIIa (FVIIIa) by cleavage at Arg(336) and Arg(562). To study substrate recognition by APC, active site-mutated APC (APC(S360A)) was used, which lacks proteolytic activity but exhibits anticoagulant activity. Experiments in model systems and in plasma show that APC(S360A), and not its zymogen protein C(S360A), expresses anticoagulant activities by competing with activated coagulation factors X and IX for binding to FVa and FVIIIa, respectively. APC(S360A) bound to FVa with a K(D) of 0.11 +/- 0.05 nm and competed with active site-labeled Oregon Green activated coagulation factor X for binding to FVa. The binding of APC(S360A) to FVa was not affected by protein S but was inhibited by prothrombin. APC(S360A) binding to FVa was critically dependent upon the presence of Arg(506) and not Arg(306) and additionally required an active site accessible to substrates. Inhibition of FVIIIa activity by APC(S360A) was >100-fold less efficient than inhibition of FVa. Our results show that despite exosite interactions near the Arg(506) cleavage site, binding of APC(S360A) to FVa is almost completely dependent on Arg(506) interacting with APC(S360A) to form a nonproductive Michaelis complex. Because docking of APC to FVa and FVIIIa constitutes the first step in the inactivation of the cofactors, we hypothesize that the observed anticoagulant activity may be important for in vivo regulation of thrombin formation.

  16. The origin of summertime crust and surface hoar formation at the WAIS Divide site, West Antarctica

    NASA Astrophysics Data System (ADS)

    Fegyveresi, J. M.; Alley, R. B.; Spencer, M. K.

    2013-12-01

    Summertime field observations at the WAIS Divide site, West Antarctica, indicate a very active surface. Over five consecutive seasons (2008-2013), daily surface measurements were made along with photography of the surface and of back-lit snowpits, where densities were measured. The Automatic Weather Station in the University of Wisconsin network was supplemented by various independent sensors deployed on site, including pyranometer sensor arrays and net-radiometers in order to better quantify the short-wave and long-wave radiation conditions surrounding near-surface metamorphism. Prominent 'glazed' crusts occur frequently. Surface and pit observations show that such crusts form in summertime during relative low-wind, low-humidity, high-temperature episodes that immediately follow a succession of strong wind events. During each documented case of formation, these episodes were also brought about during clear-sky days with maximum diurnal variability of incoming solar energy. Shallow firn temperature measurements indicate strong inversions during crust formation that likely lead to increased vapor transport. Furthermore, distinct hoar frost growth was observed on crusts that were exposed to multiple clear-sky days, likely as a result of increased insolation, humidity, and vertical vapor transport in the near-surface. There was no obvious indication of melt associated with glazed features during initial inspection. Examination of the WDC06A ice core and its associated ECM record indicates that numerous crusts are present very regularly throughout the core and in all seasons. Crusts are about 40% more abundant in summertime than in wintertime deposits, likely due to the formation of 'glazed' surfaces; formation mechanisms of the less-common wintertime crusts have not been observed and are not known. Over the ice-core record, there is little change in frequency of occurrence of wintertime crusts, but some changes in summertime, perhaps indicating changes in occurrence

  17. N44C nebula

    NASA Image and Video Library

    1999-12-03

    Resembling the hair in Botticelli famous portrait of the birth of Venus, an image from NASA Hubble Space Telescope has captured softly glowing filaments streaming from hot young stars in a nearby nebula.

  18. Geology of the Hanna Formation, Hanna Underground Coal Gasification Site, Hanna, Wyoming

    SciTech Connect

    Oliver, R.L.; Youngberg, A.D.

    1984-01-01

    The Hanna Underground Coal Gasification (UCG) study area consists of the SW1/4 of Section 29 and the E1/2SE1/4 of Section 30 in Township 22 North, Range 81 West, Wyoming. Regionally, this is located in the coal-bearing Hanna Syncline of the Hanna Basin in southeast Wyoming. The structure of the site is characterized by beds dipping gently to the northeast. An east-west fault graben complex interrupts this basic trend in the center of the area. The target coal bed of the UCG experiments was the Hanna No. 1 coal in the Hanna Formation. Sedimentary rocks comprising the Hanna Formation consist of a sequence of nonmarine shales, sandstones, coals and conglomerates. The overburden of the Hanna No. 1 coal bed at the Hanna UCG site was divided into four broad local stratigraphic units. Analytical studies were made on overburden and coal samples taken from cores to determine their mineralogical composition. Textural and mineralogical characteristics of sandstones from local stratigraphic units A, B, and C were analyzed and compared. Petrographic analyses were done on the coal including oxides, forms of sulfur, pyrite types, maceral composition, and coal rank. Semi-quantitative spectrographic and analytic geochemical analyses were done on the overburden and coal and relative element concentrations were compared. Trends within each stratigraphic unit were also presented and related to depositional environments. The spectrographic analysis was also done by lithotype. 34 references, 60 figures, 18 tables.

  19. Formation Vp Derived From LWD Sonic Data at IODP Sites U1325-U1329, Cascadia Margin

    NASA Astrophysics Data System (ADS)

    Goldberg, D.; Guerin, G.; Malinverno, A.; Tagbor, K.; Alford, J.

    2006-12-01

    LWD sonic data were acquired in very low-velocity, hydrate-bearing formations at five sites drilled during IODP Exp 311 on the Cascadia Margin. Sonic velocity logs provide one of the best means to investigate the physical properties and porosity of gas hydrates, although caution must be exercised when interpreting LWD sonic data in shallow sediments. Current LWD sonic technology is challenged to recover accurate P-wave velocity where values are extremely low, close to the fluid velocity, as in shallow marine sediments where gas hydrates typically occur. Low formation Vp makes the analysis of LWD sonic data difficult because of the strong effects of wave modes linked to the presence of a tool in the borehole, such as dipole and leaky-P modes, which typically have high amplitudes and are dispersive. Slowness vs. frequency analysis using Prony's method is used to examine the frequency dispersion of borehole leaky-P modes and establish the minimum depth below seafloor for accurate Vp estimates. A fast downhole computation method is also compared as a useful approximation for future real-time applications. During Exp 311, real time data processing was configured to identify the wave propagating through the borehole fluid for monitoring of possible gas occurrences by a loss of waveform coherence. Post-processing of the dispersive leaky-P modes allows for accurate estimation of formation Vp profiles deeper than 57-100 m below the seafloor, at the different Exp 311 LWD sites. Vp increases from ~1.6 to ~2.0 km/s at total depth (350 mbsf for the deepest hole). Gas hydrate-bearing intervals show up as high-Vp anomalies over this steady increase with depth. Vp estimates from leaky-P modes below the minimum depth compare in general with wireline sonic logs and VSP interval velocities in nearby Exp 311 holes but differ over short intervals due to local formation heterogeneity. A low-Vp transition observed at the bottom of hydrate-bearing intervals, associated with the presence

  20. Key Features of New Particle Formation Events at Background Sites in China

    NASA Astrophysics Data System (ADS)

    Shen, X.; Sun, J.; Zhang, X.; Zhang, Y.

    2016-12-01

    Long-term continuous measurements of particle number size distributions with mobility diameter sizes ranging from 3 to 800 nm were performed to study new particle formation (NPF) events at Shangdianzi (SDZ), Mt. Tai (TS), and Lin'an (LAN) stations representing the background atmospheric conditions in the North China Plain (NCP), Central East China (CEC), and Yangtze River Delta (YRD) regions, respectively. The mean formation rate of 3-nm particles was 6.3, 3.7, and 5.8 cm-3 s-1, and the mean particle growth rate was 3.6, 6.0, and 6.2 nm h-1at SDZ, TS, and LAN, respectively. The NPF event characteristics at the three sites indicate that there may be a stronger source of low volatile vapors and higher condensational sink of pre-existing particles in the YRD region. The formation rate of NPF events at these sites, as well as the condensation sink, is approximately 10 times higher than some results reported at rural/urban sites in western countries. However, the growth rates appear to be 1-2 times higher. Approximately 12%-17% of all NPF events with nucleated particles grow to a climate relevant size (>50 nm). These kinds of NPF events were normally observed with higher growth rate than the other NPF cases. Generally, the cloud condensation nuclei (CCN) number concentration can be enhanced by approximately a factor of 2-6 on these event days. The mean value of the enhancement factor is lowest at LAN (2-3) and highest at SDZ ( 4). NPF events have also been found to have greater impact on CCN production in China at the regional scale than in the other background sites worldwide. Based on the long-term measurement of NPF event at SDZ station (8-year dataset), it was found the first factor in determining the NPF occurrence was the condensation sink, and the second factor could be the concentration level of precursor vapors participating in the NPF event (e.g., sulfuric acid). Some emission control strategies applied in China will reduce the condensation sink, which is

  1. Site-specific function and regulation of Osterix in tooth root formation

    PubMed Central

    He, Y. D.; Sui, B. D.; Li, M.; Huang, J.; Chen, S.; Wu, L. A.

    2016-01-01

    Congenital diseases of tooth roots, in terms of developmental abnormalities of short and thin root phenotypes, can lead to loss of teeth. A more complete understanding of the genetic molecular pathways and biological processes controlling tooth root formation is required. Recent studies have revealed that Osterix (Osx), a key mesenchymal transcriptional factor participating in both the processes of osteogenesis and odontogenesis, plays a vital role underlying the mechanisms of developmental differences between root and crown. During tooth development, Osx expression has been identified from late embryonic to postnatal stages when the tooth root develops, particularly in odontoblasts and cementoblasts to promote their differentiation and mineralization. Furthermore, the site-specific function of Osx in tooth root formation has been confirmed, because odontoblastic Osx-conditional knockout mice demonstrate primarily short and thin root phenotypes with no apparent abnormalities in the crown (Journal of Bone and Mineral Research 30, 2014 and 742, Journal of Dental Research 94, 2015 and 430). These findings suggest that Osx functions to promote odontoblast and cementoblast differentiation and root elongation only in root, but not in crown formation. Mechanistic research shows regulatory networks of Osx expression, which can be controlled through manipulating the epithelial BMP signalling, mesenchymal Runx2 expression and cellular phosphorylation levels, indicating feasible routes of promoting Osx expression postnatally (Journal of Cellular Biochemistry 114, 2013 and 975). In this regard, a promising approach might be available to regenerate the congenitally diseased root and that regenerative therapy would be the best choice for patients with developmental tooth diseases. PMID:26599722

  2. Measurements of aerosol chemistry during new particle formation events at a remote rural mountain site.

    PubMed

    Creamean, Jessie M; Ault, Andrew P; Ten Hoeve, John E; Jacobson, Mark Z; Roberts, Gregory C; Prather, Kimberly A

    2011-10-01

    Determining the major sources of particles that act as cloud condensation nuclei (CCN) represents a critical step in the development of a more fundamental understanding of aerosol impacts on cloud formation and climate. Reported herein are direct measurements of the CCN activity of newly formed ambient particles, measured at a remote rural site in the Sierra Nevada Mountains of Northern California. Nucleation events in the winter of 2009 occurred during two pristine periods following precipitation, with higher gas-phase SO(2) concentrations during the second period, when faster particle growth occurred (7-8 nm/h). Amines, as opposed to ammonia, and sulfate were detected in the particle phase throughout new particle formation (NPF) events, increasing in number as the particles grew to larger sizes. Interestingly, long-range transport of SO(2) from Asia appeared to potentially play a role in NPF during faster particle growth. Understanding the propensity of newly formed particles to act as CCN is critical for predicting the effects of NPF on orographic cloud formation during winter storms along the Sierra Nevada Mountain range. The potential impact of newly formed particles in remote regions needs to be compared with that of transported urban aerosols when evaluating the impact of aerosols on clouds and climate.

  3. New Particle Formation Above a Loblolly Pine Forest at a New Tower Site in Central Virginia

    NASA Astrophysics Data System (ADS)

    Joerger, V.; O'Halloran, T. L.; Barr, J. G.

    2014-12-01

    We present initial results investigating the environmental controls on new particle formation events at a new research site in central Virginia. The Sweet Briar College Land-Atmosphere Research Station (SBC-LARS) became operational in July, 2014 and features a 37-meter tower within a ~30 year-old loblolly pine plantation that is surrounded by mixed deciduous forest at the eastern edge of the Blue Ridge Mountains. The tower supports meteorological instruments at three different heights (2, 26, and 37 meters) and two air sampling inlets located above the canopy. The inlets draw air samples into a climate-controlled shed where precursor gas concentrations (ozone, sulfur dioxide, and nitrogen oxides) are determined by gas analyzers. Aerosol size distributions between 10 and 470 nm are measured every 3 minutes by a Scanning Mobility Particle Sizer (SMPS). For this study, aerosol size distributions from July through November 2014 were analyzed along with HYSPLIT backwards trajectories, meteorological measurements, gas concentrations, and the condensational sink, to investigate controls on new particle formation. This station and corresponding dataset will contribute to a better understanding of the contribution of biogenic and anthropogenic emissions to aerosol formation in the southeastern United States.

  4. Investigation of frayed edge site formation in high structural charge clay minerals by Molecular Dynamics simulation

    NASA Astrophysics Data System (ADS)

    Kulasinski, K.; Bourg, I. C.; Lammers, L. N.

    2016-12-01

    The 2:1 clay minerals contribute a significant fraction of the ion exchange capacity in soils and are characterized by their layered structure with negative net charge. The edge regions of relatively high structural charge or "micaceous" clays (e.g. illites) exhibit a high affinity for radiocesium ions, which are a major environmental contaminant. Previous studies showed a clear (but unexplained) dependence of ion accessibility to edge sites on the aqueous solution composition, which may be related to the influence of interlayer thickness (d-spacing) on the kinetics of ion exchange at the edge. In particular, the presence of aqueous Ca2+ increases the availability of high-affinity frayed edge sites. We use atomistic Molecular Dynamics (MD) simulations to investigate in detail the impact of solution composition on the structure and energetics of frayed edges in micaceous clay. Our MD model is a several nm-wide K-illite particle immersed in NaCl or CaCl2 electrolyte solutions (Fig. 1a). Unconstrained MD simulations show that the near-edge d-spacing does not depend on salinity but does depend on the valence of solvated cations adsorbed at basal surfaces due to additional Coulombic repulsion. Steered MD simulations (Umbrella Sampling, Potential of Mean Force) were used to investigate the mechanism of frayed edge site formation. We find that the energy barrier for Ca2+ to enter the edge (Fig. 1b) strongly depends on the configuration of neighboring cations. Additionally, we observe the spontaneous hydration of interlayer Ca ions inserted near the edge. Exchange of hydrated ions in the near-edge region of otherwise anhydrous clay minerals makes the d-spacing increase, creating the wedge region characteristic of a frayed edge site. This exchange increases the accessibility of the interlayer to subsequent K-Cs exchange. In short, our simulations provide molecular scale insight into the formation of frayed edge sites and its dependence on solution chemistry, particularly on

  5. Cloning, localization and focus formation at DNA damage sites of canine Ku70.

    PubMed

    Koike, Manabu; Yutoku, Yasutomo; Koike, Aki

    2017-03-23

    Understanding the molecular mechanisms of DNA double-strand break (DSB) repair machinery, specifically non-homologous DNA-end joining (NHEJ), is crucial for developing next-generation radiotherapies and common chemotherapeutics for human and animal cancers. The localization, protein-protein interactions and post-translational modifications of core NHEJ factors, might play vital roles for regulation of NHEJ activity. The human Ku heterodimer (Ku70/Ku80) is a core NHEJ factor in the NHEJ pathway and is involved in sensing of DSBs. Companion animals, such as canines, have been proposed to be an excellent model for cancer research, including development of chemotherapeutics. However, the post-translational modifications, localization and complex formation of canine Ku70 have not been clarified. Here, we show that canine Ku70 localizes in the nuclei of interphase cells and that it is recruited quickly at laser-microirradiated DSB sites. Structurally, two DNA-PK phosphorylation sites (S6 and S51), an ubiquitination site (K114), two canonical sumoylation consensus motifs, a CDK phosphorylation motif, and a nuclear localization signal (NLS) in the human Ku70 are evolutionarily conserved in canine and mouse species, while the acetylation sites in human Ku70 are partially conserved. Intriguingly, the primary candidate nucleophile (K31) required for 5'dRP/AP lyase activity of human and mouse Ku70 is not conserved in canines, suggesting that canine Ku does not possess this activity. Our findings provide insights into the molecular mechanisms of Ku-dependent NHEJ in a canine model and form a platform for the development of next-generation common chemotherapeutics for human and animal cancers.

  6. Role of Criegee Intermediates in Formation of Sulfuric Acid at BVOCs-rich Cape Corsica Site

    NASA Astrophysics Data System (ADS)

    Kukui, A.; Dusanter, S.; Sauvage, S.; Gros, V.; Bourrianne, T.; Sellegri, K.; Wang, J.; Colomb, A.; Pichon, J. M.; Chen, H.; Kalogridis, C.; Zannoni, N.; Bonsang, B.; Michoud, V.; Locoge, N.; Leonardis, T.

    2015-12-01

    Oxidation of SO2 in reactions with stabilised Criegee Intermediates (sCI) was suggested as an additional source of gaseous sulfuric acid (H2SO4) in the atmosphere, complementary to the conventional H2SO4 formation in reaction of SO2 with OH radicals. Evaluation of the importance of this additional source is complicated due to large uncertainty in the mechanism and rate constants for the reactions of different sCI with SO2, water vapor and other atmospheric species. Here we present an evaluation of the role of sCI in H2SO4 production at remote site on Cape Corsica near the North tip of Corsica Island (Ersa station, Western Mediterranean). In July 2013 comprehensive field observations including gas phase (OH and RO2 radicals, H2SO4, VOCs, NOx, SO2, others) and aerosol measurements were conducted at this site in the frame of ChArMEx project. During the field campaign the site was strongly influenced by local emissions of biogenic volatile compounds (BVOCs), including isoprene and terpenes, forming different sCI in reactions with ozone and, hence, presenting additional source of H2SO4 via sCI+SO2. However, this additional source of H2SO4 at the Ersa site was found to be insignificant. The observed concentrations of H2SO4 were found to be in good agreement with those estimated from the H2SO4 condensation sink and the production of H2SO4 only in the reaction of OH with SO2, without accounting for any additional H2SO4 source. Using the BVOCs observations we present estimation of the upper limit for the rate constants of H2SO4 production via reactions of different sCI with SO2.

  7. Cloning, localization and focus formation at DNA damage sites of canine Ku70

    PubMed Central

    KOIKE, Manabu; YUTOKU, Yasutomo; KOIKE, Aki

    2017-01-01

    Understanding the molecular mechanisms of DNA double-strand break (DSB) repair machinery, specifically non-homologous DNA-end joining (NHEJ), is crucial for developing next-generation radiotherapies and common chemotherapeutics for human and animal cancers. The localization, protein-protein interactions and post-translational modifications of core NHEJ factors, might play vital roles for regulation of NHEJ activity. The human Ku heterodimer (Ku70/Ku80) is a core NHEJ factor in the NHEJ pathway and is involved in sensing of DSBs. Companion animals, such as canines, have been proposed to be an excellent model for cancer research, including development of chemotherapeutics. However, the post-translational modifications, localization and complex formation of canine Ku70 have not been clarified. Here, we show that canine Ku70 localizes in the nuclei of interphase cells and that it is recruited quickly at laser-microirradiated DSB sites. Structurally, two DNA-PK phosphorylation sites (S6 and S51), an ubiquitination site (K114), two canonical sumoylation consensus motifs, a CDK phosphorylation motif, and a nuclear localization signal (NLS) in the human Ku70 are evolutionarily conserved in canine and mouse species, while the acetylation sites in human Ku70 are partially conserved. Intriguingly, the primary candidate nucleophile (K31) required for 5’dRP/AP lyase activity of human and mouse Ku70 is not conserved in canines, suggesting that canine Ku does not possess this activity. Our findings provide insights into the molecular mechanisms of Ku-dependent NHEJ in a canine model and form a platform for the development of next-generation common chemotherapeutics for human and animal cancers. PMID:28163277

  8. Formation of target-specific binding sites in enzymes: solid-phase molecular imprinting of HRP

    NASA Astrophysics Data System (ADS)

    Czulak, J.; Guerreiro, A.; Metran, K.; Canfarotta, F.; Goddard, A.; Cowan, R. H.; Trochimczuk, A. W.; Piletsky, S.

    2016-05-01

    Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike complex protein engineering approaches commonly employed to generate affinity proteins, the method proposed can be used to produce protein-based ligands in a short time period using native protein molecules. These affinity materials are potentially useful tools especially for assays since they combine the catalytic properties of enzymes (for signaling) and molecular recognition properties of antibodies. We demonstrate this concept in an ELISA-format assay where HRP imprinted with vancomycin and ampicillin replaced traditional enzyme-antibody conjugates for selective detection of templates at micromolar concentrations. This approach can potentially provide a fast alternative to raising antibodies for targets that do not require high assay sensitivities; it can also find uses as a biochemical research tool, as a possible replacement for immunoperoxidase-conjugates.Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike

  9. Maryland power plant siting program radioecology database management system: format for coding radioecology data. Final report

    SciTech Connect

    Domotor, S.L.

    1986-01-01

    The Radioecology Laboratory of the State of Maryland Power Plant Siting Program (PPSP) conducts routine radiological monitoring programs designed to assess the environmental impact of radionuclides released by nuclear power plants affecting Maryland. The PPSP radioecology database management system was initiated to store existing and future monitoring data collected by PPSP and its subcontractors in a computer file format. From these files, SAS (Statistical Analysis System) datasets are created for qualitative and quantitative analysis of monitoring data, for modeling studies through incorporation of this data, or for predicting environmental impact. The system was designed to accommodate both gamma and beta radionuclide analyses from water, sediment, soil, air, foodstuff, and aquatic and terrestrial flora and fauna sample types. Plant releases of radionuclides and physical and chemical environmental parameters can also be stored.

  10. Osterix/Sp7 limits cranial bone initiation sites and is required for formation of sutures

    PubMed Central

    Kague, Erika; Roy, Paula; Asselin, Garrett; Hu, Gui; Stanley, Alexandra; Albertson, Craig; Simonet, Jacqueline; Fisher, Shannon

    2017-01-01

    During growth, individual skull bones overlap at sutures, where osteoblast differentiation and bone deposition occur. Mutations causing skull malformations have revealed some required genes, but many aspects of suture regulation remain poorly understood. We describe a zebrafish mutation in osterix/sp7, which causes a generalized delay in osteoblast maturation. While most of the skeleton is patterned normally, mutants have specific defects in the anterior skull and upper jaw, and the top of the skull comprises a random mosaic of bones derived from individual initiation sites. Osteoblasts at the edges of the bones are highly proliferative and fail to differentiate, consistent with global changes in gene expression. We propose that signals from the bone itself are required for orderly recruitment of precursor cells and growth along the edges. The delay in bone maturation caused by loss of Sp7 leads to unregulated bone formation, revealing a new mechanism for patterning the skull and sutures. PMID:26992365

  11. Osterix/Sp7 limits cranial bone initiation sites and is required for formation of sutures.

    PubMed

    Kague, Erika; Roy, Paula; Asselin, Garrett; Hu, Gui; Simonet, Jacqueline; Stanley, Alexandra; Albertson, Craig; Fisher, Shannon

    2016-05-15

    During growth, individual skull bones overlap at sutures, where osteoblast differentiation and bone deposition occur. Mutations causing skull malformations have revealed some required genes, but many aspects of suture regulation remain poorly understood. We describe a zebrafish mutation in osterix/sp7, which causes a generalized delay in osteoblast maturation. While most of the skeleton is patterned normally, mutants have specific defects in the anterior skull and upper jaw, and the top of the skull comprises a random mosaic of bones derived from individual initiation sites. Osteoblasts at the edges of the bones are highly proliferative and fail to differentiate, consistent with global changes in gene expression. We propose that signals from the bone itself are required for orderly recruitment of precursor cells and growth along the edges. The delay in bone maturation caused by loss of Sp7 leads to unregulated bone formation, revealing a new mechanism for patterning the skull and sutures.

  12. Location of femoral artery puncture site and the risk of postcatheterization pseudoaneurysm formation.

    PubMed

    Gabriel, Marcin; Pawlaczyk, Katarzyna; Waliszewski, Krzysztof; Krasiński, Zbigniew; Majewski, Wacław

    2007-08-21

    Iatrogenic causes constitute increasingly frequent sources of pseudoaneurysms due to endovascular interventions. However, till now, all analyses focused on evaluating different risk factors contributing to the development of pseudoaneurysm, overlooking the issue of localization of femoral puncture. The aim of this study was to assess the influence of position of femoral artery puncture on the risk of pseudoaneurysm formation. 116 patients were evaluated for the site of catheter insertion into femoral arteries. Another group of 273 patients, suspected of vascular complications after endovascular procedures, were diagnosed with pseudoaneurysms which were analyzed for the location of arterial wall disruption. Puncture sites of groin arteries, i.e. EIA (2.7%), CFA (77.5%), SFA and DFA (19.8%), correlated with pseudoaneurysm location reaching 7.6% (EIA), 54.3% (CFA) and 38.1% (SFA, DFA). Type of procedure influenced these values. Duplex ultrasound mapping of CFA before the endovascular intervention eliminated discrepancies between the incidence of pseudoaneurysm formation and the frequency of arterial puncture in the selected vascular segments. Pseudoaneurysms formed in 4.5% of patients undergoing traditional palpation-guided vessel cannulation and in 2.6% of patients after ultrasound-guided puncture of the femoral artery. Upon further analysis, we concluded that the likelihood of the development of pseudoaneurysm depends on the artery punctured in the groin. This risk increases dramatically for external iliac artery, superficial and deep femoral arteries. A simple means of prevention of this dangerous complication of femoral artery puncture is duplex ultrasound mapping of the groin arteries.

  13. The effect of drug-DNA interactions on the intercalation site formation

    NASA Astrophysics Data System (ADS)

    Miroshnychenko, K. V.; Shestopalova, A. V.

    The problem of intercalation site formation in the undistorted B-DNA of different length and sequence was considered. Three models of DNA intercalation targets were proposed that accounted for the binding features of intercalators ethidium, daunomycin and 9-amino[N-(2-dimethylamino)ethyl]-acridine-4-carboxamide (9-amino-DACA). The automated docking of ligands into the constructed DNA-targets produced correct structures of complexes for ethidium and daunomycin when asymmetrically unwound DNA was used as target. To obtain the correct structure of 9-amino-DACA-DNA complex, the manual docking was applied. The results of docking of ligands into different DNA-targets indicate that, upon formation of the intercalation target, it is sufficient to take into account only the most significant unwinding in one particular helical step: in the intercalation step (for ethidium and 9-amino-DACA) or in the adjacent helical step (for daunomycin). The unwinding or overwinding of subsequent helical steps could be refined later during the optimization of the obtained intercalation complex. The unwinding of the DNA helical step on the large angle produces the 5‧-North/3‧-South asymmetry of sugar conformations in this step. The value of the total unwinding of the DNA in the intercalation complex was found to be dependent on the sequence and length of the DNA-target.

  14. The formation and coalescence sites of the first gravitational wave events

    NASA Astrophysics Data System (ADS)

    Schneider, Raffaella; Graziani, Luca; Marassi, Stefania; Spera, Mario; Mapelli, Michela; Alparone, Matteo; de Bennassuti, Matteo

    2017-10-01

    We present a novel theoretical model to characterize the formation and coalescence sites of compact binaries in a cosmological context. This is based on the coupling between the binary population synthesis code SeBa with a simulation following the formation of a Milky Way-like halo in a well resolved cosmic volume of 4 cMpc, performed with the GAMESH pipeline. We have applied this technique to investigate when and where systems with properties similar to the recently observed LIGO/VIRGO events are more likely to form and where they are more likely to reside when they coalesce. We find that more than 70% of GW151226 and LVT151012-like systems form in galaxies with stellar mass M* > 10^8 Msun in the redshift range [0.06 - 3] and [0.14 - 11.3], respectively. All GW150914-like systems form in low-metallicity dwarfs with M* < 5 10^6 Msun at 2.4 < z < 4.2. Despite these initial differences, by the time they reach coalescence the observed events are most likely hosted by star forming galaxies with M* > 10^{10} Msun. Due to tidal stripping and radiative feedback, a non negligible fraction of GW150914-like candidates end-up in galaxies with properties similar to dwarf spheroidals and ultra-faint satellites.

  15. The Conundrum of the High-Affinity NGF Binding Site Formation Unveiled?

    PubMed Central

    Covaceuszach, Sonia; Konarev, Petr V.; Cassetta, Alberto; Paoletti, Francesca; Svergun, Dmitri I.; Lamba, Doriano; Cattaneo, Antonino

    2015-01-01

    The homodimer NGF (nerve growth factor) exerts its neuronal activity upon binding to either or both distinct transmembrane receptors TrkA and p75NTR. Functionally relevant interactions between NGF and these receptors have been proposed, on the basis of binding and signaling experiments. Namely, a ternary TrkA/NGF/p75NTR complex is assumed to be crucial for the formation of the so-called high-affinity NGF binding sites. However, the existence, on the cell surface, of direct extracellular interactions is still a matter of controversy. Here, supported by a small-angle x-ray scattering solution study of human NGF, we propose that it is the oligomerization state of the secreted NGF that may drive the formation of the ternary heterocomplex. Our data demonstrate the occurrence in solution of a concentration-dependent distribution of dimers and dimer of dimers. A head-to-head molecular assembly configuration of the NGF dimer of dimers has been validated. Overall, these findings prompted us to suggest a new, to our knowledge, model for the transient ternary heterocomplex, i.e., a TrkA/NGF/p75NTR ligand/receptors molecular assembly with a (2:4:2) stoichiometry. This model would neatly solve the problem posed by the unconventional orientation of p75NTR with respect to TrkA, as being found in the crystal structures of the TrkA/NGF and p75NTR/NGF complexes. PMID:25650935

  16. A Randomized Trial Examining Housing First in Congregate and Scattered Site Formats

    PubMed Central

    Somers, Julian M.; Moniruzzaman, Akm; Patterson, Michelle; Currie, Lauren; Rezansoff, Stefanie N.; Palepu, Anita; Fryer, Karen

    2017-01-01

    Objective No previous experimental trials have investigated Housing First (HF) in both scattered site (SHF) and congregate (CHF) formats. We hypothesized that CHF and SHF would be associated with a greater percentage of time stably housed as well as superior health and psychosocial outcomes over 24 months compared to treatment as usual (TAU). Methods Inclusion criteria were homelessness, mental illness, and high need for support. Participants were randomised to SHF, CHF, or TAU. SHF consisted of market rental apartments with support provided by Assertive Community Treatment (ACT). CHF consisted of a single building with supports equivalent to ACT. TAU included existing services and supports. Results Of 800 people screened, 297 were randomly assigned to CHF (107), SHF (90), or TAU (100). The percentage of time in stable housing over 24 months was 26.3% in TAU (reference; 95% confidence interval (CI) = 20.5, 32.0), compared to 74.3% in CHF (95% CI = 69.3, 79.3, p<0.001) and 74.5% in SHF (95% CI = 69.2, 79.7, p<0.001). Secondary outcomes favoured CHF but not SHF compared to TAU. Conclusion HF in scattered and congregate formats is capable of achieving housing stability among people experiencing major mental illness and chronic homelessness. Only CHF was associated with improvement on select secondary outcomes. Registration Current Controlled Trials: ISRCTN57595077. PMID:28076358

  17. Formation of target-specific binding sites in enzymes: solid-phase molecular imprinting of HRP.

    PubMed

    Czulak, J; Guerreiro, A; Metran, K; Canfarotta, F; Goddard, A; Cowan, R H; Trochimczuk, A W; Piletsky, S

    2016-06-07

    Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike complex protein engineering approaches commonly employed to generate affinity proteins, the method proposed can be used to produce protein-based ligands in a short time period using native protein molecules. These affinity materials are potentially useful tools especially for assays since they combine the catalytic properties of enzymes (for signaling) and molecular recognition properties of antibodies. We demonstrate this concept in an ELISA-format assay where HRP imprinted with vancomycin and ampicillin replaced traditional enzyme-antibody conjugates for selective detection of templates at micromolar concentrations. This approach can potentially provide a fast alternative to raising antibodies for targets that do not require high assay sensitivities; it can also find uses as a biochemical research tool, as a possible replacement for immunoperoxidase-conjugates.

  18. Ice Lens Formation and Frost Heave at the Phoenix Landing Site

    NASA Technical Reports Server (NTRS)

    Zent, A. P.; Sizemore, H. G.; Remple, A. W.

    2011-01-01

    Several lines of evidence indicate that the volume of shallow ground ice in the martian high latitudes exceeds the pore volume of the host regolith. Boynton et al. found an optimal fit to the Mars Odyssey Gamma Ray Spectrometer (GRS) data at the Phoenix landing site by modeling a buried layer of 50-75% ice by mass (up to 90% ice by volume). Thermal and optical observations of recent impact craters in the northern hemisphere have revealed nearly pure ice. Ice deposits containing only 1-2% soil by volume were excavated by Phoenix. The leading hypothesis for the origin of this excess ice is that it developed in situ by a mechanism analogous to the formation of terrestrial ice lenses and needle ice. Problematically, terrestrial soil-ice segregation is driven by freeze/thaw cycling and the movement of bulk water, neither of which are expected to have occurred in the geologically recent past on Mars. If however ice lens formation is possible at temperatures less than 273 K, there are possible implications for the habitability of Mars permafrost, since the same thin films of unfrozen water that lead to ice segregation are used by terrestrial psychrophiles to metabolize and grow down to temperatures of at least 258 K.

  19. Observing the formation of ice and organic crystals in active sites.

    PubMed

    Campbell, James M; Meldrum, Fiona C; Christenson, Hugo K

    2017-01-31

    Heterogeneous nucleation is vital to a wide range of areas as diverse as ice nucleation on atmospheric aerosols and the fabrication of high-performance thin films. There is excellent evidence that surface topography is a key factor in directing crystallization in real systems; however, the mechanisms by which nanoscale pits and pores promote nucleation remain unclear. Here, we use natural cleavage defects on Muscovite mica to investigate the activity of topographical features in the nucleation from vapor of ice and various organic crystals. Direct observation of crystallization within surface pockets using optical microscopy and also interferometry demonstrates that these sharply acute features provide extremely effective nucleation sites and allows us to determine the mechanism by which this occurs. A confined phase is first seen to form along the apex of the wedge and then grows out of the pocket opening to generate a bulk crystal after a threshold saturation has been achieved. Ice nucleation proceeds in a comparable manner, although our resolution is insufficient to directly observe a condensate before the growth of a bulk crystal. These results provide insight into the mechanism of crystal deposition from vapor on real surfaces, where this will ultimately enable us to use topography to control crystal deposition on surfaces. They are also particularly relevant to our understanding of processes such as cirrus cloud formation, where such topographical features are likely candidates for the "active sites" that make clay particles effective nucleants for ice in the atmosphere.

  20. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    DOE PAGES

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; ...

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with themore » metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.« less

  1. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  2. Site-specific function and regulation of Osterix in tooth root formation.

    PubMed

    He, Y D; Sui, B D; Li, M; Huang, J; Chen, S; Wu, L A

    2016-12-01

    Congenital diseases of tooth roots, in terms of developmental abnormalities of short and thin root phenotypes, can lead to loss of teeth. A more complete understanding of the genetic molecular pathways and biological processes controlling tooth root formation is required. Recent studies have revealed that Osterix (Osx), a key mesenchymal transcriptional factor participating in both the processes of osteogenesis and odontogenesis, plays a vital role underlying the mechanisms of developmental differences between root and crown. During tooth development, Osx expression has been identified from late embryonic to postnatal stages when the tooth root develops, particularly in odontoblasts and cementoblasts to promote their differentiation and mineralization. Furthermore, the site-specific function of Osx in tooth root formation has been confirmed, because odontoblastic Osx-conditional knockout mice demonstrate primarily short and thin root phenotypes with no apparent abnormalities in the crown (Journal of Bone and Mineral Research 30, 2014 and 742, Journal of Dental Research 94, 2015 and 430). These findings suggest that Osx functions to promote odontoblast and cementoblast differentiation and root elongation only in root, but not in crown formation. Mechanistic research shows regulatory networks of Osx expression, which can be controlled through manipulating the epithelial BMP signalling, mesenchymal Runx2 expression and cellular phosphorylation levels, indicating feasible routes of promoting Osx expression postnatally (Journal of Cellular Biochemistry 114, 2013 and 975). In this regard, a promising approach might be available to regenerate the congenitally diseased root and that regenerative therapy would be the best choice for patients with developmental tooth diseases. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  3. L2' loop is critical for caspase-7 active site formation.

    PubMed

    Witkowski, Witold A; Hardy, Jeanne A

    2009-07-01

    The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2') from the other half of the dimer to bind substrate. In an inactive form, the two L2' loops form a cross-dimer hydrogen-bond network over the dimer interface. Although the L2' loop has been implicated as playing a central role in the formation of the active-site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2' loop to catalytic function and enzyme stability. In wild-type and all mutants, active-site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand-free conformation, but is as stable as wild type when bound to substrate, indicating that caspase-7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2' loop are shown to be essential for substrate-binding and thus proper catalytic function of the caspase. In the crystal structure of I213A, the void created by side-chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate-binding are sufficiently strong to induce the active conformation. Thus, although the L2' loop makes no direct contacts with substrate, it is essential for buttressing the substrate-binding groove and is central to native catalytic efficiency.

  4. Environmental significance of Upper Miocene phosphorites at hominid sites in the Lukeino Formation (Tugen Hills, Kenya)

    NASA Astrophysics Data System (ADS)

    Dericquebourg, Perrine; Person, Alain; Ségalen, Loïc; Pickford, Martin; Senut, Brigitte; Fagel, Nathalie

    2015-08-01

    The Lukeino Formation contains an important sedimentary and fossiliferous record of the late Miocene (6.09-5.68 Ma), which has in particular yielded the fossil remains of the oldest East African bipedal hominid called Orrorin tugenensis. This fluvio-lacustrine sedimentary succession crops out in the Kenyan part of the East African Rift. It is mainly composed of clay to sandy clay deposits intercalated with volcanic ash horizons, and localized layers of carbonates and diatomites. A detailed sedimentological and mineralogical study of the Lukeino Formation was conducted to throw light on the environmental conditions in which the hominids lived. Several centimetric, relatively continuous and indurated phosphatic horizons, of sedimentary origin, were identified at two sites (Sunbarua and Kapcheberek). Mineralogical (XRD) and geochemical analyses as well as observations by SEM, which was coupled with an energy dispersive spectroscopy (EDS) microprobe, indicate that the autochthonous phosphate layers are composed of a micritic matrix of francolite (38-93%), with incorporation of silicates in variable proportions from one layer to another. The phosphate matrix contains very well preserved and abundant diatom frustules in the basal phosphate layer. These diatoms are identified as Aulacoseira granulata, implying a pH of 7.8-8.2 for freshwaters of the Palaeolake Lukeino. Calcitic tubular structures, linked to a possible bacterial origin, are also observed locally. Phosphate layers occur abruptly within a thick clay-sandy series, associated with an intense runoff phase during the deposition of this interval of the Lukeino Formation. The massive and cyclic input of phosphorus to the lake promoted productivity to the stage where it caused a diatom bloom. The establishment of several phosphate horizons testifies to successive phases of eutrophication of Palaeolake Lukeino. The diatom cells provided some of the organic matter, which was decomposed by bacterial activity at the

  5. Formation of nanostructured Group IIA metal activated sensors: The transformation of Group IIA metal compound sites

    NASA Astrophysics Data System (ADS)

    Tune, Travis C.; Baker, Caitlin; Hardy, Neil; Lin, Arthur; Widing, Timothy J.; Gole, James L.

    2015-05-01

    Trends in the Group IIA metal oxides and hydroxides of magnesium, calcium, and barium are unique in the periodic table. In this study we find that they display novel trends as decorating nanostructures for extrinsic semiconductor interfaces. The Group IIA metal ions are strong Lewis acids. We form these M2+ ions in aqueous solution and bring these solutions in contact with a porous silicon interface to form interfaces for conductometric measurements. Observed responses are consistent with the formation of MgO whereas the heavier elements display behaviors which suggest the effect of their more basic nature. Mg(OH)2, when formed, represents a weak base whereas the heavier metal hydroxides of Ca, Sr, and Ba are strong bases. However, the hydroxides tend to give up hydrogen and act as Brönsted acids. For the latter elements, the reversible interaction response of nanostructures deposited to the porous silicon (PS) interface is modified, as the formation of more basic sites appears to compete with M2+ Lewis acidity and hydroxide Brönsted acidity. Mg2+ forms an interface whose response to the analytes NH3 and NO is consistent with MgO and well explained by the recently developing Inverse Hard/Soft Acid/Base model. The behavior of the Ca2+ and Ba2+ decorated interfaces as they interact with the hard base NH3 follows a reversal of the model, indicating a decrease in acidic character as the observed conductometric response suggests the interaction with hydroxyl groups. A change from oxide-like to hydroxide-like constituents is supported by XPS studies. The changes in conductometric response is easily monitored in contrast to changes associated with the Group IIA oxides and hydroxides observed in XPS, EDAX, IR, and NMR measurements.

  6. Probing intein-catalyzed thioester formation by unnatural amino acid substitutions in the active site.

    PubMed

    Schwarzer, Dirk; Ludwig, Christina; Thiel, Ilka V; Mootz, Henning D

    2012-01-10

    Inteins are single-turnover catalysts that splice themselves out of a precursor polypeptide chain. For most inteins, the first step of protein splicing is the formation of a thioester through an N-S acyl shift at the upstream splice junction. However, the mechanism by which this reaction is achieved and the impact of mutations in and close to the active site remain unclear on the atomic level. To investigate these questions, we have further explored a split variant of the Ssp DnaB intein by introducing substitutions with unnatural amino acids within the short synthetic N-terminal fragment. A previously reported collapse of the oxythiazolidine anion intermediate into a thiazoline ring was found to be specificially dependent on the methyl side chain of the flanking Ala(-1). The stereoisomer d-Ala and the constitutional isomers β-Ala and sarcosine did not lead to this side reaction but rather supported splicing. Substitution of the catalytic Cys1 with homocysteine strongly inhibited protein splicing; however, thioester formation was not impaired. These results argue against the requirement of a base to deprotonate the catalytic thiol group prior to the N-S acyl shift, because it should be misaligned for optimal proton abstraction. A previously described mutant intein evolved for more general splicing in different sequence contexts could even rather efficiently splice with this homocysteine. Our findings show the large impact of some subtle structural changes on the protein splicing pathway, but also the remarkable tolerance toward other changes. Such insights will also be important for the biotechnological exploitation of inteins.

  7. Dipstick format of an improved ELISA for on-site atrazine monitoring in water in Pakistan.

    PubMed

    Maqbool, Uzma; Anwar-ul-Haq; Mahboob, Sadia

    2010-01-01

    A dipstick format was developed for on-site atrazine monitoring in water samples of different origins. It was derived from an in-house-developed ELISA based on polyclonal antibodies that also cross-react with hydroxyatrazine (30%) and terbuthylazine (17%). Test reagents were evaluated for temperature and pH stabilities and rapidity for field applications. Reagents performed well within a temperature range of 20-30 degrees C and were tolerant to alkaline pH (up to 8.5) of the assay buffering system. Tracer incubation time could be reduced to 40 min. Bovine serum albumin addition (1%) in the assay buffer improved assay performance, giving 50% B/B0 (IC50) of 65 ng/L and the lowest LOD of 2 ng/L at 90% B/B0 (IC10). The dipstick ELISA format was standardized on a membrane support. Nylon membrane, positively charged, was superior to PVDF for qualitative or semiquantitative analysis regarding color intensity and stability. Tracer incubation time was further reduced to 30 min with a lowest LOD of 0.1 microg/L. For real sample screening with dipsticks, acceptable results were obtained for water. Significant correlation was found between dipstick and plate ELISA results. Validation using GC with a nitrogen-phosphorus detector and HPLC indicated that dipstick signals in aged water samples, which were mainly due to hydroxyatrazine, were significantly above European Commission regulations of 0.1 microg/L. However, dipsticks were superior, fast, and cost-effective.

  8. Micromorphology and site formation at Die Kelders Cave I, South Africa.

    PubMed

    Goldberg, P

    2000-01-01

    The deposits of Die Kelders I were previously described and studied by Tankard & Schweitzer (1974, 1976) from the standpoint of classical granulometric analysis of sand from a coastal cave in order to infer the geological history of the cave and its environs. This paper supplements these earlier works by taking a more holistic approach toward site formation processes by including investigation of the biogenic and anthropogenic influences on the cave deposits and history. The study employs the technique of soil micromorphology, which is the study of resin-impregnated, undisturbed blocks of sediment and petrographic thin sections, in which sediments from all areas of the cave were examined. The study showed that diagenesis of the deposits in the eastern areas of the excavation resulted in decalcification, which in turn brought about slumping and compaction. Equivalent stratigraphic layers exposed in the western and central areas were only mildly decalcified and consequently, these sediments contain limestone rock fall and relatively abundant marine and terrestrial mollusks, the latter not dissimilar to the Late Stone Age (LSA) midden which covers these deposits. Thus, in spite of lowered and more distant shorelines, marine resources were exploited during Middle Stone Age (MSA) times. Observations from these calcareous units also clearly demonstrates that previously recognized "occupational horizons" (e.g. Layers 6, 8 and 10) can be resolved micromorphologically into several ephemeral events, such as burning/fire, redistribution of ashes by wind and water, and non-deposition; the latter is shown by phosphatic alteration of sediments exposed on former surfaces and accumulation of guano, or the presence of millimeter-thick truncation surfaces below which aeolian dust infiltrated. Both field and microscopic observations illustrate that the deposits in caves are highly variable from wall to center, and that excavations should not be localized in just one microenvironment

  9. Deciphering site formation processes through soil micromorphology at Contrebandiers Cave, Morocco.

    PubMed

    Aldeias, Vera; Goldberg, Paul; Dibble, Harold L; El-Hajraoui, Mohamed

    2014-04-01

    Contrebandiers Cave preserves a Late Pleistocene sequence containing Middle Stone Age (MSA) so-called Maghrebian Mousterian and Aterian occupations, spanning from ∼126 to 95 ka (thousands of years ago), followed by spatially restricted Iberomaurusian industries. Micromorphological analyses, complemented by instrumental mineralogical identification and fabric orientation, allowed for the reconstruction of the main site formation processes at the site. Initial deposition is characterized by local reworking of marine shelly sands dating to Marine Isotopic Stage 5e (MIS5e). The subsequent stratification reveals sedimentary dynamics predominantly associated with gravity-driven inputs and contributions from weathering of the encasing bedrock, at the same time that anthropogenic sediments were being accumulated. The allochthonous components reflect soil degradation and vegetation changes around the cave during the last interglacial. Human occupations seems to be somewhat ephemeral in nature, with some stratigraphic units apparently lacking archaeological components, while in others the human-associated deposits (e.g., burned bones, charcoal, and ashes) can be substantial. Ephemeral breaks in sedimentation and/or erosion followed by stabilization are mainly discernible microscopically by the presence of phosphatic-rich laminae interpreted as short-lived surfaces, peaks of increased humidity and colonization by plants. More substantial erosion affects the uppermost Aterian layers, presumably due to localized reconfigurations of the cave's roof. The subsequent Iberomaurusian deposits are not in their primary position and are associated with well-sorted silts of aeolian origin. While the effects of chemical diagenesis are limited throughout the whole stratigraphic sequence, physical bioturbation (e.g., by wasps, rodents, and earthworms) is more pervasive and leads to localized movement of the original sedimentary particles.

  10. Assessment of potential radionuclide transport in site-specific geologic formations

    SciTech Connect

    Dosch, R.G.

    1980-08-01

    Associated with the development of deep, geologic repositories for nuclear waste isolation is a need for safety assessments of the potential for nuclide migration. Frequently used in estimating migration rates is a parameter generally known as a distribution coefficient, K/sub d/, which describes the distribution of a radionuclide between a solid (rock) and a liquid (groundwater) phase. This report is intended to emphasize that the use of K/sub d/ must be coupled with a knowledge of the geology and release scenarios applicable to a repository. Selected K/sub d/ values involving rock samples from groundwater/brine simulants typical of two potential repository sites, WIPP and NTS, are used to illustrate this concern. Experimental parameters used in K/sub d/ measurements including nuclide concentration, site sampling/rock composition, and liquid-to-solid ratios are discussed. The solubility of U(VI) in WIPP brine/groundwater was addressed in order to assess the potential contribution of this phenomena to K/sub d/ values. Understanding mehanisms of sorption of radionuclides on rocks would lead to a better predictive capability. Sorption is attributed to the presence of trace constituents (often unidentified) in rocks. An attempt was made to determine if this applied to WIPP dolomite rocks by comparing sorption behavior of the natural material with that of a synthetic dolomite prepared in the laboratory with reagent grade chemicals. The results were inconclusive. The results of a study of Tc sorption by an argillite sample from the Calico Hills formation at NTS under ambient laboratory conditions were more conclusive. The Tc sorption was found to be associated with elemental carbon. Available evidence points to a reduction mechanism leading to the apparent sorption of Tc on the solid phase.

  11. Eastern-Mediterranean ventilation variability during sapropel S1 formation, evaluated at two sites influenced by deep-water formation from Adriatic and Aegean Seas

    NASA Astrophysics Data System (ADS)

    Filippidi, A.; Triantaphyllou, M. V.; De Lange, G. J.

    2016-07-01

    Present-day bottom-water ventilation in the Eastern Mediterranean basin occurs through deep-water convection originating from the two marginal basins, i.e. Adriatic and Aegean Seas. In the paleo record, long periods of enhanced deep-water formation have been alternating with shorter periods of reduced deep-water formation. The latter is related mainly to low-latitude humid climate conditions and the enhanced deposition and preservation of organic-rich sediment units (sapropels). This study focuses on sedimentary archives of the most-recent sapropel S1, retrieved from two sites under the direct influence of the two deep-water formation areas. Restricted oxygen conditions have developed rapidly at the beginning of S1 deposition in the Adriatic site, but bottom-water conditions have not persistently remained anoxic during the full interval of sapropel deposition. In fact, the variability in intensity and persistence of sedimentary redox conditions at the two deep-water formation sites is shown to be related to brief episodes of climate cooling. In the Adriatic site, sapropel deposition appears to have been interrupted twice. The 8.2 ka event, only recovered at the Adria site, is characterized by gradually increasing suboxic to possibly intermittently oxic conditions and decreasing Corg fluxes, followed by an abrupt re-establishment of anoxic conditions. Another important event that disrupted sapropel S1 formation, has taken place at ca. 7.4 cal ka BP. The latter event has been recovered at both sites. In the Adriatic site it is followed by a period of sedimentary conditions that gradually change from suboxic to more permanently oxic, as deduced from the Mn/Al pattern. Using the same proxy for suboxic/oxic sedimentary redox conditions, we observe that conditions in the Aegean Sea site shift to more permanently oxic from the 7.4 ka event onwards. However, at both sites the accumulation and preservation of enhanced amounts of organic matter have continued under these

  12. U.S. Department of Energy's site screening, site selection, and initial characterization for storage of CO2 in deep geological formations

    USGS Publications Warehouse

    Rodosta, T.D.; Litynski, J.T.; Plasynski, S.I.; Hickman, S.; Frailey, S.; Myer, L.

    2011-01-01

    The U.S. Department of Energy (DOE) is the lead Federal agency for the development and deployment of carbon sequestration technologies. As part of its mission to facilitate technology transfer and develop guidelines from lessons learned, DOE is developing a series of best practice manuals (BPMs) for carbon capture and storage (CCS). The "Site Screening, Site Selection, and Initial Characterization for Storage of CO2 in Deep Geological Formations" BPM is a compilation of best practices and includes flowchart diagrams illustrating the general decision making process for Site Screening, Site Selection, and Initial Characterization. The BPM integrates the knowledge gained from various programmatic efforts, with particular emphasis on the Characterization Phase through pilot-scale CO2 injection testing of the Validation Phase of the Regional Carbon Sequestration Partnership (RCSP) Initiative. Key geologic and surface elements that suitable candidate storage sites should possess are identified, along with example Site Screening, Site Selection, and Initial Characterization protocols for large-scale geologic storage projects located across diverse geologic and regional settings. This manual has been written as a working document, establishing a framework and methodology for proper site selection for CO2 geologic storage. This will be useful for future CO2 emitters, transporters, and storage providers. It will also be of use in informing local, regional, state, and national governmental agencies of best practices in proper sequestration site selection. Furthermore, it will educate the inquisitive general public on options and processes for geologic CO2 storage. In addition to providing best practices, the manual presents a geologic storage resource and capacity classification system. The system provides a "standard" to communicate storage and capacity estimates, uncertainty and project development risk, data guidelines and analyses for adequate site characterization, and

  13. Observing the formation of ice and organic crystals in active sites

    PubMed Central

    Campbell, James M.; Meldrum, Fiona C.; Christenson, Hugo K.

    2017-01-01

    Heterogeneous nucleation is vital to a wide range of areas as diverse as ice nucleation on atmospheric aerosols and the fabrication of high-performance thin films. There is excellent evidence that surface topography is a key factor in directing crystallization in real systems; however, the mechanisms by which nanoscale pits and pores promote nucleation remain unclear. Here, we use natural cleavage defects on Muscovite mica to investigate the activity of topographical features in the nucleation from vapor of ice and various organic crystals. Direct observation of crystallization within surface pockets using optical microscopy and also interferometry demonstrates that these sharply acute features provide extremely effective nucleation sites and allows us to determine the mechanism by which this occurs. A confined phase is first seen to form along the apex of the wedge and then grows out of the pocket opening to generate a bulk crystal after a threshold saturation has been achieved. Ice nucleation proceeds in a comparable manner, although our resolution is insufficient to directly observe a condensate before the growth of a bulk crystal. These results provide insight into the mechanism of crystal deposition from vapor on real surfaces, where this will ultimately enable us to use topography to control crystal deposition on surfaces. They are also particularly relevant to our understanding of processes such as cirrus cloud formation, where such topographical features are likely candidates for the “active sites” that make clay particles effective nucleants for ice in the atmosphere. PMID:27994140

  14. Site specific comparison of H2, CH4 and compressed air energy storage in porous formations

    NASA Astrophysics Data System (ADS)

    Tilmann Pfeiffer, Wolf; Wang, Bo; Bauer, Sebastian

    2016-04-01

    The supply of energy from renewable sources like wind or solar power is subject to fluctuations determined by the climatic and weather conditions, and shortage periods can be expected on the order of days to weeks. Energy storage is thus required if renewable energy dominates the total energy production and has to compensate the shortages. Porous formations in the subsurface could provide large storage capacities for various energy carriers, such as hydrogen (H2), synthetic methane (CH4) or compressed air (CAES). All three energy storage options have similar requirements regarding the storage site characteristics and consequently compete for suitable subsurface structures. The aim of this work is to compare the individual storage methods for an individual storage site regarding the storage capacity as well as the achievable delivery rates. This objective is pursued using numerical simulation of the individual storage operations. In a first step, a synthetic anticline with a radius of 4 km, a drop of 900 m and a formation thickness of 20 m is used to compare the individual storage methods. The storage operations are carried out using -depending on the energy carrier- 5 to 13 wells placed in the top of the structure. A homogeneous parameter distribution is assumed with permeability, porosity and residual water saturation being 500 mD, 0.35 and 0.2, respectively. N2 is used as a cushion gas in the H2 storage simulations. In case of compressed air energy storage, a high discharge rate of 400 kg/s equating to 28.8 mio. m³/d at surface conditions is required to produce 320 MW of power. Using 13 wells the storage is capable of supplying the specified gas flow rate for a period of 31 hours. Two cases using 5 and 9 wells were simulated for both the H2 and the CH4 storage operation. The target withdrawal rates of 1 mio. sm³/d are maintained for the whole extraction period of one week in all simulations. However, the power output differs with the 5 well scenario producing

  15. Effect of anthropogenic activity on formate and acetate levels in precipitation at four sites in Agra, India

    NASA Astrophysics Data System (ADS)

    Kumar, Nandini; Kulshreshta, U. C.; Saxena, A.; Kumari, K. M.; Srivastava, S. S.

    Twenty-four-hour precipitation samples from four sites: Dayalbagh (DB), Hari Parvat (HP), Taj Mahal (TM) and Udyog Kendra (UK) in Agra city, during the monsoon season (July-September) of 1991, were analysed for formate and acetate. Each site was representative of a different level of anthropogenic activity. The formate/acetate ratio observed appeared to be characteristic of the dominant activity at the site; the geometric means of the formate/acetate ratios calculated for individual samples were 0.99, 0.17, 0.83 and 0.21 for DB, HP, TM and UK, respectively. These corresponded to the level of pollution at the site. Direct acetate inputs from extensive combustion and automobile exhaust could contribute to elevated levels of the species at two of the four sites. Another possible indirect input could be from the alkaline hydrolysis of PAN, aided by relatively high pH values of rain water (volume-weighted averages = 6.79, 6.69, 7.22, 7.15) at the four sites.

  16. Molecular Study of the Effects of Chemical Processing on Heterogeneous Ice Nucleation: Role of Active Sites and Product Formation

    NASA Astrophysics Data System (ADS)

    Sihvonen, S.; Schill, G. P.; Murphy, K. A.; Mueller, K.; Tolbert, M. A.; Freedman, M. A.

    2014-12-01

    Mineral dust aerosol is the largest global source of ice nuclei, but the identity of the active sites for nucleation is unknown. During atmospheric transport, mineral dust aerosol can encounter and react with sulfuric acid, which affects the ice nucleation activity either due to changes to reactive surface sites or product formation. In this study, we reacted two types of clays found in mineral dust, kaolinite and montmorillonite, with sulfuric acid. Variation in the mineral due to acid treatment was separated from product formation through rinsing techniques. The samples were subsequently reacted with a probe molecule, (3,3,3-trifluoropropyl)dimethylchlorosilane, that selectively binds to edge hydroxyl groups that are bonded to a silicon atom with three bridging oxygens. Hydroxyl groups are considered potential active sites, because they can hydrogen bond with water and facilitate ice nucleation. Attachment to these sites was quantified by 19F magic angle spinning nuclear magnetic resonance (MAS NMR) of the 19F atoms on the probe molecule, which provided a direct correlation of the number of hydroxyl groups. Our results indicate that the number of edge-site hydroxyl groups increases with exposure to acid. Ice nucleation measurements indicate that the sulfuric acid-treated mineral is less ice active than the untreated mineral. Surprisingly, no difference between the nucleation activity of the untreated mineral and acid-treated, rinsed mineral is observed. As a result, we hypothesize that once a critical density of active sites is reached for ice nucleation, there is no further change in nucleation activity despite a continued increase in active sites. We additionally propose that the reduced activity of the acid-treated mineral is due to product formation that blocks active sites on the mineral, rather than changes to active sites.

  17. High Fat Diet Enhances β-Site Cleavage of Amyloid Precursor Protein (APP) via Promoting β-Site APP Cleaving Enzyme 1/Adaptor Protein 2/Clathrin Complex Formation

    PubMed Central

    Maesako, Masato; Uemura, Maiko; Tashiro, Yoshitaka; Sasaki, Kazuki; Watanabe, Kiwamu; Noda, Yasuha; Ueda, Karin; Asada-Utsugi, Megumi; Kubota, Masakazu; Okawa, Katsuya; Ihara, Masafumi; Shimohama, Shun; Uemura, Kengo; Kinoshita, Ayae

    2015-01-01

    Obesity and type 2 diabetes are risk factors of Alzheimer’s disease (AD). We reported that a high fat diet (HFD) promotes amyloid precursor protein (APP) cleavage by β-site APP cleaving enzyme 1 (BACE1) without increasing BACE1 levels in APP transgenic mice. However, the detailed mechanism had remained unclear. Here we demonstrate that HFD promotes BACE1/Adaptor protein-2 (AP-2)/clathrin complex formation by increasing AP-2 levels in APP transgenic mice. In Swedish APP overexpressing Chinese hamster ovary (CHO) cells as well as in SH-SY5Y cells, overexpression of AP-2 promoted the formation of BACE1/AP-2/clathrin complex, increasing the level of the soluble form of APP β (sAPPβ). On the other hand, mutant D495R BACE1, which inhibits formation of this trimeric complex, was shown to decrease the level of sAPPβ. Overexpression of AP-2 promoted the internalization of BACE1 from the cell surface, thus reducing the cell surface BACE1 level. As such, we concluded that HFD may induce the formation of the BACE1/AP-2/clathrin complex, which is followed by its transport of BACE1 from the cell surface to the intracellular compartments. These events might be associated with the enhancement of β-site cleavage of APP in APP transgenic mice. Here we present evidence that HFD, by regulation of subcellular trafficking of BACE1, promotes APP cleavage. PMID:26414661

  18. Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ(1-23) using an unnatural amino acid.

    PubMed

    Liu, Haiyang; Lantz, Richard; Cosme, Patrick; Rivera, Nelson; Andino, Carlos; Gonzalez, Walter G; Terentis, Andrew C; Wojcikiewicz, Ewa P; Oyola, Rolando; Miksovska, Jaroslava; Du, Deguo

    2015-04-25

    We identify distinct site-specific dynamics over the time course of Aβ1-23 amyloid formation by using an unnatural amino acid, p-cyanophenylalanine, as a sensitive fluorescent and Raman probe. Our results also suggest the key role of an edge-to-face aromatic interaction in the conformational conversion to form and stabilize β-sheet structure.

  19. Quarries of Culture: An Ethnohistorical and Environmental Account of Sacred Sites and Rock Formations in Southern California's Mission Indian Country

    ERIC Educational Resources Information Center

    Karr, Steven M.

    2005-01-01

    Sacred sites and Rock Formations throughout Southern California's India Country are described by Indians as ancestral markers, origin and place-name locales, areas of deity habitation, and power sources. Early ethnographers were keen to record the traditional stories and meanings related to them by their Native collaborators. Rock formations…

  20. Quarries of Culture: An Ethnohistorical and Environmental Account of Sacred Sites and Rock Formations in Southern California's Mission Indian Country

    ERIC Educational Resources Information Center

    Karr, Steven M.

    2005-01-01

    Sacred sites and Rock Formations throughout Southern California's India Country are described by Indians as ancestral markers, origin and place-name locales, areas of deity habitation, and power sources. Early ethnographers were keen to record the traditional stories and meanings related to them by their Native collaborators. Rock formations…

  1. A Study of Geological Formation on Different Sites in Batu Pahat, Malaysia Based On HVSR Method Using Microtremor Measurement

    NASA Astrophysics Data System (ADS)

    Noor, M. A. M.; Madun, A.; Kamarudin, A. F.; Daud, M. E.

    2016-07-01

    Geological formation is a one of information need to know during site reconnaissance. Conventional method like borehole has been known is very accurate to identify the formation of geology of a site. However, the problem of this technique is very expensive and not economical for large area. In the last decade, microtremor measurement has been introduced as an alternative technique and widely used in the geological formation study. Therefore, the aim in this study is to determine the geological formation underneath of surface in Batu Pahat district using microtremor measurement. There are two parameters have been carried out from microtremor measurement in term of natural frequency and HVSR curves images. Microtremor measurements are done conducted at 15 sites surrounding of Batu Pahat. Horizontal to vertical spectral ratio (HVSR) method was used for analyzing microtermor measurement data, to determine the natural frequency and also HVSR curves image. In this study, values of natural frequencies are used to classify the soil types with range in the between 0.93 to 5.35 Hz, meanwhile the pattern of HVSR curve images has been shown exists a few groups of soil types surrounding Batu Pahat district. Hence, microtremor measurement indirectly can be used as a one technique to add value in the site reconnaissance in the future.

  2. Cooperativity between Al Sites Promotes Hydrogen Transfer and Carbon–Carbon Bond Formation upon Dimethyl Ether Activation on Alumina

    PubMed Central

    2015-01-01

    The methanol-to-olefin (MTO) process allows the conversion of methanol/dimethyl ether into olefins on acidic zeolites via the so-called hydrocarbon pool mechanism. However, the site and mechanism of formation of the first carbon–carbon bond are still a matter of debate. Here, we show that the Lewis acidic Al sites on the 110 facet of γ-Al2O3 can readily activate dimethyl ether to yield CH4, alkenes, and surface formate species according to spectroscopic studies combined with a computational approach. The carbon–carbon forming step as well as the formation of methane and surface formate involves a transient oxonium ion intermediate, generated by a hydrogen transfer between surface methoxy species and coordinated methanol on adjacent Al sites. These results indicate that extra framework Al centers in acidic zeolites, which are associated with alumina, can play a key role in the formation of the first carbon–carbon bond, the initiation step of the industrial MTO process. PMID:27162986

  3. Urinary bladder matrix promotes site appropriate tissue formation following right ventricle outflow tract repair

    PubMed Central

    Remlinger, Nathaniel T; Gilbert, Thomas W; Yoshida, Masahiro; Guest, Brogan N; Hashizume, Ryotaro; Weaver, Michelle L; Wagner, William R; Brown, Bryan N; Tobita, Kimimasa; Wearden, Peter D

    2013-01-01

    The current prevalence and severity of heart defects requiring functional replacement of cardiac tissue pose a serious clinical challenge. Biologic scaffolds are an attractive tissue engineering approach to cardiac repair because they avoid sensitization associated with homograft materials and theoretically possess the potential for growth in similar patterns as surrounding native tissue. Both urinary bladder matrix (UBM) and cardiac ECM (C-ECM) have been previously investigated as scaffolds for cardiac repair with modest success, but have not been compared directly. In other tissue locations, bone marrow derived cells have been shown to play a role in the remodeling process, but this has not been investigated for UBM in the cardiac location, and has never been studied for C-ECM. The objectives of the present study were to compare the effectiveness of an organ-specific C-ECM patch with a commonly used ECM scaffold for myocardial tissue repair of the right ventricle outflow tract (RVOT), and to examine the role of bone marrow derived cells in the remodeling response. A chimeric rat model in which all bone marrow cells express green fluorescent protein (GFP) was generated and used to show the ability of ECM scaffolds derived from the heart and bladder to support cardiac function and cellular growth in the RVOT. The results from this study suggest that urinary bladder matrix may provide a more appropriate substrate for myocardial repair than cardiac derived matrices, as shown by differences in the remodeling responses following implantation, as well as the presence of site appropriate cells and the formation of immature, myocardial tissue. PMID:23974174

  4. Ice Lens Formation and Frost Heave at the Phoenix Landing Site

    NASA Astrophysics Data System (ADS)

    Zent, A.; Sizemore, H. G.; Rempel, A. W.

    2010-12-01

    Several lines of evidence indicate that the volume of shallow ground ice in the Martian high latitudes exceeds the pore volume of the host regolith. Boynton et al. (2002) found an optimal fit to the Mars Odyssey Gamma Ray Spectrometer (GRS) data at the Phoenix landing site by modeling a buried layer of 50-75% ice by mass (up to 90% by volume). Thermal and optical observations of recent impact craters in the northern hemisphere have revealed nearly pure ice. Ice deposits containing only 1-2% soil by volume were excavated by Phoenix. The leading hypothesis for the origin of this excess, or segregated, ice is that it developed in situ by a mechanism analogous to the formation of terrestrial ice lenses and needle ice. Problematically, terrestrial soil-ice segregation is driven by freeze/thaw cycling and the movement of bulk water, which are not expected to have occurred in the geologically recent past on Mars. We have developed a numerical model that applies the physics of pre-melting to track phase partitioning in soil pore spaces and test for conditions under which ice lenses could initiate. Our results indicate that diurnal cycling in the ice-cemented regolith and resultant pressure gradients in thin films at grain-ice interfaces can cause interparticle forces to unload, initiating an ice lens at temperatures as low as 245 K. These results indicate that in situ ice segregation may have occurred on Mars in the recent past, and that geologically young ice lenses may account for much of observed excess ice.

  5. Sequence of apoptosis and inflammatory necrosis within the formative ovulatory site of sheep follicles.

    PubMed

    Murdoch, W J; Wilken, C; Young, D A

    1999-11-01

    The aim of this study was to define the temporal and spatial patterns of apoptosis, necrosis and inflammation within preovulatory ovine follicles. A gonadotrophin surge was induced in pro-oestrous ewes by GnRH, and isolated follicles were hemisected into apical and basal segments at 0, 10, 18 and 22 h (the time of ovulatory stigma development) after GnRH. Ovarian surface epithelial and granulosa cells were isolated and assessed by fluorescence microscopy for membrane phosphatidylserine translocation-annexin V (early-stage apoptosis), oligonucleosomal DNA nick endlabelling (advanced apoptosis), and nuclear propidium iodide incorporation (necrotic membrane disruption). Thecal shells were analysed for interstitial blood cells. Preovulatory follicles were also hemisected and subjected to electrophoretic DNA degradation analysis. Annexin V binding and in situ DNA fragmentation among ovarian surface epithelial and granulosa cells along the follicular apex were high 18 and 22 h after GnRH. Propidium iodide staining of apical ovarian surface and granulosa cells was apparent at 22 h. There was a coincident increase within the apical theca as the time of ovulation approached in extravasated leucocytes (18 and 22 h) and erythrocytes (22 h). Apoptotic DNA laddering and necrotic DNA smears within the follicular apex were evident on agarose gels at 18 and 22 h, respectively. In contrast, ovarian surface epithelium not associated with the ovulation site and the basal follicular wall were largely unafflicted. It is suggested that both modalities of cellular death, apoptosis and necrosis (with acute inflammation and vascular injury), contribute progressively to follicular stigma formation and ovarian rupture.

  6. Electroporation-induced formation of individual calcium entry sites in the cell body and processes of adherent cells.

    PubMed Central

    Teruel, M N; Meyer, T

    1997-01-01

    Electroporation is a widely used method for introducing macromolecules into cells. We developed an electroporation device that requires only 1 microl of sample to load adherent cells in a 10-mm2 surface area while retaining greater than 90% cell survivability. To better understand this device, field-induced permeabilization of adherent rat basophilic leukemia and neocortical neuroblastoma cells was investigated by using fluorescent calcium and voltage indicators. Rectangular field pulses led to the formation of only a few calcium entry sites, preferentially in the hyperpolarized parts of the cell body and processes. Individual entry sites were formed at the same locations when field pulses were repeated. Before calcium entry, a partial breakdown of the membrane potential was observed in both polar regions. Based on our results, a model is proposed for the formation and closure of macromolecule entry sites in adherent cells. First, the rapid formation of a large number of small pores leads to a partial membrane potential breakdown in both polar regions of the cell. Second, over tens of milliseconds, a few entry sites for macromolecules are formed, preferentially in the hyperpolarized part of cell body and processes, at locations defined by the local membrane structure. These entry sites reseal on a time scale of 50 ms to several seconds, with residual small pores remaining open for several minutes. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 8 FIGURE 9 PMID:9336174

  7. Upper Devonian vertebrate taphonomy and sedimentology from the Klunas fossil site, Tervete Formation, Latvia

    NASA Astrophysics Data System (ADS)

    Vasiļkova, J.; Lukševičs, E.; Stinkulis, Ä.¢.; Zupinš, I.

    2012-04-01

    The deposits of the Tervete Formation, Famennian Stage of Latvia, comprising weakly cemented sandstone and sand intercalated with dolomitic marls, siltstone and clay, have been traditionally interpreted as having formed in a shallow, rather restricted sea with lowered salinity. During seven field seasons the excavations took place in the south-western part of Latvia, at the Klunas site, and resulted in extensive palaeontological and sedimentological data. The taphonomical analysis has been performed, having evaluated the size, sorting, orientation of the fossils, articulation and skeletal preservation as well as the degree of fragmentation and abrasion. The sedimentological analysis involved interpretation of sedimentary structures, palaeocurrent direction reconstruction, grain-size analysis and approximate water depth calculations. The vertebrate assemblage of the Klunas site represents all known taxa of the Sparnene Regional Stage of the Baltic Devonian, comprising placoderms Bothriolepis ornata Eichwald, B. jani Lukševičs, Phyllolepis tolli Vasiliauskas, Dunkleosteus sp. and Chelyophorus sp., sarcopterygians Holoptychius nobilissimus Agassiz, Platycephalichthys skuenicus Vorobyeva, Cryptolepis sp., Conchodus sp., Glyptopomus ? sp., "Strunius" ? sp., and Dipterus sp., as well as an undetermined actinopterygian. Placoderms Bothriolepis ornata and B. jani dominate the assemblage. The fossils are represented in the main by fully disarticulated placoderm plates and plate fragments, sarcopterygian scales and teeth, rarely bones of the head and shoulder girdle, and acanthodian spines and scales. The characteristic feature is the great amount of fragmentary remains several times exceeding the number of intact bones. The horizontal distribution of the bones over the studied area is not homogenous, distinct zones of increased or decreased density of fossils can be traced. Zones of the increased density usually contain many elements of various sizes, whereas zones of the

  8. Active Site Formation, Not Bond Kinetics, Limits Adhesion Rate between Human Neutrophils and Immobilized Vascular Cell Adhesion Molecule 1

    PubMed Central

    Waugh, Richard E.; Lomakina, Elena B.

    2009-01-01

    Abstract The formation of receptor ligand bonds at the interface between different cells and between cells and substrates is a widespread phenomenon in biological systems. Physical measurements of bond formation rates between cells and substrates have been exploited to increase our understanding of the biophysical mechanisms that regulate bond formation at interfaces. Heretofore, these measurements have been interpreted in terms of simple bimolecular reaction kinetics. Discrepancies between this simple framework and the behavior of neutrophils adhering to surfaces expressing vascular cell adhesion molecule 1 (VCAM-1) motivated the development of a new kinetic framework in which the explicit formation of active bond formation sites (reaction zones) are a prerequisite for bond formation to occur. Measurements of cells interacting with surfaces having a wide range of VCAM-1 concentrations, and for different durations of contact, enabled the determination of novel kinetic rate constants for the formation of reaction zones and for the intrinsic bond kinetics. Comparison of these rates with rates determined previously for other receptor-ligand pairs points to a predominant role of extrinsic factors such as surface topography and accessibility of active molecules to regions of close contact in determining forward rates of bond formation at cell interfaces. PMID:19134479

  9. Probing Enhanced Double-Strand Break Formation at Abasic Sites within Clustered Lesions in Nucleosome Core Particles.

    PubMed

    Banerjee, Samya; Chakraborty, Supratim; Jacinto, Marco Paolo; Paul, Michael D; Balster, Morgan V; Greenberg, Marc M

    2017-01-10

    DNA is rapidly cleaved under mild alkaline conditions at apyrimidinic/apurinic sites, but the half-life is several weeks in phosphate buffer (pH 7.5). However, abasic sites are ∼100-fold more reactive within nucleosome core particles (NCPs). Histone proteins catalyze the strand scission, and at superhelical location 1.5, the histone H4 tail is largely responsible for the accelerated cleavage. The rate constant for strand scission at an abasic site is enhanced further in a nucleosome core particle when it is part of a bistranded lesion containing a proximal strand break. Cleavage of this form results in a highly deleterious double-strand break. This acceleration is dependent upon the position of the abasic lesion in the NCP and its structure. The enhancement in cleavage rate at an apurinic/apyrimidinic site rapidly drops off as the distance between the strand break and abasic site increases and is negligible once the two forms of damage are separated by 7 bp. However, the enhancement of the rate of double-strand break formation increases when the size of the gap is increased from one to two nucleotides. In contrast, the cleavage rate enhancement at 2-deoxyribonolactone within bistranded lesions is more modest, and it is similar in free DNA and nucleosome core particles. We postulate that the enhanced rate of double-strand break formation at bistranded lesions containing apurinic/apyrimidinic sites within nucleosome core particles is a general phenomenon and is due to increased DNA flexibility.

  10. Site-specific glycoproteomics confirms that protein structure dictates formation of N-glycan type, core fucosylation and branching.

    PubMed

    Thaysen-Andersen, Morten; Packer, Nicolle H

    2012-11-01

    Growing evidence indicates that the individualized and highly reproducible N-glycan repertoires on each protein glycosylation site modulate function. Relationships between protein structures and the resulting N-glycoforms have previously been observed, but remain to be quantitatively confirmed and examined in detail to define the responsible mechanisms in the conserved mammalian glycosylation machinery. Here, we investigate this relationship by manually extracting and analyzing quantitative and qualitative site-specific glycoprofiling data from 117 research papers. Specifically, N-glycan structural motifs were correlated with the structure of the protein carriers, focusing on the solvent accessibility of the individual glycosylation sites and the physicochemical properties of the surrounding polypeptide chains. In total, 474 glycosylation sites from 169 mammalian N-glycoproteins originating from different tissues/body fluids were investigated. It was confirmed statistically that the N-glycan type, degree of core fucosylation and branching are strongly influenced by the glycosylation site accessibility. For these three N-glycan features, glycosylation sites carrying highly processed glycans were significantly more solvent-accessible than those carrying less processed counterparts. The glycosylation site accessibilities could be linked to molecular signatures at the primary and secondary protein levels, most notably to the glycoprotein size and the proportion of glycosylation sites located in accessible β-turns. In addition, the subcellular location of the glycoproteins influenced the formation of the N-glycan structures. These data confirm that protein structures dictate site-specific formation of several features of N-glycan structures by affecting the biosynthetic pathway. Mammals have, as such, evolved mechanisms enabling proteins to influence the N-glycans they present to the extracellular environment.

  11. Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases

    PubMed Central

    Bellini, Dom; Horrell, Sam; Hutchin, Andrew; Phippen, Curtis W.; Strange, Richard W.; Cai, Yuming; Wagner, Armin; Webb, Jeremy S.; Tews, Ivo; Walsh, Martin A.

    2017-01-01

    The bacterial second messenger cyclic di-3′,5′-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825EAL) and PA1727 (MucREAL). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825EAL in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5′-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation. PMID:28186120

  12. Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases.

    PubMed

    Bellini, Dom; Horrell, Sam; Hutchin, Andrew; Phippen, Curtis W; Strange, Richard W; Cai, Yuming; Wagner, Armin; Webb, Jeremy S; Tews, Ivo; Walsh, Martin A

    2017-02-10

    The bacterial second messenger cyclic di-3',5'-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825(EAL)) and PA1727 (MucR(EAL)). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825(EAL) in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5'-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation.

  13. Role of soil macrofauna in soil formation in post mining sites along climatic and litter quality gradients

    NASA Astrophysics Data System (ADS)

    Frouz, Jan

    2014-05-01

    Soil macrofauna can play important role in soil formation. Here we used thin soil sections to study this process in two environmental gradients, climatic gradient, and liter quality gradient. Climatic gradient consist from four chronosequences of post mining sites in the USA, covering hardwood forest (TN, IN), tallgrass prairie (IL), or shortgrass prairie (WY). Earthworms and other saprophages were absent in such shortgrass sites but were present in the wetter, eastern sites. Absence of saprophagous groups, and especially earthworms, resulted in the absence of bioturbation in shortgrass prairie sites while worm casts and other biogenic structures formed an important part of the soil profile in other chronosequences, in short grass prairie in turn physical processes, such as erosion may play important role in soil mixing. Litter quality gradient consists from set of 28 sites planted with six kind of tree stand (pine, larch, spruce, oak, lime and alder) and unreclaimed sites (covered by willow, birch, aspen dominated forest) on one large heap in Czech Republic. Earthworm density on these sites negatively correlate with CN ratio, the same relationships was shown for proportion of earthworm cast in soil volume. In sites with high earthworm density Oe layer was absent and A layer formed by worm casts was well developed, in the contrary when earthworm were absent Oe layer was thick and A layer absent. Development of A layer correlate with soil carbon storage.

  14. Influence of the Heterogeneous Nucleation Sites on the Kinetics of Intermetallic Phase Formation in Aged Duplex Stainless Steel

    NASA Astrophysics Data System (ADS)

    Melo, Elis Almeida; Magnabosco, Rodrigo

    2017-09-01

    The aim of this work is to study the influence of the heterogeneous nucleation site quantity, observed in different ferrite and austenite grain size samples, on the phase transformations that result in intermetallic phases in a UNS S31803 duplex stainless steel (DSS). Solution treatment was conducted for 1, 24, 96, or 192 hours at 1373 K (1100 °C) to obtain different ferrite and austenite grain sizes. After solution treatment, isothermal aging treatments for 5, 8, 10, 20, 30, or 60 minutes at 1123 K (850 °C) were performed to verify the influence of different amounts of heterogeneous nucleation sites in the kinetics of intermetallic phase formation. The sample solution treated for 1 hour, with the highest surface area between matrix phases, was the one that presented, after 60 minutes at 1123 K (850 °C), the smaller volume fraction of ferrite (indicative of greater intermetallic phase formation), higher volume of sigma (that was present in coral-like and compact morphologies), and chi phase. It was not possible to identify which was the first nucleated phase, sigma or chi. It was also observed that the phase formation kinetics is higher for the sample solution treated for 1 hour. It was evidenced that, from a certain moment on, the chi phase begins to be consumed due to the sigma phase formation, and the austenite/ferrite interface presents higher S V for all solution treatment times. It was also observed that intermetallic phases form preferably in austenite-ferrite interfaces, although the higher occupation rate occurs at triple junction ferrite-ferrite-ferrite. It was verified that there was no saturation of nucleation sites in any interface type nor triple junction, and the equilibrium after 1 hour of aging at 1123 K (850 °C) was not achieved. It was then concluded that sigma phase formation is possibly controlled by diffusional processes, without saturation of nucleation sites.

  15. Kawasaki disease patients with redness or crust formation at the Bacille Calmette-Guérin inoculation site.

    PubMed

    Uehara, Ritei; Igarashi, Hiroshi; Yashiro, Mayumi; Nakamura, Yosikazu; Yanagawa, Hiroshi

    2010-05-01

    A specific diagnostic test for Kawasaki disease (KD) is currently unavailable. Redness or crust formation at the Bacille Calmette-Guérin (BCG) inoculation site is listed as a positive sign in the diagnostic guidelines of KD. The purpose of this study was to investigate the epidemiologic features of KD patients with such changes at the BCG inoculation site and to evaluate the specificity of this sign in KD diagnosis. Data on KD patients who received BCG vaccination were analyzed from a Japanese nationwide epidemiologic survey on KD conducted in 2007. Patients who had 5 or 6 principal signs (complete cases) with redness or crust formation at the BCG inoculation site were compared by sex, year of hospital visit, day of first hospital visit, recurrent status, and presence of KD in siblings. To evaluate the specificity of the sign for KD diagnosis, patients aged 2 years or younger who were diagnosed as having respiratory syncytial virus or rotavirus infection using a commercial rapid test and who required hospitalization were observed. Of the 15,524 KD patients with a history of BCG vaccination, 7745 (49.9%) had redness or crust formation at the BCG inoculation site. This was observed in more than 70% of complete KD patients aged 3 to 20 months. Of these patients, the proportion with this sign in the group whose first day of hospital visit was within 1 to 4 days from the onset was significantly larger than that of the other patients groups (5-9 or 10+ days) (52.1%, P < 0.001). Among the patients with respiratory syncytial virus or rotavirus infection, none showed these changes at BCG inoculation site. Redness or crust formation at the BCG inoculation site is a useful diagnostic sign for KD among children aged 3 to 20 months in countries with a BCG vaccination program. Even if patients have 4 or fewer signs of the clinical criteria for KD, physicians should consider that patients with redness or crust formation at the BCG inoculation site could suffer from KD.

  16. DDT Vertical Migration and Formation of Accumulation Layer in Pesticide-Producing Sites.

    PubMed

    Liu, Li; Bai, Liping; Man, Changgeng; Liang, Wuhong; Li, Fasheng; Meng, Xiaoguang

    2015-08-04

    Soil samples were collected at various depths (0.5-21.5 m) from ten boreholes that were drilled with a SH-30 Model Rig, four of which were at a dicofol production site while six were at a dichlorodiphenyltrichloroethane (DDT) production site. In industrial sites, the shallow soils at depths of 0-2 m were mostly backfill soils, which cannot represent the contamination situation of the sites. The contaminated levels in the deep original soil can represent the situation in contaminated sites. All the soil samples investigated at the DDT and dicofol production sites were found to be seriously polluted. The contents of both DDT (0.6-6071 mg/kg) and dicofol (0.5-1440 mg/kg) were much higher at the dicofol production site than at the DDT production site (DDTs, 0.01-664.6 mg/kg; dicofol, <0.1 mg/kg), even in the deep soil. DDTs had a different distribution in the soil of the pesticide production site from that in the soil outside the sites and that in agricultural soils. The results of the investigation revealed that DDTs were easily enriched in cohesive soil and in the bottom zone of aquifers, where the concentration was higher than in above the layers. DDTs were found to be hard to degrade, and their degradation speed was slower than their vertical migration, despite the fact that hydrophobic DDTs did not migrate easily in soils. In the dicofol production site, the value of DDE/DDD cannot indicate the degradation condition of DDTs, nor can the value of (DDE + DDD)/DDT identify how long DDTs have remained in the soil. It is debatable that the half-life of DDT inputted to soils is about 20-30 years, maybe longer than the generally recognized time.

  17. Site- and bond-selective H- formation in methylated pyrimidine bases driven by potassium-molecule collisions

    NASA Astrophysics Data System (ADS)

    Ferreira da Silva, F.; Almeida, D.; Garcia, G.; Limão-Vieira, P.

    2012-11-01

    Electron transfer in alkali-molecule collisions to gas phase thymine and uracil yielding H- formation is selectively controlled in the energy range between 5 and 65 eV. By tuning the collision energy, electron transfer from the alkali to methylated thymine (at the N1 position), methylated uracil (at the N3 position) and partly deuterated thymine, enables H-formation. Such process proceeds not only through the breaking of the (C-H) against (N-H) bonds but also through N1 against N3 sites. Such selectivity, as far as bond and site are concerned, is here reported for the first time in collision induced dissociation experiments by alkali-molecule interactions.

  18. Roles of target site location and sequence complementarity in trans-acting siRNA formation in Arabidopsis.

    PubMed

    Zhang, Changqing; Ng, Danny W-K; Lu, Jie; Chen, Z Jeffrey

    2012-01-01

    In plants, many mRNAs and non-coding RNAs are cleaved by RNA-induced silencing complexes. After cleavage, only a limited number of RNAs are processed into trans-acting siRNAs (tasiRNAs). One reason is that 22 nt small RNAs, but not the more common 21 nt small RNAs, can efficiently trigger tasiRNA formation. The characteristics of the target transcripts may also affect tasiRNA production. Here we report the effects of target site location and sequence complementarity on tasiRNA formation. A synthetic sequence that included a miR173 target site and two siRNAs targeting an endogenous mRNA encoding PHYTOENE DESATURASE3 was introduced into a protein-coding (GFP) gene in the coding region or 3' UTR. tasiRNAs were generated in the transgenic seedlings, and the PDS3 mRNA level was reduced, leading to a photobleaching phenotype. It was found that tasiRNAs were most efficiently produced when the miR173 target site was placed immediately after the stop codon. Introducing premature stop codons caused a dramatic reduction of tasiRNAs and over-accumulation of 3' cleavage products, suggesting positive effects of translation on processing the 3' cleavage products into tasiRNAs. By systematically mutating the miR173 target site, we found that perfect complementarity between the 3' end of miR173 and the 5' end of the target sequence was crucial. Mismatches at that position abolished tasiRNA formation, but mismatches at the 5' end of miR173 had less effect. These data suggest important roles for translation and specific sequence complementarity in tasiRNA formation, providing new insights into tasiRNA biogenesis as well as a strategy for improving the efficiency of RNA interference (RNAi) using tasiRNAs. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  19. Mid-infrared observations of methanol maser sites and ultracompact H ii regions: signposts of high-mass star formation

    NASA Astrophysics Data System (ADS)

    Walsh, A. J.; Bertoldi, F.; Burton, M. G.; Nikola, T.

    2001-09-01

    N-band (10.5μm) and/or Q-band (20.0μm) images taken with MANIAC on the ESO/MPI 2.2-m telescope are presented for 31 methanol maser sites and 19 ultracompact (UC) Hii regions. Most of the maser sites and UC Hii regions are coincident with mid-infrared (MIR) sources to within the positional uncertainties of ~3arcsec, consistent with the maser emission being powered by the MIR source. The IRAS source positions, however, do not always coincide with the MIR sources. Based on an average infrared spectral energy distribution, we deduce that the MIR objects are luminous enough that they should also produce a strong ionizing radiation. Some sources are consistent with stars of later spectral type, but not all can be. A number of maser sites show no detectable radio continuum emission associated with MIR emission, despite a powering source luminous enough potentially to produce an UC Hii region. Since no signs of an UC Hii region are detected here, these maser sites might be produced during a very early stage of stellar evolution. We present objects that show evidence of outflow activity stemming from a maser site, exhibiting CO and/or CS line profiles indicative of outflows coincident with the MIR source. These cases are promising examples of maser sites signposting the earliest stages of high-mass star formation.

  20. Radial Glial Cell-Neuron Interaction Directs Axon Formation at the Opposite Side of the Neuron from the Contact Site.

    PubMed

    Xu, Chundi; Funahashi, Yasuhiro; Watanabe, Takashi; Takano, Tetsuya; Nakamuta, Shinichi; Namba, Takashi; Kaibuchi, Kozo

    2015-10-28

    How extracellular cues direct axon-dendrite polarization in mouse developing neurons is not fully understood. Here, we report that the radial glial cell (RGC)-cortical neuron interaction directs axon formation at the opposite side of the neuron from the contact site. N-cadherin accumulates at the contact site between the RGC and cortical neuron. Inhibition of the N-cadherin-mediated adhesion decreases this oriented axon formation in vitro, and disrupts the axon-dendrite polarization in vivo. Furthermore, the RGC-neuron interaction induces the polarized distribution of active RhoA at the contacting neurite and active Rac1 at the opposite neurite. Inhibition of Rho-Rho-kinase signaling in a neuron impairs the oriented axon formation in vitro, and prevents axon-dendrite polarization in vivo. Collectively, these results suggest that the N-cadherin-mediated radial glia-neuron interaction determines the contacting neurite as the leading process for radial glia-guided neuronal migration and directs axon formation to the opposite side acting through the Rho family GTPases.

  1. Mechanism of site-specific psoralen photoadducts formation in triplex DNA directed by psoralen-conjugated oligonucleotides.

    PubMed

    Ping, Yueh-Hsin; Rana, Tariq M

    2005-02-22

    Triplex-formation oligonucleotides attached with a photoreactive psoralen molecule (psoTFO) can be used to induce site-specific DNA damage and to control gene expression. Inhibition of transcription by psoralen-cross-linked triplexes results in both arrest and termination of RNA Pol II transcriptional complexes during elongation. To understand the relationship between triplex psoralen cross-linking products and the fate of RNA Pol II elongation complexes, it is important to delineate the mechanism for creating site-specific psoralen photoadducts in a target duplex DNA. To investigate the mechanism of photoadduct-formation by psoralen photo-cross-linking, triplex structures were generated by targeting a DNA duplex with psoTFOs of different lengths. The psoralen photoadducts were then analyzed after UV irradiation, which initiates the psoralen cross-linking reaction. Our results demonstrated that UV irradiation of triplexes formed between a psoTFO and a DNA duplex generated two distinct groups of psoralen photoadducts: monoadducts and psoralen interstrand cross-link products. The formation of these psoralen photoadducts was also photoreversible through exposure to short wavelength UV irradiation. The length of a psoTFO was shown to establish the position at which psoralen was added to the target DNA duplex and determined which photoadducts products formed predominantly. Kinetic experiments that monitored the formation of the psoralen photoadducts also suggested that the length of the psoTFO influenced which photoadducts were preferentially formed at faster rates. Taken together, these studies provide new insight into the mechanism associated with the formation of psoralen photoadducts that are directed by psoTFO during triplex formation.

  2. Insights into site formation at Rose Cottage Cave, South Africa, based on the analysis of sediment peels

    NASA Astrophysics Data System (ADS)

    Kloos, Peter; Miller, Christopher E.; Kritikakis, Panagiotis; Wadley, Lyn

    2016-04-01

    Rose Cottage Cave (RCC), in South Africa, has been a key site for explaining the origins of modern human behaviour and movement of early modern humans out of Africa. Nine sediment peels were made previously from the profile sections, preserving original materials that provide a record of cultural and environmental change during the late Pleistocene and Holocene. Here, we present the preliminary results of the study of the RCC sediment peels which aims to investigate site formation processes and the implications for site interpretation. Methods used include micromorphology and Fourier Transform Infrared spectroscopy coupled with detailed observations of the peels. The predominance of geogenic processes is demonstrated by the abundance of silt- and sand-sized quartz grains, which entered the site primarily through a crevice at the back of the cave. RCC lacks rich anthropogenic deposits as noted at other Middle Stone Age sites in southern Africa, but anthropogenic input to the sediment is indicated by the presence of charcoal, burnt bone, lithic fragments, fat-derived char and ashes. Clay coating fragments and chaotic microstructures demonstrate that bioturbation and colluvial reworking homogenised much of the deposit and may explain the absence of preserved bedding and rarity of combustion features. Downward movement of water through the sequence, indicated by clay coatings, is the likely cause for poor bone preservation and near lack of ashes at the site, as well as fluctuations in dose rate that have complicated luminescence dating studies. Evidence for diagenesis at the site is in the form of secondary apatite and gypsum. Sedimentary structures such as channel lag deposits and (silt and sand) laminae observed in peels dating between 60 and 35 ka BP suggest a high-energy sedimentary environment, which experienced flooding events that eroded underlying deposits and deposited large volumes of sediment. This explains why some of the post-Howiesons Poort layers contain

  3. The homing of bone marrow MSCs to non-osseous sites for ectopic bone formation induced by osteoinductive calcium phosphate

    PubMed Central

    Song, Guodong; Habibovic, Pamela; Bao, Chongyun; Hu, Jing; van Blitterswijk, Clemens A.; Yuan, Huipin; Chen, Wenchuan; Xu, Hockin H.K.

    2013-01-01

    Osteoinductive biomaterials are promising for bone repair. There is no direct proof that bone marrow mesenchymal stem cells (BMSCs) home to non-osseous sites and participate in ectopic bone formation induced by osteoinductive bioceramics. The objective of this study was to use a sex-mismatched beagle dog model to investigate BMSC homing via blood circulation to participate in ectopic bone formation via osteoinductive biomaterial. BMSCs of male dogs were injected into female femoral marrow cavity. The survival and stable chimerism of donor BMSCs in recipients were confirmed with polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH). Biphasic calcium phosphate (BCP) granules were implanted in dorsal muscles of female dogs. Y chromosomes were detected in samples harvested from female dogs which had received male BMSCs. At 4 weeks, cells with Y-chromosomes were distributed in the new bone matrix throughout the BCP granule implant. At 6 weeks, cells with Y chromosomes were present in newly mineralized woven bone. TRAP positive osteoclast-like cells were observed in 4-week implants, and the number of such cells decreased from 4 to 6 weeks. These results show that osteoprogenitors were recruited from bone marrow and homed to ectopic site to serve as a cell source for calcium phosphate-induced bone formation. In conclusion, BMSCs were demonstrated to migrate from bone marrow through blood circulation to non-osseous bioceramic implant site to contribute to ectopic bone formation in a canine model. BCP induced new bone in muscles without growth factor delivery, showing excellent osteoinductivity that could be useful for bone tissue engineering. PMID:23298780

  4. Impact of Internet Images: Impression-Formation Effects of University Web Site Images

    ERIC Educational Resources Information Center

    Ramasubramanian, Srividya; Gyure, James F.; Mursi, Nasreen M.

    2002-01-01

    Institutions of higher education are increasingly becoming dependent on Web-based marketing to reach out to their target audiences. The current empirical study examines the types of impressions formed by prospective students based on exposure to different university Web site images. A between-subjects experiment was conducted using four identical…

  5. Impact of Internet Images: Impression-Formation Effects of University Web Site Images

    ERIC Educational Resources Information Center

    Ramasubramanian, Srividya; Gyure, James F.; Mursi, Nasreen M.

    2002-01-01

    Institutions of higher education are increasingly becoming dependent on Web-based marketing to reach out to their target audiences. The current empirical study examines the types of impressions formed by prospective students based on exposure to different university Web site images. A between-subjects experiment was conducted using four identical…

  6. Genetic alterations and cancer formation in a European flatfish at sites of different contaminant burdens.

    PubMed

    Lerebours, Adélaïde; Stentiford, Grant D; Lyons, Brett P; Bignell, John P; Derocles, Stéphane A P; Rotchell, Jeanette M

    2014-09-02

    Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological "normal" fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis.

  7. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3'-end formation.

    PubMed Central

    Hyman, L E; Seiler, S H; Whoriskey, J; Moore, C L

    1991-01-01

    The sequences directing formation of mRNA 3' ends in Saccharomyces cerevisiae are not well defined. This is in contrast to the situation in higher eukaryotes in which the sequence AAUAAA is known to be crucial to proper 3'-end formation. The AAUAAA hexanucleotide is found upstream of the poly(A) site in some but not all yeast genes. One of these is the gene coding for alcohol dehydrogenase, ADH2. Deletion or a double point mutation of the AAUAAA has only a small effect on the efficiency of the reaction, and in contrast to the mammalian system, it is most likely not operating as a major processing signal in the yeast cell. However, we isolated point mutations which reveal that a region located approximately 80 nucleotides upstream of the poly(A) site plays a critical role in either transcription termination, polyadenylation, or both. These mutations represent the first point mutations in yeasts which significantly reduce the efficiency of 3'-end formation. Images PMID:2005893

  8. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3'-end formation.

    PubMed

    Hyman, L E; Seiler, S H; Whoriskey, J; Moore, C L

    1991-04-01

    The sequences directing formation of mRNA 3' ends in Saccharomyces cerevisiae are not well defined. This is in contrast to the situation in higher eukaryotes in which the sequence AAUAAA is known to be crucial to proper 3'-end formation. The AAUAAA hexanucleotide is found upstream of the poly(A) site in some but not all yeast genes. One of these is the gene coding for alcohol dehydrogenase, ADH2. Deletion or a double point mutation of the AAUAAA has only a small effect on the efficiency of the reaction, and in contrast to the mammalian system, it is most likely not operating as a major processing signal in the yeast cell. However, we isolated point mutations which reveal that a region located approximately 80 nucleotides upstream of the poly(A) site plays a critical role in either transcription termination, polyadenylation, or both. These mutations represent the first point mutations in yeasts which significantly reduce the efficiency of 3'-end formation.

  9. Addition of Adipose-Derived Stem Cells to Mesenchymal Stem Cell Sheets Improves Bone Formation at an Ectopic Site.

    PubMed

    Wang, Zhifa; Li, Zhijin; Dai, Taiqiang; Zong, Chunlin; Liu, Yanpu; Liu, Bin

    2016-02-02

    To determine the effect of adipose-derived stem cells (ADSCs) added to bone marrow-derived mesenchymal stem cell (MSC) sheets on bone formation at an ectopic site. We isolated MSCs and ADSCs from the same rabbits. We then prepared MSC sheets for implantation with or without ADSCs subcutaneously in the backs of severe combined immunodeficiency (SCID) mice. We assessed bone formation at eight weeks after implantation by micro-computed tomography and histological analysis. In osteogenic medium, MSCs grew to form multilayer sheets containing many calcium nodules. MSC sheets without ADSCs formed bone-like tissue; although neo-bone and cartilage-like tissues were sparse and unevenly distributed by eight weeks after implantation. In comparison, MSC sheets with ADSCs promoted better bone regeneration as evidenced by the greater density of bone, increased mineral deposition, obvious formation of blood vessels, large number of interconnected ossified trabeculae and woven bone structures, and greater bone volume/total volume within the composite constructs. Our results indicate that although sheets of only MSCs have the potential to form tissue engineered bone at an ectopic site, the addition of ADSCs can significantly increase the osteogenic potential of MSC sheets. Thus, the combination of MSC sheets with ADSCs may be regarded as a promising therapeutic strategy to stimulate bone regeneration.

  10. Active site remodelling accompanies thioester bond formation in the SUMO E1.

    PubMed

    Olsen, Shaun K; Capili, Allan D; Lu, Xuequan; Tan, Derek S; Lima, Christopher D

    2010-02-18

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.

  11. Active site remodelling accompanies thioester bond formation in the SUMO E1

    SciTech Connect

    Olsen, Shaun K.; Capili, Allan D.; Lu, Xuequan; Tan, Derek S.; Lima, Christopher D.

    2010-03-30

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 {angstrom}, respectively. These structures show that side chain contacts to ATP-Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.

  12. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    PubMed Central

    Wang, Yang-Gang; Mei, Donghai; Glezakou, Vassiliki-Alexandra; Li, Jun; Rousseau, Roger

    2015-01-01

    Catalysis by gold supported on reducible oxides has been extensively studied, yet issues such as the nature of the catalytic site and the role of the reducible support remain fiercely debated topics. Here we present ab initio molecular dynamics simulations of an unprecedented dynamic single-atom catalytic mechanism for the oxidation of carbon monoxide by ceria-supported gold clusters. The reported dynamic single-atom catalytic mechanism results from the ability of the gold cation to strongly couple with the redox properties of the ceria in a synergistic manner, thereby lowering the energy of redox reactions. The gold cation can break away from the gold nanoparticle to catalyse carbon monoxide oxidation, adjacent to the metal/oxide interface and subsequently reintegrate back into the nanoparticle after the reaction is completed. Our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in catalysis. PMID:25735407

  13. Barometric pressure transient testing applications at the Nevada Test Site: formation permeability analysis. Final report

    SciTech Connect

    Hanson, J.M.

    1984-12-01

    The report evaluates previous investigations of the gas permeability of the rock surrounding emplacement holes at the Nevada Test Site. The discussion sets the framework from which the present uncertainty in gas permeability can be overcome. The usefulness of the barometric pressure testing method has been established. Flow models were used to evaluate barometric pressure transients taken at NTS holes U2fe, U19ac and U20ai. 31 refs., 103 figs., 18 tabs. (ACR)

  14. Possibility of microscopic liquid water formation at landing sites on Mars and their observational potential

    NASA Astrophysics Data System (ADS)

    Pál, B.; Kereszturi, Á.

    2017-01-01

    Microscopic liquid brines, especially calcium-perchlorate could emerge by deliquescence on Mars during night time hours. Using climate model computations and orbital humidity observations, the ideal periods and their annual plus daily characteristics at various past, current and future landing sites were compared. Such results provide context for future analysis and targeting the related observations by the next missions for Mars. Based on the analysis, at most (but not all) past missions' landing sites, microscopic brine could emerge during night time for different durations. Analysing the conditions at ExoMars rover's primary landing site at Oxia Planum, the best annual period was found to be between Ls 115-225, and in Local Time 2-5, after midnight. In an ideal case, 4 h of continuous liquid phase can emerge there. Local conditions might cause values to differ from those estimated by the model. Thermal inertia could especially make such differences (low TI values favour fast cooling and H2O cold trapping at loose surfaces) and the concentration of calcium-perchlorate salt in the regolith also influences the process (it might occur preferentially at long-term exposed surfaces without recent loose dust coverage). These factors should be taken into account while targeting future liquid water observations on Mars.

  15. Active mutants of the TCR-mediated p38α alternative activation site show changes in the phosphorylation lip and DEF site formation.

    PubMed

    Tzarum, Netanel; Diskin, Ron; Engelberg, David; Livnah, Oded

    2011-02-04

    The p38α mitogen-activated protein kinase is commonly activated by dual (Thr and Tyr) phosphorylation catalyzed by mitogen-activated protein kinase kinases. However, in T-cells, upon stimulation of the T-cell receptor, p38α is activated via an alternative pathway, involving its phosphorylation by zeta-chain-associated protein kinase 70 on Tyr323, distal from the phosphorylation lip. Tyr323-phosphorylated p38α is autoactivated, resulting in monophosphorylation of Thr180. The conformational changes induced by pTyr323 mediating autoactivation are not known. The lack of pTyr323 p38α for structural studies promoted the search for Tyr323 mutations that may functionally emulate its effect when phosphorylated. Via a comprehensive mutagenesis of Tyr323, we identified mutations that rendered the kinase intrinsically active and others that displayed no activity. Crystallographic studies of selected active (p38α(Y323Q), p38α(Y323T), and p38α(Y323R)) and inactive (p38α(Y323F)) mutants revealed that substantial changes in interlobe orientation, extended conformation of the activation loop, and formation of substrate docking DEF site (docking site for extracellular signal-regulated kinase FXF) interaction pocket are associated with p38α activation. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. In site bioimaging of hydrogen sulfide uncovers its pivotal role in regulating nitric oxide-induced lateral root formation.

    PubMed

    Li, Yan-Jun; Chen, Jian; Xian, Ming; Zhou, Li-Gang; Han, Fengxiang X; Gan, Li-Jun; Shi, Zhi-Qi

    2014-01-01

    Hydrogen sulfide (H2S) is an important gasotransmitter in mammals. Despite physiological changes induced by exogenous H2S donor NaHS to plants, whether and how H2S works as a true cellular signal in plants need to be examined. A self-developed specific fluorescent probe (WSP-1) was applied to track endogenous H2S in tomato (Solanum lycopersicum) roots in site. Bioimaging combined with pharmacological and biochemical approaches were used to investigate the cross-talk among H2S, nitric oxide (NO), and Ca(2+) in regulating lateral root formation. Endogenous H2S accumulation was clearly associated with primordium initiation and lateral root emergence. NO donor SNP stimulated the generation of endogenous H2S and the expression of the gene coding for the enzyme responsible for endogenous H2S synthesis. Scavenging H2S or inhibiting H2S synthesis partially blocked SNP-induced lateral root formation and the expression of lateral root-related genes. The stimulatory effect of SNP on Ca(2+) accumulation and CaM1 (calmodulin 1) expression could be abolished by inhibiting H2S synthesis. Ca(2+) chelator or Ca(2+) channel blocker attenuated NaHS-induced lateral root formation. Our study confirmed the role of H2S as a cellular signal in plants being a mediator between NO and Ca(2+) in regulating lateral root formation.

  17. Radial Glial Cell–Neuron Interaction Directs Axon Formation at the Opposite Side of the Neuron from the Contact Site

    PubMed Central

    Xu, Chundi; Funahashi, Yasuhiro; Watanabe, Takashi; Takano, Tetsuya; Nakamuta, Shinichi; Namba, Takashi

    2015-01-01

    How extracellular cues direct axon–dendrite polarization in mouse developing neurons is not fully understood. Here, we report that the radial glial cell (RGC)–cortical neuron interaction directs axon formation at the opposite side of the neuron from the contact site. N-cadherin accumulates at the contact site between the RGC and cortical neuron. Inhibition of the N-cadherin-mediated adhesion decreases this oriented axon formation in vitro, and disrupts the axon–dendrite polarization in vivo. Furthermore, the RGC–neuron interaction induces the polarized distribution of active RhoA at the contacting neurite and active Rac1 at the opposite neurite. Inhibition of Rho–Rho-kinase signaling in a neuron impairs the oriented axon formation in vitro, and prevents axon–dendrite polarization in vivo. Collectively, these results suggest that the N-cadherin-mediated radial glia–neuron interaction determines the contacting neurite as the leading process for radial glia-guided neuronal migration and directs axon formation to the opposite side acting through the Rho family GTPases. SIGNIFICANCE STATEMENT Neurons are highly polarized cell lines typically with a single axon and multiple dendrites, which underlies the ability of integrating and transmitting the information in the brain. How is the axon–dendrite polarity of neurons established in the developing neocortex? Here we show that the N-cadherin-mediated radial glial cell–neuron interaction directs axon–dendrite polarization, the radial glial cell–neuron interaction induces polarized distribution of active RhoA and active Rac1 in neurons, and Rho–Rho-kinase signaling is required for axon–dendrite polarization. Our work advances the overall understanding of how extracellular cues direct axon–dendrite polarization in mouse developing neurons. PMID:26511243

  18. Formation of pi, tau-dimethylhistidine on alkylation of trypsin with active-site-directed sulfonic acid methyl esters.

    PubMed

    Schubert, C; Fiedler, F

    1994-01-01

    The possibility of synthesizing stable alkyl analogues of acyl trypsins by introducing the alkyl residue by means of active-site-directed sulfonic acid esters was studied. Nine amidino- or guanidino-substituted sulfonic acids of different geometries and their methyl esters were prepared. The time-dependent inhibition of bovine trypsin by these esters, indicating modification at the active site of the enzyme, was followed. With the exception of p-guanidinobenzenesulfonic acid methyl ester, all the esters acted as irreversible inhibitors. The site of methylation, Ser-195 or His-57 (chymotrypsinogen numbering), was determine by analyzing for O-methylserine and methylhistidines. With four of the esters indications of a possible formation of, at most, 0.1 residue of O-methylserine per inactivated trypsin molecule were obtained. tau-Methylhistidine (but no pi-methylhistidine) was, however, always observed as the main product of the modification reaction. A further product, hitherto not yet described in active site methylations of serine proteinases, was pi, tau-dimethylhistidine (1,3-dimethylhistidine). The failure of an attempted synthesis of the N-acetyl-ethanolamine ester of p-toluene-sulfonic acid reported in the literature is shown to be due to the high instability of this ester.

  19. Mutations within potential glycosylation sites in the capsid protein of hepatitis E virus prevent the formation of infectious virus particles.

    PubMed

    Graff, Judith; Zhou, Yi-Hua; Torian, Udana; Nguyen, Hanh; St Claire, Marisa; Yu, Claro; Purcell, Robert H; Emerson, Suzanne U

    2008-02-01

    Hepatitis E virus is a nonenveloped RNA virus. However, the single capsid protein resembles a typical glycoprotein in that it contains a signal sequence and potential glycosylation sites that are utilized when recombinant capsid protein is overexpressed in cell culture. In order to determine whether these unexpected observations were biologically relevant or were artifacts of overexpression, we analyzed capsid protein produced during a normal viral replication cycle. In vitro transcripts from an infectious cDNA clone mutated to eliminate potential glycosylation sites were transfected into cultured Huh-7 cells and into the livers of rhesus macaques. The mutations did not detectably affect genome replication or capsid protein synthesis in cell culture. However, none of the mutants infected rhesus macaques. Velocity sedimentation analyses of transfected cell lysates revealed that mutation of the first two glycosylation sites prevented virion assembly, whereas mutation of the third site permitted particle formation and RNA encapsidation, but the particles were not infectious. However, conservative mutations that did not destroy glycosylation motifs also prevented infection. Overall, the data suggested that the mutations were lethal because they perturbed protein structure rather than because they eliminated glycosylation.

  20. Force mapping during the formation and maturation of cell adhesion sites with multiple optical tweezers.

    PubMed

    Schwingel, Melanie; Bastmeyer, Martin

    2013-01-01

    Focal contacts act as mechanosensors allowing cells to respond to their biomechanical environment. Force transmission through newly formed contact sites is a highly dynamic process requiring a stable link between the intracellular cytoskeleton and the extracellular environment. To simultaneously investigate cellular traction forces in several individual maturing adhesion sites within the same cell, we established a custom-built multiple trap optical tweezers setup. Beads functionalized with fibronectin or RGD-peptides were placed onto the apical surface of a cell and trapped with a maximum force of 160 pN. Cells form adhesion contacts around the beads as demonstrated by vinculin accumulation and start to apply traction forces after 30 seconds. Force transmission was found to strongly depend on bead size, surface density of integrin ligands and bead location on the cell surface. Highest traction forces were measured for beads positioned on the leading edge. For mouse embryonic fibroblasts, traction forces acting on single beads are in the range of 80 pN after 5 minutes. If two beads were positioned parallel to the leading edge and with a center-to-center distance less than 10 µm, traction forces acting on single beads were reduced by 40%. This indicates a spatial and temporal coordination of force development in closely related adhesion sites. We also used our setup to compare traction forces, retrograde transport velocities, and migration velocities between two cell lines (mouse melanoma and fibroblasts) and primary chick fibroblasts. We find that maximal force development differs considerably between the three cell types with the primary cells being the strongest. In addition, we observe a linear relation between force and retrograde transport velocity: a high retrograde transport velocity is associated with strong cellular traction forces. In contrast, migration velocity is inversely related to traction forces and retrograde transport velocity.

  1. Force Mapping during the Formation and Maturation of Cell Adhesion Sites with Multiple Optical Tweezers

    PubMed Central

    Schwingel, Melanie; Bastmeyer, Martin

    2013-01-01

    Focal contacts act as mechanosensors allowing cells to respond to their biomechanical environment. Force transmission through newly formed contact sites is a highly dynamic process requiring a stable link between the intracellular cytoskeleton and the extracellular environment. To simultaneously investigate cellular traction forces in several individual maturing adhesion sites within the same cell, we established a custom-built multiple trap optical tweezers setup. Beads functionalized with fibronectin or RGD-peptides were placed onto the apical surface of a cell and trapped with a maximum force of 160 pN. Cells form adhesion contacts around the beads as demonstrated by vinculin accumulation and start to apply traction forces after 30 seconds. Force transmission was found to strongly depend on bead size, surface density of integrin ligands and bead location on the cell surface. Highest traction forces were measured for beads positioned on the leading edge. For mouse embryonic fibroblasts, traction forces acting on single beads are in the range of 80 pN after 5 minutes. If two beads were positioned parallel to the leading edge and with a center-to-center distance less than 10 µm, traction forces acting on single beads were reduced by 40%. This indicates a spatial and temporal coordination of force development in closely related adhesion sites. We also used our setup to compare traction forces, retrograde transport velocities, and migration velocities between two cell lines (mouse melanoma and fibroblasts) and primary chick fibroblasts. We find that maximal force development differs considerably between the three cell types with the primary cells being the strongest. In addition, we observe a linear relation between force and retrograde transport velocity: a high retrograde transport velocity is associated with strong cellular traction forces. In contrast, migration velocity is inversely related to traction forces and retrograde transport velocity. PMID:23372781

  2. Cloning, localization and focus formation at DNA damage sites of canine XLF.

    PubMed

    Koike, Manabu; Yutoku, Yasutomo; Koike, Aki

    2017-01-20

    Understanding the molecular mechanisms of DNA double-strand break (DSB) repair processes, especially nonhomologous DNA-end joining (NHEJ), is critical for developing next-generation radiotherapies and chemotherapeutics for human and animal cancers. The localization, protein-protein interactions and post-translational modifications of core NHEJ factors, such as human Ku70 and Ku80, might play critical roles in controlling NHEJ activity. XRCC4-like factor (XLF) is a core NHEJ factor and plays a key role in the Ku-dependent NHEJ repair process in human cells. Recently, companion animals, such as canines, have been proposed to be a good model for many aspects of cancer research, including the development of chemotherapeutics. However, the localization and regulation of core NHEJ factors in canine cells have not been elucidated. Here, we show that the localization of canine XLF changes dynamically during the cell cycle. EYFP-canine XLF localizes in the nuclei of interphase cells and accumulates immediately at microirradiated DSB sites. The structure of a putative human XLF nuclear localization signal (NLS) and a putative 14-3-3 binding motif are evolutionarily conserved in canine, chimpanzee and mouse XLF. However, the putative β-TRCP-recognizable degron of human XLF is not conserved in canine and mouse. Additionally, some vital human XLF phosphorylation sites, including the ATM major phosphorylation site (S251), are not conserved in canine XLF. Our findings might be useful for the study of the molecular mechanisms of NHEJ in canine cells and for the development of new radiosensitizers that target XLF.

  3. Direct observation of hydrogen adsorption sites and nanocage formation in metal-organic frameworks.

    PubMed

    Yildirim, T; Hartman, M R

    2005-11-18

    The hydrogen adsorption sites in MOF5 were determined using neutron powder diffraction along with first-principles calculations. The metal-oxide cluster is primarily responsible for the adsorption while the organic linker plays only a secondary role. Equally important, at low temperatures and high-concentration, molecules form unique interlinked high-symmetry nanoclusters with intermolecular distances as small as 3.0 Angstrom and H(2) uptake as high as 11 wt %. These results hold the key to optimizing metal-organic framework (MOF) materials for hydrogen storage applications and also suggest that MOFs can be used as templates to create artificial interlinked hydrogen nanocages with novel properties.

  4. Direct Observation of Hydrogen Adsorption Sites and Nanocage Formation in Metal-Organic Frameworks

    NASA Astrophysics Data System (ADS)

    Yildirim, T.; Hartman, M. R.

    2005-11-01

    The hydrogen adsorption sites in MOF5 were determined using neutron powder diffraction along with first-principles calculations. The metal-oxide cluster is primarily responsible for the adsorption while the organic linker plays only a secondary role. Equally important, at low temperatures and high-concentration, H2 molecules form unique interlinked high-symmetry nanoclusters with intermolecular distances as small as 3.0 Å and H2 uptake as high as 11 wt %. These results hold the key to optimizing metal-organic framework (MOF) materials for hydrogen storage applications and also suggest that MOFs can be used as templates to create artificial interlinked hydrogen nanocages with novel properties.

  5. Malignant tumor formation at the site of previously irradiated acanthomatous epulides in four dogs

    SciTech Connect

    Thrall, D.E.; Goldschmidt, M.H.; Biery, D.N.

    1981-01-15

    The radiation response of acanthomatous epulis in 32 dogs was good, with an estimated median survival time of 21 months. Of the 32 patients, 14 have died. In 4 of those 14, malignant tumors developed at the site of the acanthomatous epulis. The tumors were of epithelial origin in 3 patients and of mesenchymal origin in 1 patient. Possibilities explaining the appearance of the malignancies included spontaneous malignant transformation, radiation induction of neoplasms, and radiation induction of malignant transformation. This uncommon complication was not considered contradictory to radiotherapy of acanthomatous epulides, because of their excellent response to irradiation and the long latent period between irradiation and appearance of the malignant tumor.

  6. BOREAS TE-1 Soils Data Over The SSA Tower Sites in Raster Format

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Anderson, Darwin; Knapp, David E.

    2000-01-01

    The BOREAS TE-1 team collected various data to characterize the soil-plant systems in the BOREAS SSA. This data set was gridded from vector layers of soil maps that were received from Dr. Darwin Anderson (TE-1), who did the original soil mapping in the field during 1994. The vector layers were gridded into raster files that cover approximately 1 square kilometer over each of the tower sites in the SSA. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  7. BOREAS TE-20 Soils Data Over the NSA-MSA and Tower Sites in Vector Format

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Veldhuis, Hugo; Knapp, David

    2000-01-01

    The BOREAS TE-20 team collected several data sets for use in developing and testing models of forest ecosystem dynamics. This data set contains vector layers of soil maps that were received from Dr. Hugo Veldhuis, who did the original mapping in the field during 1994. The vector layers were converted to ARCANFO EXPORT files. These data cover 1-kilometer diameters around each of the NSA tower sites, and another layer covers the NSA-MSA. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Center (DAAC).

  8. Stratigraphy of mid-Cretaceous formations at drilling sites in Weston and Johnson counties, northeastern Wyoming

    USGS Publications Warehouse

    Mereweather, E.A.

    1980-01-01

    The sedimentary rocks of early Late Cretaceous age in Weston County, Wyo., on the east flank of the Powder River Basin, are assigned, in ascending order, to the Belle Fourche Shale, Greenhorn Formation, and Carlile Shale. In Johnson County, on the west flank of the basin, the lower Upper Cretaceous strata are included in the Frontier Formation and the overlying Cody Shale. The Frontier Formation and some of the laterally equivalent strata in the Rocky Mountain region contain major resources of oil and gas. These rocks also include commercial deposits of bentonite. Outcrop sections, borehole logs, and core studies of the lower Upper Cretaceous rocks near Osage, in Weston County, and Kaycee, in Johnson County, supplement comparative studies of the fossils in the formations. Fossils of Cenomanian, Turonian, and Coniacian Age are abundant at these localities and form sequences of species which can be used for the zonation and correlation of strata throughout the region. The Belle Fourche Shale near Osage is about 115 m (meters) thick and consists mainly of noncalcareous shale, which was deposited in offshore-marine environments during Cenomanian time. These strata are overlain by calcareous shale and limestone of the Greenhorn Formation. In this area, the Greenhorn is about 85 m thick and accumulated in offshore, open-marine environments during the Cenomanian and early Turonian. The Carlile Shale overlies the Greenhorn and is composed of, from oldest to youngest, the Pool Creek Member, Turner Sandy Member, and Sage Breaks Member. In boreholes, the Pool Creek Member is about 23 m thick and consists largely of shale. The member was deposited in offshoremarine environments in Turonian time. These rocks are disconformably overlain by the Turner Sandy Member, a sequence about 50 m thick of interstratified shale, siltstone, and sandstone. The Turner accumulated during the Turonian in several shallow-marine environments. Conformably overlying the Turner is the slightly

  9. Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates.

    PubMed

    Siegmund, Vanessa; Piater, Birgit; Zakeri, Bijan; Eichhorn, Thomas; Fischer, Frank; Deutsch, Carl; Becker, Stefan; Toleikis, Lars; Hock, Björn; Betz, Ulrich A K; Kolmar, Harald

    2016-12-16

    Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.

  10. An evaluation of water quality in private drinking water wells near natural gas extraction sites in the Barnett Shale formation.

    PubMed

    Fontenot, Brian E; Hunt, Laura R; Hildenbrand, Zacariah L; Carlton, Doug D; Oka, Hyppolite; Walton, Jayme L; Hopkins, Dan; Osorio, Alexandra; Bjorndal, Bryan; Hu, Qinhong H; Schug, Kevin A

    2013-09-03

    Natural gas has become a leading source of alternative energy with the advent of techniques to economically extract gas reserves from deep shale formations. Here, we present an assessment of private well water quality in aquifers overlying the Barnett Shale formation of North Texas. We evaluated samples from 100 private drinking water wells using analytical chemistry techniques. Analyses revealed that arsenic, selenium, strontium and total dissolved solids (TDS) exceeded the Environmental Protection Agency's Drinking Water Maximum Contaminant Limit (MCL) in some samples from private water wells located within 3 km of active natural gas wells. Lower levels of arsenic, selenium, strontium, and barium were detected at reference sites outside the Barnett Shale region as well as sites within the Barnett Shale region located more than 3 km from active natural gas wells. Methanol and ethanol were also detected in 29% of samples. Samples exceeding MCL levels were randomly distributed within areas of active natural gas extraction, and the spatial patterns in our data suggest that elevated constituent levels could be due to a variety of factors including mobilization of natural constituents, hydrogeochemical changes from lowering of the water table, or industrial accidents such as faulty gas well casings.

  11. Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates

    PubMed Central

    Siegmund, Vanessa; Piater, Birgit; Zakeri, Bijan; Eichhorn, Thomas; Fischer, Frank; Deutsch, Carl; Becker, Stefan; Toleikis, Lars; Hock, Björn; Betz, Ulrich A. K.; Kolmar, Harald

    2016-01-01

    Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation. PMID:27982100

  12. Ground-water flow model of the Boone formation at the Tar Creek superfund site, Oklahoma and Kansas

    USGS Publications Warehouse

    Reed, T.B.; Czarnecki, John B.

    2006-01-01

    Extensive mining activities conducted at the Tar Creek Superfund site, one of the largest Superfund sites in the United States, pose substantial health and safety risks. Mining activities removed a total of about 6,000,000 tons of lead and zinc by 1949. To evaluate the effect of this mining on the ground-water flow, a MODFLOW 2000 digital model has been developed to simulate ground-water flow in the carbonate formations of Mississippian age underlying the Tar Creek Superfund site. The model consists of three layers of variable thickness and a grid of 580 rows by 680 columns of cells 164 feet (50 meters) on a side. Model flux boundary conditions are specified for rivers and general head boundaries along the northern boundary of the Boone Formation. Selected cells in layer 1 are simulated as drain cells. Model calibration has been performed to minimize the difference between simulated and observed water levels in the Boone Formation. Hydraulic conductivity values specified during calibration range from 1.3 to 35 feet per day for the Boone Formation with the larger values occurring along the axis of the Miami Syncline where horizontal anisotropy is specified as 10 to 1. Hydraulic conductivity associated with the mine void is set at 50,000 feet per day and a specific yield of 1.0 is specified to represent that the mine void is filled completely with water. Residuals (the difference between measured and simulated ground-water altitudes) has a root-mean-squared value of 8.53 feet and an absolute mean value of 7.29 feet for 17 observed values of water levels in the Boone Formation. The utility of the model for simulating and evaluating the possible consequences of remediation activities has been demonstrated. The model was used to simulate the emplacement of chat (mine waste consisting of fines and fragments of chert) back into the mine. Scenarios using 1,800,000 and 6,500,000 tons of chat were run. Hydraulic conductivity was reduced from 50,000 feet per day to 35 feet

  13. Cubic Siloxanes with Both Si-H and Si-OtBu Groups for Site-Selective Siloxane Bond Formation.

    PubMed

    Saito, Shohei; Yamasue, Nao; Wada, Hiroaki; Shimojima, Atsushi; Kuroda, Kazuyuki

    2016-09-19

    Cage-type siloxanes have attracted increasing attention as building blocks for silica-based nanomaterials as their corners can be modified with various functional groups. Cubic octasiloxanes incorporating both Si-H and Si-OtBu groups [(tBuO)n H8-n Si8 O12 ; n=1, 2 or 7] have been synthesized by the reaction of octa(hydridosilsesquioxane) (H8 Si8 O12 ) and tert-butyl alcohol in the presence of a Et2 NOH catalyst. The Si-H and Si-OtBu groups are useful for site-selective formation of Si-O-Si linkages without cage structure deterioration. The Si-H group can be selectively hydrolyzed to form a Si-OH group in the presence of Et2 NOH, enabling the formation of the monosilanol compound (tBuO)7 (HO)Si8 O12 . The Si-OH group can be used for either intermolecular condensation to form a dimeric cage compound or silylation to introduce new reaction sites. Additionally, the alkoxy groups of (tBuO)7 HSi8 O12 can be treated with organochlorosilanes in the presence of a BiCl3 catalyst to form Si-O-Si linkages, while the Si-H group remains intact. These results indicate that such bifunctional cage siloxanes allow for stepwise Si-O-Si bond formation to design new siloxane-based nanomaterials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. The Link between Rare-Earth Peak Formation and the Astrophysical Site of the R Process

    NASA Astrophysics Data System (ADS)

    Mumpower, Matthew R.; McLaughlin, Gail C.; Surman, Rebecca; Steiner, Andrew W.

    2016-12-01

    The primary astrophysical source of the rare-earth elements is the rapid neutron capture process (r process). The rare-earth peak that is seen in the solar r-process residuals has been proposed to originate as a pile-up of nuclei during the end of the r process. We introduce a new method utilizing Monte Carlo studies of nuclear masses in the rare-earth region, that includes self-consistently adjusting β-decay rates and neutron capture rates, to find the mass surfaces necessary for the formation of the rare-earth peak. We demonstrate our method with two types of astrophysical scenario, one corresponding to conditions typical of hot winds from core-collapse supernovae and stellar-mass accretion disks, and one corresponding to conditions typical of the ejection of the material from the tidal tails of neutron star mergers. In each type of astrophysical condition, this method successfully locates a region of enhanced stability in the mass surface that is responsible for the rare-earth peak. For each scenario, we find that the change in the mass surface has qualitatively different features, thus future measurements can shed light on the type of environment in which the r process occurred.

  15. Use of Modeling for Prevention of Solids Formation During Canyon Processing of Legacy Nuclear Materials at the Savannah River Site

    SciTech Connect

    Rhodes, W. D.; Crooks III, W. J.; Christian, J. D.

    2002-02-26

    The Savannah River Site (SRS) Environmental Management (EM) nuclear material stabilization program includes the dissolution and processing of legacy materials from various DOE sites. The SRS canyon facilities were designed to dissolve and process spent nuclear fuel and targets. As the processing of typical materials is completed, unusual and exotic nuclear materials are being targeted for stabilization. These unusual materials are often difficult to dissolve using historical flowsheet conditions and require more aggressive dissolver solutions. Solids must be prevented in the dissolver to avoid expensive delays associated with the build-up of insoluble material in downstream process equipment. Moreover, it is vital to prevent precipitation of all solids, especially plutonium-bearing solids, since their presence in dissolver solutions raises criticality safety issues. To prevent precipitation of undesirable solids in aqueous process solutions, the accuracy of computer models to predict precipitate formation requires incorporation of plant specific fundamental data. These data are incorporated into a previously developed thermodynamic computer program that applies the Pitzer correlation to derive activity coefficient parameters. This improved predictive model will reduce unwanted precipitation in process solutions at DOE sites working with EM nuclear materials in aqueous solutions.

  16. Memo-RhoA-mDia1 signaling controls microtubules, the actin network, and adhesion site formation in migrating cells.

    PubMed

    Zaoui, Kossay; Honoré, Stéphane; Isnardon, Daniel; Braguer, Diane; Badache, Ali

    2008-11-03

    Actin assembly at the cell front drives membrane protrusion and initiates the cell migration cycle. Microtubules (MTs) extend within forward protrusions to sustain cell polarity and promote adhesion site turnover. Memo is an effector of the ErbB2 receptor tyrosine kinase involved in breast carcinoma cell migration. However, its mechanism of action remained unknown. We report in this study that Memo controls ErbB2-regulated MT dynamics by altering the transition frequency between MT growth and shortening phases. Moreover, although Memo-depleted cells can assemble the Rac1-dependent actin meshwork and form lamellipodia, they show defective localization of lamellipodial markers such as alpha-actinin-1 and a reduced number of short-lived adhesion sites underlying the advancing edge of migrating cells. Finally, we demonstrate that Memo is required for the localization of the RhoA guanosine triphosphatase and its effector mDia1 to the plasma membrane and that Memo-RhoA-mDia1 signaling coordinates the organization of the lamellipodial actin network, adhesion site formation, and MT outgrowth within the cell leading edge to sustain cell motility.

  17. Site characterization of the highest-priority geologic formations for CO2 storage in Wyoming

    SciTech Connect

    Surdam, Ronald C.; Bentley, Ramsey; Campbell-Stone, Erin; Dahl, Shanna; Deiss, Allory; Ganshin, Yuri; Jiao, Zunsheng; Kaszuba, John; Mallick, Subhashis; McLaughlin, Fred; Myers, James; Quillinan, Scott

    2013-12-07

    This study, funded by U.S. Department of Energy National Energy Technology Laboratory award DE-FE0002142 along with the state of Wyoming, uses outcrop and core observations, a diverse electric log suite, a VSP survey, in-bore testing (DST, injection tests, and fluid sampling), a variety of rock/fluid analyses, and a wide range of seismic attributes derived from a 3-D seismic survey to thoroughly characterize the highest-potential storage reservoirs and confining layers at the premier CO2 geological storage site in Wyoming. An accurate site characterization was essential to assessing the following critical aspects of the storage site: (1) more accurately estimate the CO2 reservoir storage capacity (Madison Limestone and Weber Sandstone at the Rock Springs Uplift (RSU)), (2) evaluate the distribution, long-term integrity, and permanence of the confining layers, (3) manage CO2 injection pressures by removing formation fluids (brine production/treatment), and (4) evaluate potential utilization of the stored CO2

  18. GALFA HI: Candidate Sites for H2 Formation in Cold HI Emission and Other Tracers

    NASA Astrophysics Data System (ADS)

    Newton, Jonathan; Gibson, S. J.; Douglas, K. A.; Koo, B.; Kang, J.; Park, G.; Peek, J. E. G.; Korpela, E. J.; Heiles, C.; Dame, T. M.

    2012-01-01

    Interstellar gas has a variety of temperature phases, but only the coldest clouds are dense enough to collapse gravitationally and form stars. How do such clouds form? A key step in this process is the transition from neutral atomic hydrogen (HI) to molecular hydrogen (H2). To identify candidate sites where this HI-to-H2 transition may be underway, we have developed a method of fitting isolated HI 21cm emission features to constrain their spin temperature and other properties vs. position 21cm-line data cubes. Our method uses the Nelder-Meade `amoeba' method to solve the relevant radiative transfer equation by identifying the absolute chi-squared minimum in the parameter space. As other investigators have noted, this approach requires a very high signal-to-noise ratio, so we are using sensitive Arecibo L-band Feed Array (ALFA) observations, starting with narrow-line HI emission clouds in the inner-Galaxy ALFA (I-GALFA) survey, and we have also tested the reliability of our method with a large suite of model spectra. Cold HI clouds confirmed by the fit will be compared to tracers of molecular gas, including CO lines and FIR dust emission. The I-GALFA survey is part of the Galactic ALFA HI data set obtained with the Arecibo 305m telescope. Arecibo Observatory is part of the National Astronomy and Ionosphere Center, operated sequentially by Cornell University and Stanford Research Institute under Cooperative Agreement with the U.S. National Science Foundation.

  19. Cloning, localization and focus formation at DNA damage sites of canine XRCC4.

    PubMed

    Koike, Manabu; Yutoku, Yasutomo; Koike, Aki

    2017-01-10

    Various chemotherapies and radiation therapies are useful for killing cancer cells mainly by inducing DNA double-strand breaks (DSBs). Uncovering the molecular mechanisms of DSB repair processes is crucial for developing next-generation radiotherapies and chemotherapeutics for human and animal cancers. XRCC4 plays a critical role in Ku-dependent nonhomologous DNA-end joining (NHEJ) in human cells, and is one of the core NHEJ factors. The localization of core NHEJ factors, such as human Ku70 and Ku80, might play a crucial role in regulating NHEJ activity. Recently, companion animals, such as canines, have been proposed to be a good model in many aspects of cancer research. However, the localization and regulation mechanisms of core NHEJ factors in canine cells have not been elucidated. Here, we show that the expression and subcellular localization of canine XRCC4 changes dynamically during the cell cycle. Furthermore, EYFP-canine XRCC4 accumulates quickly at laser-microirradiated DSB sites. The structure of a putative human XRCC4 nuclear localization signal (NLS) is highly conserved in canine, chimpanzee and mouse XRCC4. However, the amino acid residue corresponding to the human XRCC4 K210, thought to be important for nuclear localization, is not conserved in canine XRCC4. Our findings might be useful for the study of the molecular mechanisms of Ku-dependent NHEJ in canine cells and the development of new radiosensitizers that target XRCC4.

  20. Evaluation of tritiated water diffusion through the Toarcian clayey formation of the Tournemire experimental site (France).

    PubMed

    Motellier, S; Devol-Brown, I; Savoye, S; Thoby, D; Alberto, J-C

    2007-10-30

    Through-diffusion experiments with tritiated water were performed on argillaceous samples from various zones of the Tournemire test site. It was intended to evaluate the homogeneity of the transport property of unfracturated samples and the influence of the orientation and the nature of the samples (presence of an opened fracture or a pre-existing tectonic fracture filled with calcite and pyrite). Homogeneous values of the tritiated water (HTO) effective diffusion coefficients were deduced from experiments carried out when diffusion occurred parallel to the stratigraphic bedding, with an apparent sensitivity to experimental conditions. Anisotropy was significant, De(HTO) perpendicular to the bedding being 1/3 lower than that parallel to the bedding. The observed fractures of the samples created by mechanical stress and partial dehydration during sawing and the presence of a pre-existing opened fracture did not affect the effective diffusion coefficients of tritiated water, which is probably due to the healing ability of the clayey medium during the re-saturation phases of the equilibrium steps performed prior to the diffusion experiments. On the contrary, a significant decrease of this transport parameter was induced by the occurrence of a pre-existing tectonic fracture, which was assigned to the dense structure of the filling phases.

  1. Notch3 Activation Promotes Invasive Glioma Formation in a Tissue Site-Specific Manner

    PubMed Central

    Pierfelice, Tarran J.; Schreck, Karisa C.; Dang, Louis; Asnaghi, Laura; Gaiano, Nicholas; Eberhart, Charles G.

    2010-01-01

    While Notch signaling has been widely implicated in neoplastic growth, direct evidence for in vivo initiation of neoplasia by the pathway in murine models has been limited to tumors of lymphoid, breast, and choroid plexus cells. To examine tumorigenic potential in the eye and brain, we injected retroviruses encoding activated forms of Notch1, Notch2, or Notch3 into embryonic mice. Interestingly, the majority of animals infected with active Notch3 developed proliferative lesions comprised of pigmented ocular choroid cells, retinal and optic nerve glia, and lens epithelium. Notch3-induced lesions in the choroid, retina, and optic nerve were capable of invading adjacent tissues, suggesting that they were malignant tumors. While Notch3 activation induced choroidal tumors in up to 67% of eyes, Notch1 or Notch2 activation never resulted in such tumors. Active forms of Notch1 and Notch2 did generate a few small proliferative glial nodules in the retina and optic nerve, while Notch3 was ten-fold more efficient at generating growths, many of which were large invasive gliomas. Expression of active Notch1/Notch3 chimeric receptors implicated the RAM (RBPjk-association molecule) and transactivation domains (TAD) of Notch3 in generating choroidal and glial tumors, respectively. In contrast to our findings in the optic nerve and retina, introduction of active Notch receptors, including Notch3, into the brain never caused glial tumors. Our results highlight the differential ability of Notch receptor paralogs to initiate malignant tumor formation, and suggest that glial precursors of the optic nerve, but not the brain, are susceptible to transformation by Notch3. PMID:21245095

  2. Dust Seds And Processing Near Sites Of High Mass Star Formation In The LMC

    NASA Astrophysics Data System (ADS)

    Hony, Sacha; Galliano, F.; Madden, S. M.; SAGE Consortium

    2010-01-01

    We present a study into the properties of the dust and complex molecules in and around selected HII regions in the Large Magellanic Cloud. The analysis is based on the Spitzer program SAGE (Surveying the Agents of a Galaxy's Evolution). Because of the lower metallicity environment, dust shielding is reduced and the effects of the ultraviolet radiation carry further than in the Milky way. Because of this these HII regions may better represent star forming regions in the more distant universe. We present the near- to far-IR spectral energy distributions (SEDs) as a function of radial distance to the center of the several clusters. The regions span a wide range in luminosities. We have developed a self consistent spherical clumpy dust radiative transfer model to interpret the observed trends. The model treats the detailed dust optical properties and transient grain heating as well as IR absorption and reprocession. This allows us to interpret the observed variations in SED in terms of the clumpiness, varying incident radiation-field and changing abundances of polycyclic aromatic hydrocarbons (PAHs), transiently heated very small grains (VSG) to submicron-sized grains in thermal equilibrium, i.e. in terms of the varying grain-size distribution. We find that the LMC massive star forming sites are typified by a several parsec sized void and clumpiness and PAH abundance which increases with distance from the central illuminating source. The inner void may be the result of massive star winds. The observed flat mid-IR SEDs require a grain-size distribution skewed to a higher fraction of smaller grains compared to the Milky Way dust.

  3. Climatology and Formation of Tropical Midlevel Clouds at the Darwin ARM Site

    SciTech Connect

    Riihimaki, Laura D.; McFarlane, Sally A.; Comstock, Jennifer M.

    2012-10-01

    A 4-yr climatology of midlevel clouds is presented from vertically pointing cloud lidar and radar measurements at the Atmospheric Radiation Measurement Program (ARM) site at Darwin, Australia. Few studies exist of tropical midlevel clouds using a dataset of this length. Seventy percent of clouds with top heights between 4 and 8 km are less than 2 km thick. These thin layer clouds have a peak in cloud-top temperature around the melting level (0°C) and also a second peak around -12.5°C. The diurnal frequency of thin clouds is highest during the night and reaches a minimum around noon, consistent with variation caused by solar heating. Using a 1.5-yr subset of the observations, the authors found that thin clouds have a high probability of containing supercooled liquid water at low temperatures: ~20% of clouds at -30°C, ~50% of clouds at -20°C, and ~65% of clouds at -10°C contain supercooled liquid water. The authors hypothesize that thin midlevel clouds formed at the melting level are formed differently during active and break monsoon periods and test this over three monsoon seasons. A greater frequency of thin midlevel clouds are likely formed by increased condensation following the latent cooling of melting during active monsoon periods when stratiform precipitation is most frequent. This is supported by the high percentage (65%) of midlevel clouds with preceding stratiform precipitation and the high frequency of stable layers slightly warmer than 0°C. In the break monsoon, a distinct peak in the frequency of stable layers at 0°C matches the peak in thin midlevel cloudiness, consistent with detrainment from convection.

  4. A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation.

    PubMed Central

    Leviev, I G; Rodriguez-Fonseca, C; Phan, H; Garrett, R A; Heilek, G; Noller, H F; Mankin, A S

    1994-01-01

    The binding site and probable site of action have been determined for the universal antibiotic amicetin which inhibits peptide bond formation. Evidence from in vivo mutants, site-directed mutations and chemical footprinting all implicate a highly conserved motif in the secondary structure of the 23S-like rRNA close to the central circle of domain V. We infer that this motif lies at, or close to, the catalytic site in the peptidyl transfer centre. The binding site of amicetin is the first of a group of functionally related hexose-cytosine inhibitors to be localized on the ribosome. Images PMID:8157007

  5. Fast helix formation in the B domain of protein A revealed by site-specific infrared probes.

    PubMed

    Davis, Caitlin M; Cooper, A Kat; Dyer, R Brian

    2015-03-10

    Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). (13)C═(18)O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1-3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.

  6. Fast Helix Formation in the B Domain of Protein A Revealed by Site-Specific Infrared Probes

    PubMed Central

    Davis, Caitlin M.; Cooper, A. Kat; Dyer, R. Brian

    2015-01-01

    Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). 13C=18O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1–3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations. PMID:25706439

  7. Site-specific inhibition of the SUMO-conjugating enzyme Ubc9 selectively impairs SUMO chain formation.

    PubMed

    Wiechmann, Svenja; Gärtner, Anne; Kniss, Andreas; Stengl, Andreas; Behrends, Christian; Rogov, Vladimir V; Rodriguez, Manuel S; Dötsch, Volker; Müller, Stefan; Ernst, Andreas

    2017-08-07

    Posttranslational modifications by small ubiquitin-like modifiers (SUMOs) regulate many cellular processes, including genome integrity, gene expression, and ribosome biogenesis. The E2-conjugating enzyme Ubc9 catalyzes the conjugation of SUMOs to ϵ-amino groups of lysine residues in target proteins. Attachment of SUMO moieties to internal lysines in Ubc9 itself can further lead to the formation of polymeric SUMO chains. Mono- and poly-SUMOylations of target proteins provide docking sites for distinct adapter and effector proteins important for regulating discrete SUMO-regulated pathways. However, molecular tools to dissect pathways depending on either mono- or poly-SUMOylation are largely missing. Using a protein-engineering approach, we generated high-affinity SUMO2 variants by phage display that bind the backside of Ubc9 and function as SUMO-based Ubc9 inhibitors (SUBINs). Importantly, we found that distinct SUBINs primarily inhibit poly-SUMO chain formation, while mono-SUMOylation is not impaired. Proof-of-principle experiments demonstrated that in a cellular context, SUBINs largely prevent heat shock-triggered poly-SUMOylation. Moreover, SUBINs abrogated arsenic-induced degradation of promyelocytic leukemia protein. We propose that the availability of the new chain-selective SUMO inhibitors reported here will enable thorough investigation of poly-SUMO-mediated cellular processes, such as DNA damage responses and cell cycle progression. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  8. Phosphatidylglycerol of rat lung. Intracellular sites of formation de novo and acyl species pattern in mitochondria, microsomes and surfactant.

    PubMed Central

    Schlame, M; Rüstow, B; Kunze, D; Rabe, H; Reichmann, G

    1986-01-01

    The subcellular site of phosphatidylglycerol (PG) formation for lung surfactant has not been convincingly clarified. To approach this problem we analysed the acyl species pattern of lung PG in mitochondria, microsomes and surfactant by h.p.l.c. separation of its 1,2-diacyl-3-naphthylurethane derivatives. Both mitochondrial and microsomal PG proved identical with surfactant PG, containing the major species 1-palmitoyl-2-oleoyl-PG and 1,2-dipalmitoyl-PG. The fatty acid composition of mitochondrial PG differs markedly from that of diphosphatidylglycerol. This may be taken as an indication that mitochondrial PG is synthesized on purpose to form surfactant, rather than being only the precursor of diphosphatidylglycerol. In vitro, sn-[U-14C]glycerol 3-phosphate incorporation into PG of mitochondria or microsomes occurs in the presence of CTP, ATP and CoA but independently of the supply of exogenous lipoidic precursors. Although the rate in vitro of autonomous PG synthesis, and the endogenous PG content, are higher in mitochondria than in microsomes, it is assumed that both subcellular fractions are involved in PG formation for surfactant. PMID:3827844

  9. Analysis of solutes in groundwaters from the Rustler Formation at and near the Waste Isolation Pilot Plant site

    SciTech Connect

    Robinson, K.L.

    1997-09-01

    Between 1976 and 1986, groundwater samples from more than 60 locations in the vicinity of the Waste Isolation Pilot Plant site were collected and analyzed for a variety of major, minor, and trace solutes. Most of the samples were from the Rustler Formation (the Culebra Dolomite, the Magenta Dolomite, or the zone at the contact between the Rustler and underlying Salado Formations) or the Dewey Lake Red Beds. The analytical data from the laboratories are presented here with accompanying discussions of sample collection methods, supporting field measurements, and laboratory analytical methods. A comparison of four data sets and a preliminary evaluation of the data for the major solutes (Cl{sup {minus}}, SO{sub 4}{sup {minus}2}, Na, K, Ca, and Mg) shows that the data for samples analyzed by UNC/Bendix for SNL seem to be the most reliable, but that at some locations, samples representative of the native, unperturbed groundwater have not been collected. At other locations, the water chemistry has apparently changed between sampling episodes.

  10. Organic geochemical characterization of reservoir rocks, cap rocks and formation fluids from the CO2 storage site at Ketzin, Germany

    NASA Astrophysics Data System (ADS)

    Scherf, A.-K.; Morozova, D.; Wandrey, M.; Mangelsdorf, K.; Würdemann, H.; Vieth, A.

    2009-04-01

    The European project CO2SINK (CO2 Storage by Injection into a natural saline Aquifer at Ketzin) is the first project on the on-shore underground storage of carbon dioxide in Europe. Near the city Ketzin (north-east Germany) a geological formation of the younger Triassic (Stuttgart Formation) was chosen as reservoir for the long-term storage of the carbon dioxide. Within the scope of the Ketzin project we will analyse the organic matter in core rock and fluid samples to investigate the biogeochemical effects and changes on the geological formation caused by the injection of carbon dioxide. These investigations will help to evaluate the efficiency and reliability of the long-term storage of CO2 in such a geological system. Organic geochemical analyses will be performed on core rock samples drilled in 2007 at the Ketzin CO2 storage site in Germany. In total, three bore holes were constructed: one injection well and two observation wells. In addition to the molecular analysis of the microbial community we will investigate rock samples from different depths for total, dissolved and extractable organic carbon including lipid biomarkers, such as organic acids and intact polar lipids as well as the isotopic analysis of individual organic compounds. With the analysis of intact phospholipids (IPL) we will be able to further characterize the indigenous microbial community. Intact phospholipids are found in all living cells as membrane components (Zelles, 1999). Their interpretation is based on the premise that different microorganisms contain different phospholipids with ester- and/or ether-bound fatty acids (White et al., 1979) and thus, the distribution of IPLs and PLFAs (phospholipids fatty acid) can be applied to characterise and compare microbial communities. The data obtained from these analyses will provide valuable information on the active microorganisms as well as shifts in community composition. The characterization of the organic matter in the reservoir rock

  11. A FEEDBACK-DRIVEN BUBBLE G24.136+00.436: A POSSIBLE SITE OF TRIGGERED STAR FORMATION

    SciTech Connect

    Liu, Hong-Li; Li, JinZeng; Yuan, Jing-Hua; Wu, Yuefang; Dong, Xiaoyi; Liu, Tie E-mail: yfwu.pku@gmail.com

    2015-01-01

    We present a multi-wavelength study of the IR bubble G24.136+00.436. The J = 1-0 observations of {sup 12}CO, {sup 13}CO, and C{sup 18}O were carried out with the Purple Mountain Observatory 13.7 m telescope. Molecular gas with a velocity of 94.8 km s{sup –1} is found prominently in the southeast of the bubble, shaped as a shell with a total mass of ∼2 × 10{sup 4} M {sub ☉}. It was likely assembled during the expansion of the bubble. The expanding shell consists of six dense cores, whose dense (a few of 10{sup 3} cm{sup –3}) and massive (a few of 10{sup 3} M {sub ☉}) characteristics coupled with the broad linewidths (>2.5 km s{sup –1}) suggest that they are promising sites for forming high-mass stars or clusters. This could be further consolidated by the detection of compact H II regions in Cores A and E. We tentatively identified and classified 63 candidate young stellar objects (YSOs) based on the Spitzer and UKIDSS data. They are found to be dominantly distributed in regions with strong molecular gas emission, indicative of active star formation, especially in the shell. The H II region inside the bubble is mainly ionized by a ∼O8V star(s), of the dynamical age of ∼1.6 Myr. The enhanced number of candidate YSOs and secondary star formation in the shell as well as the timescales involved, indicate a possible scenario for triggering star formation, signified by the ''collect and collapse'' process.

  12. MECHANISMS OF PHASE FORMATION IN THE VITRIFICATION OF HIGH-FERROUS SAVANNAH RIVER SITE SB2 HLW SLUDGE SURROGATE - 9300

    SciTech Connect

    Marra, J

    2008-08-27

    Phase formation mechanisms associated with the vitrification of high-ferrous Savannah River Site (SRS) Sludge Batch 2 (SB2) high level waste surrogate were studied by infrared spectroscopy (IRS) and X-ray diffraction (XRD). Two mixtures at 50 wt% waste loading with commercially available Frit 320 (Li{sub 2}O - 8 wt %, B{sub 2}O{sub 3} - 8 wt %, Na{sub 2}O - 12 wt %, SiO{sub 2} - 72 wt %) and batch chemicals (LiOH {center_dot} H{sub 2}O, H{sub 3}BO{sub 3}, NaNO{sub 3}, SiO{sub 2}) to represent the frit formulation were prepared as slurries with a water content of {approx}50 wt%. The mixtures were air-dried at a temperature of 115 C and heat-treated at 500, 700, 900, 1000, 1100, 1200, and 1300 C for 1 hr at each temperature. Infrared spectra and XRD patterns of the products produced at each temperature were recorded. In both mixtures prepared using frit and batch chemicals to represent the frit, phase formation reactions were completed within the temperature range between 900 and 1000 C. However, residual quartz was still present in glass produced from the mixture with batch chemicals even at 1100 C. Although, the phase composition and structure of the glassy products obtained from both mixtures at temperatures over 1000 C were similar, the products obtained from the mixture using actual frit were more homogeneous than those from the mixture with batch chemicals. Thus, the use of frit rather than batch chemicals reduced the temperature range of phase formation and provided for production of higher quality glass.

  13. A parasitic nematode releases cytokinin that controls cell division and orchestrates feeding site formation in host plants

    PubMed Central

    Siddique, Shahid; Radakovic, Zoran S.; De La Torre, Carola M.; Chronis, Demosthenis; Novák, Ondřej; Ramireddy, Eswarayya; Holbein, Julia; Matera, Christiane; Hütten, Marion; Gutbrod, Philipp; Anjam, Muhammad Shahzad; Rozanska, Elzbieta; Habash, Samer; Elashry, Abdelnaser; Sobczak, Miroslaw; Kakimoto, Tatsuo; Strnad, Miroslav; Schmülling, Thomas; Mitchum, Melissa G.; Grundler, Florian M. W.

    2015-01-01

    Sedentary plant-parasitic cyst nematodes are biotrophs that cause significant losses in agriculture. Parasitism is based on modifications of host root cells that lead to the formation of a hypermetabolic feeding site (a syncytium) from which nematodes withdraw nutrients. The host cell cycle is activated in an initial cell selected by the nematode for feeding, followed by activation of neighboring cells and subsequent expansion of feeding site through fusion of hundreds of cells. It is generally assumed that nematodes manipulate production and signaling of the plant hormone cytokinin to activate cell division. In fact, nematodes have been shown to produce cytokinin in vitro; however, whether the hormone is secreted into host plants and plays a role in parasitism remained unknown. Here, we analyzed the spatiotemporal activation of cytokinin signaling during interaction between the cyst nematode, Heterodera schachtii, and Arabidopsis using cytokinin-responsive promoter:reporter lines. Our results showed that cytokinin signaling is activated not only in the syncytium but also in neighboring cells to be incorporated into syncytium. An analysis of nematode infection on mutants that are deficient in cytokinin or cytokinin signaling revealed a significant decrease in susceptibility of these plants to nematodes. Further, we identified a cytokinin-synthesizing isopentenyltransferase gene in H. schachtii and show that silencing of this gene in nematodes leads to a significant decrease in virulence due to a reduced expansion of feeding sites. Our findings demonstrate the ability of a plant-parasitic nematode to synthesize a functional plant hormone to manipulate the host system and establish a long-term parasitic interaction. PMID:26417108

  14. A parasitic nematode releases cytokinin that controls cell division and orchestrates feeding site formation in host plants.

    PubMed

    Siddique, Shahid; Radakovic, Zoran S; De La Torre, Carola M; Chronis, Demosthenis; Novák, Ondřej; Ramireddy, Eswarayya; Holbein, Julia; Matera, Christiane; Hütten, Marion; Gutbrod, Philipp; Anjam, Muhammad Shahzad; Rozanska, Elzbieta; Habash, Samer; Elashry, Abdelnaser; Sobczak, Miroslaw; Kakimoto, Tatsuo; Strnad, Miroslav; Schmülling, Thomas; Mitchum, Melissa G; Grundler, Florian M W

    2015-10-13

    Sedentary plant-parasitic cyst nematodes are biotrophs that cause significant losses in agriculture. Parasitism is based on modifications of host root cells that lead to the formation of a hypermetabolic feeding site (a syncytium) from which nematodes withdraw nutrients. The host cell cycle is activated in an initial cell selected by the nematode for feeding, followed by activation of neighboring cells and subsequent expansion of feeding site through fusion of hundreds of cells. It is generally assumed that nematodes manipulate production and signaling of the plant hormone cytokinin to activate cell division. In fact, nematodes have been shown to produce cytokinin in vitro; however, whether the hormone is secreted into host plants and plays a role in parasitism remained unknown. Here, we analyzed the spatiotemporal activation of cytokinin signaling during interaction between the cyst nematode, Heterodera schachtii, and Arabidopsis using cytokinin-responsive promoter:reporter lines. Our results showed that cytokinin signaling is activated not only in the syncytium but also in neighboring cells to be incorporated into syncytium. An analysis of nematode infection on mutants that are deficient in cytokinin or cytokinin signaling revealed a significant decrease in susceptibility of these plants to nematodes. Further, we identified a cytokinin-synthesizing isopentenyltransferase gene in H. schachtii and show that silencing of this gene in nematodes leads to a significant decrease in virulence due to a reduced expansion of feeding sites. Our findings demonstrate the ability of a plant-parasitic nematode to synthesize a functional plant hormone to manipulate the host system and establish a long-term parasitic interaction.

  15. Identification of catalysis, substrate, and coenzyme binding sites and improvement catalytic efficiency of formate dehydrogenase from Candida boidinii.

    PubMed

    Jiang, Wei; Lin, Peng; Yang, Ruonan; Fang, Baishan

    2016-10-01

    Formate dehydrogenases (FDHs) are continually used for the cofactor regeneration in biocatalysis and biotransformation with hiring NAD(P)H-dependent oxidoreductases. Major weaknesses of most native FDHs are their low activity and operational stability in the catalytic reaction. In this work, the FDH from Candida boidinii (CboFDH) was engineered in order to gain an enzyme with high activity and better operational stability. Through comparing and analyzing its spatial structure with other FDHs, the catalysis, substrate, and coenzyme binding sites of the CboFDH were identified. To improve its performance, amino acids, which concentrated on the enzyme active site or in the conserved NAD(+) and substrate binding motif, were mutated. The mutant V120S had the highest catalytic efficiency (k cat/K m ) with COONH4 as it enhanced the catalytic velocity (k cat) and k cat/K m 3.48-fold and 1.60-fold, respectively, than that of the wild type. And, the double-mutant V120S-N187D had the highest k cat/K m with NAD(+) as it displayed an approximately 1.50-fold increase in k cat/K m . The mutants showed higher catalytic efficiency than other reported FDHs, suggesting that the mutation has achieved good results. The single and double mutants exhibited higher thermostability than the wild type. The structure-function relationship of single and double mutants was analyzed by homology models and site parsing. Asymmetric synthesis of L-tert-leucine was executed to evaluate the ability of cofactor regeneration of the mutants with about 100 % conversion rates. This work provides a helpful theoretical reference for the evolution of an enzyme in vitro and promotion of the industrial production of chiral compounds, e.g., amino acid and chiral amine.

  16. The roles of vertical shear and topography on the eddy formation near the site of origin of the Brazil Current

    NASA Astrophysics Data System (ADS)

    Soutelino, R. G.; Gangopadhyay, A.; da Silveira, I. C. A.

    2013-11-01

    The site of origin of the Brazil Current (BC) is currently one of the less explored aspects of regional circulation and mesoscale activity in the west side of the South Atlantic Subtropical gyre. The few studies that are available, based either on in situ data or on numerical modeling, seems to agree that the region is characterized by relatively weak baroclinic flow, with substantial mesoscale activity, which is quite different from other western boundary current systems (e.g. Florida Current, in the North Atlantic). We present numerical simulations that show that the main realistic mesoscale features in the eddy-rich vicinities of the BC site of origin can be successfully modeled through the dynamical interaction between parameterized versions of two opposing mean western boundary currents (BC and North Brazil Undercurrent—NBUC) and local topography, with no influence of remote dynamics or atmospheric forcing. Large BC-related anticyclones observed in previous work were reproduced and recurrently formed during the model run. Two additional sensitivity experiments were performed. When NBUC is removed from the physical setting, the BC interaction with topography is not sufficient to generate eddies similar to observations. When an idealized flat-bottom and a physiographic configuration with no Abrolhos and Royal Charlotte Banks are considered, the BC-NBUC interaction is also not capable of developing realistic mesoscale structures. Our geophysical instability analyses suggest that BC-NBUC vertical shear is promoting baroclinic energy fluxes from the mean flow to the perturbations, resulting in eddy formation and growth in the region.

  17. An intramembranous ossification model for the in silico analysis of bone tissue formation in tooth extraction sites.

    PubMed

    Corredor-Gómez, Jennifer Paola; Rueda-Ramírez, Andrés Mauricio; Gamboa-Márquez, Miguel Alejandro; Torres-Rodríguez, Carolina; Cortés-Rodríguez, Carlos Julio

    2016-07-21

    The accurate modeling of biological processes allows us to predict the spatiotemporal behavior of living tissues by computer-aided (in silico) testing, a useful tool for the development of medical strategies, avoiding the expenses and potential ethical implications of in vivo experimentation. A model for bone healing in mouth would be useful for selecting proper surgical techniques in dental procedures. In this paper, the formulation and implementation of a model for Intramembranous Ossification is presented aiming to describe the complex process of bone tissue formation in tooth extraction sites. The model consists in a mathematical description of the mechanisms in which different types of cells interact, synthesize and degrade extracellular matrices under the influence of biochemical factors. Special attention is given to angiogenesis, oxygen-dependent effects and growth factor-induced apoptosis of fibroblasts. Furthermore, considering the depth-dependent vascularization of mandibular bone and its influence on bone healing, a functional description of the cell distribution on the severed periodontal ligament (PDL) is proposed. The developed model was implemented using the finite element method (FEM) and successfully validated by simulating an animal in vivo experiment on dogs reported in the literature. A good fit between model outcome and experimental data was obtained with a mean absolute error of 3.04%. The mathematical framework presented here may represent an important tool for the design of future in vitro and in vivo tests, as well as a precedent for future in silico studies on osseointegration and mechanobiology.

  18. Active site formation mechanism of carbon-based oxygen reduction catalysts derived from a hyperbranched iron phthalocyanine polymer

    NASA Astrophysics Data System (ADS)

    Hiraike, Yusuke; Saito, Makoto; Niwa, Hideharu; Kobayashi, Masaki; Harada, Yoshihisa; Oshima, Masaharu; Kim, Jaehong; Nabae, Yuta; Kakimoto, Masa-aki

    2015-04-01

    Carbon-based cathode catalysts derived from a hyperbranched iron phthalocyanine polymer (HB-FePc) were characterized, and their active-site formation mechanism was studied by synchrotron-based spectroscopy. The properties of the HB-FePc catalyst are compared with those of a catalyst with high oxygen reduction reaction (ORR) activity synthesized from a mixture of iron phthalocyanine and phenolic resin (FePc/PhRs). Electrochemical measurements demonstrate that the HB-FePc catalyst does not lose its ORR activity up to 900°C, whereas that of the FePc/PhRs catalyst decreases above 700°C. Hard X-ray photoemission spectra reveal that the HB-FePc catalysts retain more nitrogen components than the FePc/PhRs catalysts between pyrolysis temperatures of 600°C and 800°C. This is because the linked structure of the HB-FePc precursor has high thermostability against nitrogen desorption. Consequently, effective doping of active nitrogen species into the sp 2 carbon network of the HB-FePc catalysts may occur up to 900°C.

  19. Active site formation mechanism of carbon-based oxygen reduction catalysts derived from a hyperbranched iron phthalocyanine polymer.

    PubMed

    Hiraike, Yusuke; Saito, Makoto; Niwa, Hideharu; Kobayashi, Masaki; Harada, Yoshihisa; Oshima, Masaharu; Kim, Jaehong; Nabae, Yuta; Kakimoto, Masa-Aki

    2015-01-01

    Carbon-based cathode catalysts derived from a hyperbranched iron phthalocyanine polymer (HB-FePc) were characterized, and their active-site formation mechanism was studied by synchrotron-based spectroscopy. The properties of the HB-FePc catalyst are compared with those of a catalyst with high oxygen reduction reaction (ORR) activity synthesized from a mixture of iron phthalocyanine and phenolic resin (FePc/PhRs). Electrochemical measurements demonstrate that the HB-FePc catalyst does not lose its ORR activity up to 900°C, whereas that of the FePc/PhRs catalyst decreases above 700°C. Hard X-ray photoemission spectra reveal that the HB-FePc catalysts retain more nitrogen components than the FePc/PhRs catalysts between pyrolysis temperatures of 600°C and 800°C. This is because the linked structure of the HB-FePc precursor has high thermostability against nitrogen desorption. Consequently, effective doping of active nitrogen species into the sp (2) carbon network of the HB-FePc catalysts may occur up to 900°C.

  20. A search for water on the moon at the Reiner Gamma Formation - A possible site of cometary coma impact

    NASA Technical Reports Server (NTRS)

    Roush, Ted L.; Lucey, Paul G.

    1988-01-01

    Earth-based telescopic measurements of the Reiner Gamma Formation in the 3-micron region were made to search for evidence of water at this proposed site of cometary interaction with the lunar surface. Comparison of the spectra of Reiner Gamma and laboratory measurements of a variety of minerals with adsorbed water or structural OH(-) show that there is no evidence for water at the locations measured. While these measurements rule out the presence of abundant bound H2O at these locations, they do not exclude the presence of OH(-) bearing minerals that have absorptions not detectable through the wet terrestrial atmosphere. The possible effects of high lunar temperatures on the reflectance spectra were examined, and it was concluded that these effects would not obscure a bound water absorption if it were present. Upper limits on the amount of water that could be present at the locations observed and remain undetected are 2.25 average wt pct for a mixture consisting of discrete patches of water-bearing and water-free minerals and 0.01 wt pct for an intimate mixture of these two materials.

  1. Searching for Sites of Recent Star Formation Towards the Central Molecular Zone: Surveys of Water and Methanol Masers

    NASA Astrophysics Data System (ADS)

    Rickert, Matthew

    The Central Molecular Zone (CMZ) spans the inner 450 pc ( 3°) of our Galaxy. This region displays enhanced molecular emission and contains 5% of the entire Galaxy's gas mass. However, the number of detected star forming sites towards the CMZ is low for the amount of molecular gas that is present. We have conducted four sets of observations of this region in order to detect new sites of star formation. These observations can be broken into two types of surveys: blind (that span a wide region of the sky) and targeted (that point at specific sources). We use two telescopes (the Very Large Array and the Australia Telescope Compact Array) to observe two types of masers: the 6.7 GHz methanol maser and the 22 GHz water maser. Both are tracers of recent (<0.05 Myr) star formation. The 6.7 GHz methanol maser is a radiatively pumped maser that traces recent high mass star formation, while the 22 GHz water maser is collisionally pumped and can also be produced by evolved stars. Our only 6.7 GHz CH3OH maser survey used the Jansky Very Large Array (VLA) to conduct a blind survey of the inner 3° x 40' (450 pc x 100 pc) of the Galaxy. We detect 42 CH3OH masers towards 30 distinct locations. 16 of these masers are new detections. A majority of all the detected CH3OH masers are located towards positive Galactic longitudes, similar to how 2/3 of the molecular gas mass in the CMZ is also located at positive Galactic longitudes. The first of our 22 GHz observations used the VLA to target 22 GHz water masers that were previously detected with the Mopra telescope. We detect 293 water masers towards 31 distinct locations. This is a vast increase over the 37 water masers that had been detected by Mopra towards 29 distinct locations, demonstrating the benefit of observations with high spatial (<2") and spectral (< 1 km/s) resolutions for detecting masers. As part of the Search for Water and Ammonia in the Galactic Center (SWAG) collaboration, we then conducted a blind survey of the inner

  2. Submicron aerosols at thirteen diversified sites in China: size distribution, new particle formation and corresponding contribution to cloud condensation nuclei production

    NASA Astrophysics Data System (ADS)

    Peng, J. F.; Hu, M.; Wang, Z. B.; Huang, X. F.; Kumar, P.; Wu, Z. J.; Yue, D. L.; Guo, S.; Shang, D. J.; Zheng, Z.; He, L. Y.

    2014-06-01

    Understanding the particle number size distributions in diversified atmospheric environments is important in order to design mitigation strategies related to submicron particles and their effect on regional air quality, haze and human health. In this study, we conducted 15 different field measurement campaigns, each one-month long, between 2007 and 2011 at 13 individual sites in China. These were 5 urban sites, 4 regional sites, 3 coastal/background sites and one ship cruise measurement along eastern coastline of China. Size resolved particles were measured in the 15-600 nm size range. The median particle number concentrations (PNC) were found to vary in the range of 1.1-2.2 × 104 cm-3 at urban sites, 0.8-1.5 × 104 cm-3 at regional sites, 0.4-0.6 × 104 cm-3 at coastal/background sites, and 0.5 × 104 cm-3 during cruise measurements. Peak diameters at each of these sites varied greatly from 24 nm to 115 nm. Particles in the 15-25 nm (nucleation mode), 25-100 nm (Aitken mode) and 100-600 nm (accumulation mode) range showed different characteristics at each of the studied sites, indicating the features of primary emissions and secondary formation in these diversified atmospheric environments. Diurnal variations show a build-up of accumulation mode particles belt at regional sites, suggesting the contribution of regional secondary aerosol pollution. Frequencies of new particle formation (NPF) events were much higher at urban and regional sites than at coastal sites and cruise measurement. The average growth rates (GRs) of nucleation mode particles were 8.0-10.9 nm h-1 at urban sites, 7.4-13.6 nm h-1 at regional sites and 2.8-7.5 nm h-1 at both coastal and cruise measurement sites. The high gaseous precursors and strong oxidation at urban and regional sites not only favored the formation of particles, but also accelerated the growth rate of the nucleation mode particles. No significant difference in condensation sink (CS) during NPF days were observed among different

  3. Submicron aerosols at thirteen diversified sites in China: size distribution, new particle formation and corresponding contribution to cloud condensation nuclei production

    NASA Astrophysics Data System (ADS)

    Peng, J. F.; Hu, M.; Wang, Z. B.; Huang, X. F.; Kumar, P.; Wu, Z. J.; Guo, S.; Yue, D. L.; Shang, D. J.; Zheng, Z.; He, L. Y.

    2014-09-01

    Understanding the particle number size distributions in diversified atmospheric environments is important in order to design mitigation strategies related to submicron particles and their effects on regional air quality, haze and human health. In this study, we conducted 15 different field measurement campaigns between 2007 and 2011 at 13 individual sites in China, including five urban sites, four regional sites, three coastal/background sites and one ship cruise measurement along eastern coastline of China. Size resolved particles were measured in the 15-600 nm size range. The median particle number concentrations (PNCs) were found to vary in the range of 1.1-2.2 × 104 cm-3 at urban sites, 0.8-1.5 × 104 cm-3 at regional sites, 0.4-0.6 × 104 cm-3 at coastal/background sites, and 0.5 × 104 cm-3 during cruise measurement. Peak diameters at each of these sites varied greatly from 24 to 115 nm. Particles in the 15-25 nm (nucleation mode), 25-100 nm (Aitken mode) and 100-600 nm (accumulation mode) range showed different characteristics at each sites, indicating the features of primary emissions and secondary formation in these diversified atmospheric environments. Diurnal variations show a build-up of accumulation mode particles belt at regional sites, suggesting the contribution of regional secondary aerosol pollution. Frequencies of new particle formation (NPF) events were much higher at urban and regional sites than at coastal sites and during cruise measurement. The average growth rates (GRs) of nucleation mode particles were 8.0-10.9 nm h-1 at urban sites, 7.4-13.6 nm h-1 at regional sites and 2.8-7.5 nm h-1 at coastal sites and during cruise measurement. The high gaseous precursors and strong oxidation at urban and regional sites not only favored the formation of particles, but also accelerated the growth rate of the nucleation mode particles. No significant difference in condensation sink (CS) during NPF days were observed among different site types

  4. Modulation of an active-site cysteine pKa allows PDI to act as a catalyst of both disulfide bond formation and isomerization.

    PubMed

    Karala, Anna-Riikka; Lappi, Anna-Kaisa; Ruddock, Lloyd W

    2010-03-05

    Protein disulfide isomerase (PDI) plays a central role in disulfide bond formation in the endoplasmic reticulum. It is implicated both in disulfide bond formation and in disulfide bond reduction and isomerization. To be an efficient catalyst of all three reactions requires complex mechanisms. These include mechanisms to modulate the pK(a) values of the active-site cysteines of PDI. Here, we examined the role of arginine 120 in modulating the pK(a) values of these cysteines. We find that arginine 120 plays a significant role in modulating the pK(a) of the C-terminal active-site cysteine in the a domain of PDI and plays a role in determining the reactivity of the N-terminal active-site cysteine but not via direct modulation of its pK(a). Mutation of arginine 120 and the corresponding residue, arginine 461, in the a' domain severely reduces the ability of PDI to catalyze disulfide bond formation and reduction but enhances the ability to catalyze disulfide bond isomerization due to the formation of more stable PDI-substrate mixed disulfides. These results suggest that the modulation of pK(a) of the C-terminal active cysteine by the movement of the side chain of these arginine residues into the active-site locales has evolved to allow PDI to efficiently catalyze both oxidation and isomerization reactions. (c) 2009 Elsevier Ltd. All rights reserved.

  5. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions.

    PubMed

    Hartmann, Tobias; Schrapers, Peer; Utesch, Tillmann; Nimtz, Manfred; Rippers, Yvonne; Dau, Holger; Mroginski, Maria Andrea; Haumann, Michael; Leimkühler, Silke

    2016-04-26

    Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal-containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pKa of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase.

  6. Evidence of formation of submicrometer water-soluble organic aerosols at a deciduous forest site in northern Japan in summer

    NASA Astrophysics Data System (ADS)

    Miyazaki, Yuzo; Jung, Jinsang; Fu, Pingqing; Mizoguchi, Yasuko; Yamanoi, Katsumi; Kawamura, Kimitaka

    2012-10-01

    Semicontinuous measurements of submicrometer water-soluble organic aerosols and particle size distributions were conducted at a deciduous forest site in northern Japan in August 2010. Increases in particle number concentration were frequently observed in daytime, accompanied by an increase in the concentrations of water-soluble organic carbon (WSOC). We found that daily averaged WSOC concentrations positively correlated with gross primary production of CO2 by the forest ecosystem (r2 = 0.63) and ambient temperature during daytime. These relations suggest that the formation of WSOC is closely linked to photosynthetic activity by the forest ecosystem, which depends on both temperature and solar radiation. Off-line chemical analysis of samples of particles with aerodynamic diameter smaller than 1 μm collected during a 2 day event of elevated WSOC levels suggests that photochemical aging of both α- andβ-pinene and isoprene oxidation products contributes to the particle growth and the WSOC mass. Organic tracers of primary biological aerosol particles (PBAPs) showed distinct diurnal variations with a maximum around noontime, also indicating that higher temperature and light intensity induce emissions of PBAPs. However, their contribution to the submicrometer WSOC mass was likely insignificant. During the day, the concentrations of 3-methyl-1,2,3-butanetricarboxylic acid (3-MBTCA) showed a strong dependence on temperature, and the ratios of WSOC to particle volume concentration increased with an increase in the concentration ratios of 3-MBTCA to pinonic acid (PA). This result supports a previous proposal that the 3-MBTCA/PA ratios in submicrometer particles can be a useful tracer for chemical aging of biogenic secondary organic aerosol from forest vegetation.

  7. Lung deposited surface area in Leicester urban background site/UK: Sources and contribution of new particle formation

    NASA Astrophysics Data System (ADS)

    Hama, Sarkawt M. L.; Ma, Nan; Cordell, Rebecca L.; Kos, Gerard P. A.; Wiedensohler, Alfred; Monks, Paul S.

    2017-02-01

    Lung Deposited Surface Area (LDSA) has been identified as a potential metric for the correlation of a physical aerosol particle properties with health outcomes. Currently, there is little urban LDSA data. As a case study, we investigated measurements of LDSA (alveolar) concentrations in a mid-size European city. LDSA and associated measurements were carried out over 1.5 years at an urban background site in Leicester, UK. Average LDSA concentrations in the cold (November-April) and warm (May-October) seasons of UK were 37 and 23 μm2 cm-3, respectively. LDSA correlates well (R2 = 0.65-0.7, r = 0.77-0.8) with traffic related pollutants, such as equivalent black carbon (eBC) and NOX. We also report for the first time in the UK the correlation between an empirically derived LDSA and eBC. Furthermore, the effect of wind speed and direction on the LDSA was explored. Higher LDSA concentrations are observed at low wind speeds (1-2 m s-1), owing to local traffic emissions. In addition, the diurnal variation of LDSA showed a second peak in the afternoon under warm and relatively clean atmospheric conditions, which can be attributed to photochemical new particle formation (NPF) and growth into the Aitken mode range. These NPF events increased the average background LDSA concentrations from 15.5 to 35.5 μm2 cm-3, although they might not be health-relevant. Overall, the results support the notion that local traffic emissions are a major contributor to observed LDSA concentrations with a clear seasonal pattern with higher values during winter.

  8. Interpretation of brine-permeability tests of the Salado Formation at the Waste Isolation Pilot Plant site: First interim report

    SciTech Connect

    Beauheim, R.L. ); Saulnier, G.J. Jr.; Avis, J.D. )

    1991-08-01

    Pressure-pulse tests have been performed in bedded evaporites of the Salado Formation at the Waste Isolation Pilot Plant (WIPP) site to evaluate the hydraulic properties controlling brine flow through the Salado. Hydraulic conductivities ranging from about 10{sup {minus}14} to 10{sup {minus}11} m/s (permeabilities of about 10{sup {minus}21} to 10{sup {minus}18} m{sup 2}) have been interpreted from nine tests conducted on five stratigraphic intervals within eleven meters of the WIPP underground excavations. Tests of a pure halite layer showed no measurable permeability. Pore pressures in the stratigraphic intervals range from about 0.5 to 9.3 MPa. An anhydrite interbed (Marker Bed 139) appears to be one or more orders of magnitude more permeable than the surrounding halite. Hydraulic conductivities appear to increase, and pore pressures decrease, with increasing proximity to the excavations. These effects are particularly evident within two to three meters of the excavations. Two tests indicated the presence of apparent zero-flow boundaries about two to three meters from the boreholes. The other tests revealed no apparent boundaries within the radii of influence of the tests, which were calculated to range from about four to thirty-five meters from the test holes. The data are insufficient to determine if brine flow through evaporites results from Darcy-like flow driven by pressure gradients within naturally interconnected porosity or from shear deformation around excavations connecting previously isolated pores, thereby providing pathways for fluids at or near lithostatic pressure to be driven towards the low-pressure excavations. Future testing will be performed at greater distances from the excavations to evaluate hydraulic properties and processes beyond the range of excavation effects.

  9. Evidence for sites of methylmercury formation in a flowing water system: impact of anthropogenic barriers and water management.

    PubMed

    Pizarro-Barraza, Claudia; Gustin, Mae Sexauer; Peacock, Mary; Miller, Matthieu

    2014-04-15

    The Truckee River, California-Nevada, USA is impacted by mercury (Hg) contamination associated with legacy gold mining. In this work, we investigated the potential for hot-spots of methylmercury (MeHg) formation in the river. Mercury concentrations in multiple media were also used to assess the impacts of anthropogenic barriers, restoration, and water management in this flowing water ecosystem. Water samples were collected on a seasonal time step over 3 years, and analyzed for total Hg (THg) and MeHg concentrations, along with a variety of other water quality parameters. In addition, we measured THg and MeHg in sediments, THg in macroinvertebrates, and THg and δ(15)N and δ(13)C concentrations in fish. Differences in stable isotopes and Hg concentrations in fish were applied to understand the mobility of fish in the river. Mercury concentrations of specific macroinvertebrate species were used to identify sites of MeHg production. In general, loads of Hg and nutrients in the river reach above the Reno-Sparks metropolitan area were similar to that reported for pristine systems, while within and below the city, water quality impacts were observed. Fish isotope data showed that in the city reach food resources were different than those upriver and downriver. Based on Hg and isotope data, mobility of the fish in the river is impacted by anthropogenic obstructions and water manipulation. Below the city, particle bound Hg, derived from the legacy mining, continues to be input to the Truckee River. This Hg is deposited in riparian habitats and areas of river restoration, where it is methylated and becomes available to biota. During spring, when flows were highest, MeHg produced and stored in the sediments is mobilized and transported downriver. Fish and macroinvertebrate concentrations increased downriver indicating passive uptake from water. The information presented here could be useful for those doing river restoration and water manipulation in mercury contaminated

  10. Arterial wall degeneration plus hemodynamic insult cause arterial wall remodeling and nascent aneurysm formation at specific sites in dogs.

    PubMed

    Zhu, Yue-Qi; Li, Ming-Hua; Yan, Lei; Tan, Hua-Qiao; Cheng, Ying-Sheng

    2014-09-01

    To determine whether arterial wall degeneration, in combination with hemodynamic insult, causes cerebral artery aneurysms in a dog model, we simulated the geometry and hemodynamics of a human artery by surgical reconstruction of both common carotid arteries in 12 dogs. The dogs were then randomly assigned to one of the following groups: hemodynamic insult + elastase insult group ( n = 6), hemodynamic insult group (n = 6), or elastase control group (n = 3), in which the straight common carotid arteries were subjected to elastase alone. Angiography and hemodynamic analysis were performed immediately and at 12 weeks after surgery; the animals were then killed for histologic evaluation. The 12 surgically reconstructed distal internal carotid arteries simulated the human artery well with respect to geometric and hemodynamic measurements, with the intended aneurysm sites exposed to higher wall shear stress and velocity, lower pressure, turbulent flow, and changes in wall shear stress gradient. Nascent aneurysms developed in 4 hemodynamic insult + elastase insult group dogs at 12 weeks; blood flow analysis demonstrated decreased wall shear stress, increased pressure, and wall shear stress gradient from the neck to the dome. Arterial wall remodeling or nascent aneurysm formation in the hemodynamic insult + elastase insult group versus the other groups was indicated by internal elastic lamina/elastic fiber disruption, muscular layer thinning, increased smooth muscle cell proliferation, macrophage infiltration, and high expression of matrix metalloproteinase-2 and matrix metalloproteinase-9 in the media. These data suggest that nascent aneurysms were caused by the combination of arterial wall degeneration and hemodynamic perturbations in this distal internal carotid artery dog model.

  11. Bundle formation of smooth muscle desmin intermediate filaments by calponin and its binding site on the desmin molecule.

    PubMed

    Fujii, T; Takagi, H; Arimoto, M; Ootani, H; Ueeda, T

    2000-03-01

    Smooth muscle basic calponin, a major actin-, tropomyosin-, and calmodulin-binding protein, has been examined for its ability to interact with desmin intermediate filaments from smooth muscle cells using sedimentation analysis, turbidity changes, chemical cross-linking, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF/MS), and electron microscopic observations. Calponin interacted with desmin intermediate filaments in a concentration-dependent manner in vitro. The binding of calponin to desmin produced dense aggregates at 30 degrees C. The dense aggregates were observed by electron microscopy to be composed of large anisotropic bundles of desmin filaments, indicating that calponin forms bundles of desmin filaments. The addition of calmodulin or S100 to the mixture of calponin and desmin caused the removal of calponin from the desmin filaments and inhibited bundle formation in the presence of Ca(2+), but not in the presence of EGTA. Calponin-related proteins including G-actin, tropomyosin, and SM22, had little effect on the binding of calponin to desmin filaments, whereas tubulin weakly inhibited the binding. Desmin had little influence on the calponin-actin and calponin-tubulin interactions using the zero-length cross-linker, EDC. Domain mapping with chymotryptic digestion showed that the binding site of calponin resides within the central a-helical rod domain of the desmin molecule. The chemical cross-linked products of calponin and synthetic peptides (TQ27, TNEKVELQELNDRFANYIEKVRFLEQQ; EE24, EEELRELRRQVDALTGQRARVEVE) derived from the rod domain were detected by MALDI TOF/MS. Furthermore, the calponin-desmin interaction was significantly inhibited by the addition of EE24, but only slightly by TQ27. These results suggest that calponin may act as a cross-linking protein between desmin filaments as well as among intermediate filaments, microfilaments and microtubules in smooth muscle cells.

  12. Maternal Wnt/β-Catenin Signaling Coactivates Transcription through NF-κB Binding Sites during Xenopus Axis Formation

    PubMed Central

    Armstrong, Neil J.; Fagotto, François; Prothmann, Christian; Rupp, Ralph A. W.

    2012-01-01

    Maternal Wnt/β-Catenin signaling establishes a program of dorsal-specific gene expression required for axial patterning in Xenopus. We previously reported that a subset of dorsally expressed genes depends not only on Wnt/β-Catenin stimulation, but also on a MyD88-dependent Toll-like receptor/IL1-receptor (TLR/IL1-R) signaling pathway. Here we show that these two signal transduction cascades converge in the nucleus to coactivate gene transcription in blastulae through a direct interaction between β-Catenin and NF-κB proteins. A transdominant inhibitor of NF-κB, ΔNIκBα, phenocopies loss of MyD88 protein function, implicating Rel/NF-κB proteins as selective activators of dorsal-specific gene expression. Sensitive axis formation assays in the embryo demonstrate that dorsalization by Wnt/β-Catenin requires NF-κB protein activity, and vice versa. Xenopus nodal-related 3 (Xnr3) is one of the genes with dual β-Catenin/NF-κB input, and a proximal NF-κB consensus site contributes to the regional activity of its promoter. We demonstrate in vitro binding of Xenopus β-Catenin to several XRel proteins. This interaction is observed in vivo upon Wnt-stimulation. Finally, we show that a synthetic luciferase reporter gene responds to both endogenous and exogenous β-Catenin levels in an NF-κB motif dependent manner. These results suggest that β-Catenin acts as a transcriptional co-activator of NF-κB-dependent transcription in frog primary embryonic cells. PMID:22590521

  13. Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors

    NASA Astrophysics Data System (ADS)

    Sato, Ryuma; Kitoh-Nishioka, Hirotaka; Ando, Koji; Yamato, Takahisa

    2015-07-01

    To examine the functional roles of the active site methionine (M-site) and glutamic acid (E-site) residues of blue-light photoreceptors, we performed in silico mutation at the M-site in a systematic manner and focused on the hydrogen bonding between the E-site and the substrate: the cyclobutane-pyrimidine dimer (CPD). Fragment molecular orbital calculations with electron correlations demonstrated that substitution of the M-site methionine with either alanine or glutamine always destabilizes the interaction energy between the E-site and the CPD by more than 12.0 kcal/mol, indicating that the methionine and glutamic acid residues cooperatively facilitate the enzymatic reaction in the active site.

  14. EphrinA4 mimetic peptide targeted to EphA binding site impairs the formation of long-term fear memory in lateral amygdala

    PubMed Central

    Dines, M; Lamprecht, R

    2014-01-01

    Fear conditioning leads to long-term fear memory formation and is a model for studying fear-related psychopathologies conditions such as phobias and posttraumatic stress disorder. Long-term fear memory formation is believed to involve alterations of synaptic efficacy mediated by changes in synaptic transmission and morphology in lateral amygdala (LA). EphrinA4 and its cognate Eph receptors are intimately involved in regulating neuronal morphogenesis, synaptic transmission and plasticity. To assess possible roles of ephrinA4 in fear memory formation we designed and used a specific inhibitory ephrinA4 mimetic peptide (pep-ephrinA4) targeted to EphA binding site. We show that this peptide, composed of the ephrinA4 binding domain, interacts with EphA4 and inhibits ephrinA4-induced phosphorylation of EphA4. Microinjection of the pep-ephrinA4 into rat LA 30 min before training impaired long- but not short-term fear conditioning memory. Microinjection of a control peptide derived from a nonbinding E helix site of ephrinA4, that does not interact with EphA, had no effect on fear memory formation. Microinjection of pep-ephrinA4 into areas adjacent to the amygdala had no effect on fear memory. Acute systemic administration of pep-ephrinA4 1 h after training also impaired long-term fear conditioning memory formation. These results demonstrate that ephrinA4 binding sites in LA are essential for long-term fear memory formation. Moreover, our research shows that ephrinA4 binding sites may serve as a target for pharmacological treatment of fear and anxiety disorders. PMID:25268254

  15. EphrinA4 mimetic peptide targeted to EphA binding site impairs the formation of long-term fear memory in lateral amygdala.

    PubMed

    Dines, M; Lamprecht, R

    2014-09-30

    Fear conditioning leads to long-term fear memory formation and is a model for studying fear-related psychopathologies conditions such as phobias and posttraumatic stress disorder. Long-term fear memory formation is believed to involve alterations of synaptic efficacy mediated by changes in synaptic transmission and morphology in lateral amygdala (LA). EphrinA4 and its cognate Eph receptors are intimately involved in regulating neuronal morphogenesis, synaptic transmission and plasticity. To assess possible roles of ephrinA4 in fear memory formation we designed and used a specific inhibitory ephrinA4 mimetic peptide (pep-ephrinA4) targeted to EphA binding site. We show that this peptide, composed of the ephrinA4 binding domain, interacts with EphA4 and inhibits ephrinA4-induced phosphorylation of EphA4. Microinjection of the pep-ephrinA4 into rat LA 30 min before training impaired long- but not short-term fear conditioning memory. Microinjection of a control peptide derived from a nonbinding E helix site of ephrinA4, that does not interact with EphA, had no effect on fear memory formation. Microinjection of pep-ephrinA4 into areas adjacent to the amygdala had no effect on fear memory. Acute systemic administration of pep-ephrinA4 1 h after training also impaired long-term fear conditioning memory formation. These results demonstrate that ephrinA4 binding sites in LA are essential for long-term fear memory formation. Moreover, our research shows that ephrinA4 binding sites may serve as a target for pharmacological treatment of fear and anxiety disorders.

  16. The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites.

    PubMed

    Zhang, Zheng Z; Pannunzio, Nicholas R; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R

    2014-07-24

    R loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R loop formation, and on the number of WGCW sites.

  17. The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

    PubMed Central

    Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

    2014-01-01

    SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

  18. Size-resolved aerosol composition at an urban and a rural site in the Po Valley in summertime: implications for secondary aerosol formation

    NASA Astrophysics Data System (ADS)

    Sandrini, Silvia; van Pinxteren, Dominik; Giulianelli, Lara; Herrmann, Hartmut; Poulain, Laurent; Facchini, Maria Cristina; Gilardoni, Stefania; Rinaldi, Matteo; Paglione, Marco; Turpin, Barbara J.; Pollini, Francesca; Bucci, Silvia; Zanca, Nicola; Decesari, Stefano

    2016-09-01

    The aerosol size-segregated chemical composition was analyzed at an urban (Bologna) and a rural (San Pietro Capofiume) site in the Po Valley, Italy, during June and July 2012, by ion-chromatography (major water-soluble ions and organic acids) and evolved gas analysis (total and water-soluble carbon), to investigate sources and mechanisms of secondary aerosol formation during the summer. A significant enhancement of secondary organic and inorganic aerosol mass was observed under anticyclonic conditions with recirculation of planetary boundary layer air but with substantial differences between the urban and the rural site. The data analysis, including a principal component analysis (PCA) on the size-resolved dataset of chemical concentrations, indicated that the photochemical oxidation of inorganic and organic gaseous precursors was an important mechanism of secondary aerosol formation at both sites. In addition, at the rural site a second formation process, explaining the largest fraction (22 %) of the total variance, was active at nighttime, especially under stagnant conditions. Nocturnal chemistry in the rural Po Valley was associated with the formation of ammonium nitrate in large accumulation-mode (0.42-1.2 µm) aerosols favored by local thermodynamic conditions (higher relative humidity and lower temperature compared to the urban site). Nocturnal concentrations of fine nitrate were, in fact, on average 5 times higher at the rural site than in Bologna. The water uptake by this highly hygroscopic compound under high RH conditions provided the medium for increased nocturnal aerosol uptake of water-soluble organic gases and possibly also for aqueous chemistry, as revealed by the shifting of peak concentrations of secondary compounds (water-soluble organic carbon (WSOC) and sulfate) toward the large accumulation mode (0.42-1.2 µm). Contrarily, the diurnal production of WSOC (proxy for secondary organic aerosol) by photochemistry was similar at the two sites but

  19. Influences of aerosol physiochemical properties and new particle formation on CCN activity from observation at a suburban site of China

    NASA Astrophysics Data System (ADS)

    Li, Yanan; Zhang, Fang; Li, Zhanqing; Sun, Li; Wang, Zhenzhu; Li, Ping; Sun, Yele; Ren, Jingye; Wang, Yuying; Cribb, Maureen; Yuan, Cheng

    2017-05-01

    With the aim of understanding the impact of aerosol particle size and chemical composition on CCN activity, the size-resolved cloud condensation nuclei (CCN) number concentration (NCCN), particle number size distribution (PSD) (10-600 nm), and bulk chemical composition of particles with a diameter < 1.0 μm (PM1) were measured simultaneously at Xinzhou, a suburban site in northern China, from 22 July to 26 August 2014. The NCCN was measured at five different supersaturations (SS) ranging from 0.075%-0.76%. Diurnal variations in the aerosol number concentration (NCN), NCCN, the bulk aerosol activation ratio (AR), the hygroscopicity parameter (κchem), and the ratio of 44 mass to charge ration (m/z 44) to total organic signal in the component spectrum (f44), and the PSD were examined integrally to study the influence of particle size and chemical composition on CCN activation. We found that particle size was more related to the CCN activation ratios in the morning, whereas in the afternoon ( 1400 LST), κchem and f44 were more closely associated with the bulk AR. Assuming the internal mixing of aerosol particles, NCCN was estimated using the bulk chemical composition and real-time PSD. We found that the predicted CCN number concentrations were underestimated by 20-30% at SS < 0.2% probably due to the measurement uncertainties. Estimates were more accurate at higher SS levels, suggesting that the hygroscopicity parameter based on bulk chemical composition information can provide a good estimate of CCN number concentrations. We studied the impacts of new particle formation (NPF) events on size-resolved CCN activity at the ;growth; stage and ;leveling-off; stage during a typical NPF event by comparing with the case during non-NPF event. It has been found that CCN activation was restrained at the ;growth; stage during which larger particle diameters were needed to reach an activation diameter(Da), and the bulk AR decreased as well. However, during the ;leveling

  20. Post burial alteration of the Permian Rustler Formation Evaporites, WIPP (Waste Isolation Pilot Plant) site, New Mexico: Textural, stratigraphic and chemical evidence

    SciTech Connect

    Lowenstein, T.K.

    1987-04-01

    The Rustler Formation is a Late Permian (Ochoan Series) evaporite found in the subsurface and in outcrop in New Mexico and west Texas. The main rock types of the Rustler Formation are anhydrite, gypsum, halite, dolostone and siliciclastic sandstone and mudstone. Across the WIPP site, located in southeastern New Mexico, some of the Rustler rock types and their thicknesses change dramatically over short lateral distances. These lateral variations have mainly been attributed to post-burial dissolution of evaporites. The aim of the present study is to distinguish syndepositional features from post burial alteration features in the Rustler Formation. Four borehole cores of the complete Rustler Formation were examined. Primary sedimentary structures, textures and fabrics were identified, based on comparison with modern evaporite deposits. Vertical and lateral patterns of primary sedimentary features were recorded. From this information, depositional settings have been assembled which best account for the observed types of primary features and their vertical and lateral distribution. With this framework, post-depositional diagenetic overprints were identified in the Rustler Formation. The question of whether subsurface diagenetic alteration is presently active at the WIPP site is addressed.

  1. Different characteristics of new particle formation between urban and deciduous forest sites in Northern Japan during the summers of 2010-2011

    NASA Astrophysics Data System (ADS)

    Jung, J.; Miyazaki, Y.; Kawamura, K.

    2013-01-01

    To investigate new particle formation (NPF) events in urban and forest environments, number size distributions of ultrafine particles were measured at an urban site and a deciduous forest site in Sapporo, Northern Japan, during the summers of 2011 and 2010, respectively. The burst of nucleation mode particles at the urban site typically started in the morning (07:00-11:30 local time, LT) with simultaneous increases in SO2 and O3 concentrations and the UV index under clear (sunny) weather conditions. The growth rates of nucleated particles at the urban site ranged from 5.0 to 7.8 nm h-1 with an average of 6.3 ± 1.1 nm h-1. NPF events at the urban site were separated into events with or without subsequent particle growth after the burst of nucleation mode particles. This division was found to relate to prevailing wind direction because the subsequent growth of freshly nucleated particles typically occurred when wind direction shifted to northwesterly (from residential and public park areas), whereas it did not occur under southeasterly winds (from the downtown area). During the periods with NPF events, elevated concentrations of non-methane hydrocarbons (NMHC) were obtained under conditions of northwesterly winds when compared to southeasterly winds, whereas no difference in SO2 levels was recorded. These results suggest that variations in NMHC concentration may play an important role in the growth of freshly nucleated particles at the urban site. The burst of nucleation mode particles at the forest site typically started around noon (10:30-14:30 LT), which was 3-4 h later than that at the urban site. Interestingly, at the forest site the burst of nucleation mode particles usually started when air masses originating from urban Sapporo arrived at the forest site. The present study indicates that the inflow of these urban air masses acted as a trigger for the initiation of the burst of nucleation mode particles in the deciduous forest.

  2. Different characteristics of new particle formation between urban and deciduous forest sites in Northern Japan during the summers of 2010-2011

    NASA Astrophysics Data System (ADS)

    Jung, J.; Miyazaki, Y.; Kawamura, K.

    2012-06-01

    To investigate new particle formation (NPF) events in urban and forest environments, number size distributions of ultrafine particles were measured at an urban site and a deciduous forest site in Sapporo, Northern Japan, during the summers of 2011 and 2010, respectively. The burst of nucleation mode particles at the urban site typically started in the morning (7:00-11:30 local time, LT) with simultaneous increases in SO2 and O3 concentrations and the UV index under clear (sunny) weather conditions. The growth rates of nucleated particles at the urban site ranged from 5.0 to 7.8 nm h-1 with an average of 6.3 ± 1.1 nm h-1. NPF events at the urban site were separated into events with or without subsequent particle growth after the burst of nucleation mode particles. This division was related to prevailing wind direction as the subsequent growth of freshly nucleated particles typically occurred when wind direction shifted to northwesterly (from residential and public park areas), whereas it did not occur under southeasterly winds (from the downtown area). During the periods with NPF events, elevated concentrations of non-methane hydrocarbons (NMHC) were obtained under conditions of northwesterly winds when compared to southeasterly winds, whereas no difference in SO2 levels was recorded. These results suggest that variations in NMHC concentration may play an important role in the growth of freshly nucleated particles at the urban site. The burst of nucleation mode particles at the forest site typically started around noon (10:30-14:30 LT), which was 3-4 h later than that at the urban site. Interestingly, at the forest site the burst of nucleation mode particles usually started when air masses originating from urban Sapporo arrived at the forest site. The present study indicates that the inflow of these urban air masses acted as a trigger for the initiation of the burst of nucleation mode particles in the deciduous forest.

  3. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline

    NASA Astrophysics Data System (ADS)

    Park, Ki Soo; Oh, Seung Soo; Soh, H. Tom; Park, Hyun Gyu

    2014-08-01

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to

  4. [[superscript 3]H]-Flunitrazepam-Labeled Benzodiazepine Binding Sites in the Hippocampal Formation in Autism: A Multiple Concentration Autoradiographic Study

    ERIC Educational Resources Information Center

    Guptill, Jeffrey T.; Booker, Anne B.; Gibbs, Terrell T.; Kemper, Thomas L.; Bauman, Margaret L.; Blatt, Gene J.

    2007-01-01

    Increasing evidence indicates that the GABAergic system in cerebellar and limbic structures is affected in autism. We extended our previous study that found reduced [[superscript 3]H] flunitrazepam-labeled benzodiazepine sites in the autistic hippocampus to determine whether this reduction was due to a decrease in binding site number (B [subscript…

  5. [[superscript 3]H]-Flunitrazepam-Labeled Benzodiazepine Binding Sites in the Hippocampal Formation in Autism: A Multiple Concentration Autoradiographic Study

    ERIC Educational Resources Information Center

    Guptill, Jeffrey T.; Booker, Anne B.; Gibbs, Terrell T.; Kemper, Thomas L.; Bauman, Margaret L.; Blatt, Gene J.

    2007-01-01

    Increasing evidence indicates that the GABAergic system in cerebellar and limbic structures is affected in autism. We extended our previous study that found reduced [[superscript 3]H] flunitrazepam-labeled benzodiazepine sites in the autistic hippocampus to determine whether this reduction was due to a decrease in binding site number (B [subscript…

  6. Exploration of the 1891 Foerstner submarine vent site (Pantelleria, Italy): insights into the formation of basaltic balloons

    NASA Astrophysics Data System (ADS)

    Kelly, Joshua T.; Carey, Steven; Pistolesi, Marco; Rosi, Mauro; Croff-Bell, Katherine Lynn; Roman, Chris; Marani, Michael

    2014-07-01

    On October 17, 1891, a submarine eruption started at Foerstner volcano located within the Pantelleria Rift of the Strait of Sicily (Italy). Activity occurred for a period of 1 week from an eruptive vent located 4 km northwest of the island of Pantelleria at a water depth of 250 m. The eruption produced lava balloons that discharged gas at the surface and eventually sank to the seafloor. Remotely operated vehicle (ROV) video footage and high-resolution multi-beam mapping of the Foerstner vent site were used to create a geologic map of the AD 1891 deposits and conduct the first detailed study of the source area associated with this unusual type of submarine volcanism. The main Foerstner vent consists of two overlapping circular mounds with a total volume of 6.3 × 105 m3 and relief of 60 m. It is dominantly constructed of clastic scoriaceous deposits with some interbedded pillow lavas. Petrographic and geochemical analyses of Foerstner samples by X-ray fluorescence and inductively coupled plasma mass spectrometry reveal that the majority of the deposits are vesicular, hypocrystalline basanite scoria that display porphyritic, hyaloophitic, and vitrophyric textures. An intact lava balloon recovered from the seafloor consists of a large interior gas cavity surrounded by a thin lava shell comprising two distinct layers: a thin, oxidized, quenched crust surrounding the exterior of the balloon and a dark gray, tachylite layer lying beneath it. Ostwald ripening is proposed to be the dominant bubble growth mechanism of four representative Foerstner scoria samples as inferred by vesicle size distributions. Characterization of the diversity of deposit facies observed at Foerstner in conjunction with quantitative rock texture analysis indicates that submarine Strombolian-like activity is the most likely mechanism for the formation of lava balloons. The deposit facies observed at the main Foerstner vent are very similar to those produced by other known submarine Strombolian

  7. NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region.

    PubMed Central

    Stamatoyannopoulos, J A; Goodwin, A; Joyce, T; Lowrey, C H

    1995-01-01

    The beta-like globin genes require the upstream locus control region (LCR) for proper expression. The active elements of the LCR coincide with strong erythroid-specific DNase I-hypersensitive sites (HSs). We have used 5' HS4 as a model to study the formation of these HSs. Previously, we identified a 101 bp element that is required for the formation of this HS. This element binds six proteins in vitro. We now report a mutational analysis of the HS4 HS-forming element (HSFE). This analysis indicates that binding sites for the hematopoietic transcription factors NF-E2 and GATA-1 are required for the formation of the characteristic chromatin structure of the HS following stable transfection into murine erythroleukemia cells. Similarly arranged NF-E2 and GATA binding sites are present in the other HSs of the human LCR, as well as in the homologous mouse and goat sequences and the chicken beta-globin enhancer. A combination of DNase I and micrococcal nuclease sensitivity assays indicates that the characteristic erythroid-specific hypersensitivity of HS4 to DNase I is the result of tissue-specific alterations in both nucleosome positioning and tertiary DNA structure. Images PMID:7828582

  8. Measurements of hygroscopicity and volatility of atmospheric ultrafine particles during ultrafine particle formation events at urban, industrial, and coastal sites.

    PubMed

    Park, Kihong; Kim, Jae-Seok; Park, Seung Ho

    2009-09-01

    The tandem differential mobility analyzer (TDMA) technique was applied to determine the hygroscopicity and volatility of atmospheric ultrafine particles in three sites of urban Gwangju, industrial Yeosu, and coastal Taean in South Korea. A database for the hygroscopicity and volatility of the known compositions and sizes of the laboratory-generated particles wasfirst constructed for comparison with the measured properties of atmospheric ultrafine particles. Distinct differences in hygroscopicity and volatility of atmospheric ultrafine particles werefound between a "photochemical event" and a "combustion event" as well as among different sites. At the Gwangju site, ultrafine particles in the "photochemical event" were determined to be more hygroscopic (growth factor (GF) = 1.05-1.33) than those in the "combustion event" (GF = 1.02-1.12), but their hygroscopicity was not as high as pure ammonium sulfate or sulfuric acid particles in the laboratory-generated database, suggesting they were internally mixed with less soluble species. Ultrafine particles in the "photochemical event" at the Yeosu site, having a variety of SO2, CO, and VOC emission sources, were more hygroscopic (GF = 1.34-1.60) and had a higher amount of volatile species (47-75%)than those observed at the Gwangju site. Ultrafine particle concentration at the Taean site increased during daylight hours with low tide, having a higher GF (1.34-1.80) than the Gwangju site and a lower amount of volatile species (17-34%) than the Yeosu site. Occasionally ultrafine particles were externally mixed according to their hygroscopicity and volatility, and TEM/EDS data showed that each type of particle had a distinct morphology and elemental composition.

  9. Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi-functional c-di-GMP regulator.

    PubMed

    Phippen, Curtis William; Mikolajek, Halina; Schlaefli, Henry George; Keevil, Charles William; Webb, Jeremy Stephen; Tews, Ivo

    2014-12-20

    Diguanylate cyclases (DGC) and phosphodiesterases (PDE), respectively synthesise and hydrolyse the secondary messenger cyclic dimeric GMP (c-di-GMP), and both activities are often found in a single protein. Intracellular c-di-GMP levels in turn regulate bacterial motility, virulence and biofilm formation. We report the first structure of a tandem DGC-PDE fragment, in which the catalytic domains are shown to be active. Two phosphodiesterase states are distinguished by active site formation. The structures, in the presence or absence of c-di-GMP, suggest that dimerisation and binding pocket formation are linked, with dimerisation being required for catalytic activity. An understanding of PDE activation is important, as biofilm dispersal via c-di-GMP hydrolysis has therapeutic effects on chronic infections. Copyright © 2014. Published by Elsevier B.V.

  10. Synergistic modulation of cyclobutane pyrimidine dimer photoproduct formation and deamination at a TmCG site over a full helical DNA turn in a nucleosome core particle.

    PubMed

    Song, Qian; Cannistraro, Vincent J; Taylor, John-Stephen

    2014-12-01

    Sunlight-induced C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C or 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by DNA polymerase η and defines a probable mechanism for the origin of UV-induced C to T mutations. We have now determined the photoproduct formation and deamination rates for 10 consecutive T=(m)CG CPDs over a full helical turn at the dyad axis of a nucleosome and find that whereas photoproduct formation and deamination is greatly inhibited for the CPDs closest to the histone surface, it is greatly enhanced for the outermost CPDs. Replacing the G in a T=(m)CG CPD with A greatly decreased the deamination rate. These results show that rotational position and flanking sequence in a nucleosome can significantly and synergistically modulate CPD formation and deamination that contribute to C to T mutations associated with skin cancer induction and may have influenced the evolution of the human genome. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

    PubMed Central

    Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jérôme; Legault, Pascale

    2011-01-01

    The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme. PMID:21266483

  12. Formation energy and photoelectrochemical properties of BiVO4 after doping at Bi3+ or V5+ sites with higher valence metal ions.

    PubMed

    Luo, Wenjun; Wang, Jiajia; Zhao, Xin; Zhao, Zongyan; Li, Zhaosheng; Zou, Zhigang

    2013-01-21

    Photoelectrochemical water splitting is an attractive method to produce H(2) fuel from solar energy and water. Ion doping with higher valence states was used widely to enhance the photocurrent of an n-type oxide semiconductor. In this study, the different doping sites and the photoelectrochemical properties of Mo(6+), W(6+) and Sn(4+)-doped BiVO(4) were studied systematically. The results suggested that Mo(6+) or W(6+)-doped BiVO(4) had a much higher photocurrent while the photocurrent of Sn(4+)-doped BiVO(4) did not change obviously. Raman and XPS were used to identify the doping sites in the BiVO(4) crystal lattice. It was found that Mo or W substituted V sites but Sn did not substitute Bi sites. Results of theoretical calculation indicated that a higher formation energy and lower solubility of impurity ions led to serious SnO(2) segregation on the surface of the Sn(4+)-doped BiVO(4) thin film, which was the main reason for the poor performance of Sn-doped BiVO(4). The higher formation energy of Sn(4+) came from the large mismatch of ion radius and different outer shell electron distribution. These results can offer guidance in choosing suitable doping ions for other semiconductor photoelectrodes.

  13. Geology, coal resources, and chemical analyses of coal from the Fruitland Formation, Kimbeto EMRIA study site, San Juan County, New Mexico

    USGS Publications Warehouse

    Schneider, Gary B.; Hildebrand, Rick T.; Affolter, Ronald H.

    1979-01-01

    The Kimbeto EMRIA study site, an area of about 20 square miles (52 km2), is located on the south margin of the San Juan Basin on the gently northward-dipping strata of the Upper Cretaceous Fruitland Formation and the Kirtland Shale. The coal beds are mainly in the lower 150 feet (45 m) of the Fruitland Format ion. Coal resources--measured, indicated, and inferred--with less than 400 feet (120 m) of overburden in the site are 69,085,000 short tons (62,660,100 metric tons), 369,078,000 short tons (334,754,000 metric tons), and 177,803,000 short tons (161,267,000 metric tons) respectively. About 68 percent of these resources are overlain by 200 feet (60 m) or less of overburden. The apparent rank of the coal ranges from subbituminous B to subbituminous A. The average Btu/lb value of 14 core samples from the site on the as-received basis is 8,240 (4580 Kcal/kg), average ash content is 23.4 percent, and average sulfur content is 0.5 percent. Analyses of coal from the Kimbeto EMRIA study site show significantly higher ash content and significantly lower contents of volatile matter, fixed carbon, carbon, and a significantly lower heat of combustion when compared with other coal analyses from the Rocky Mountain province.

  14. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline.

    PubMed

    Park, Ki Soo; Oh, Seung Soo; Soh, H Tom; Park, Hyun Gyu

    2014-09-07

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.

  15. A site-specific phosphorylation of the focal adhesion kinase controls the formation of spheroid cell clusters.

    PubMed

    Beck, Hans Christian; Gosau, Martin; Kristensen, Lars Peter; Morsczeck, Christian

    2014-07-01

    Human dental follicle cells (DFCs) are ectomesenchymal multipotent stem cells that form spheroid cell clusters (SCCs) under serum free medium cell culture conditions (SFM). Until today, molecular mechanisms for the formation of SCCs are unknown. In this study a quantitative phosphoproteomics approach revealed regulated phosphorylated proteins in SCCs, which were derived from DFCs after 24 and 48 h in SFM. These regulated proteins were categorized using the Kyoto encyclopedia of genes and genomes program. Here, cellular processes and signaling pathway were identified such as the focal adhesion kinase (FAK) signaling pathway. In addition to the phosphoproteomics approach we showed that a specific phosphorylation of FAK (Y397) was required for the formation of SCCs. In conclusion, this study disclosed the phosphoproteome of SCCs for the first time and showed that the FAK signaling pathway is required for the formation of SCCs.

  16. A new design of highly reversible LiNiO2: Defect formation in transition metal site

    NASA Astrophysics Data System (ADS)

    Kobayashi, Yo; Tabuchi, Mitsuharu; Miyashiro, Hajime; Kuriyama, Nobuhiro

    2017-10-01

    LiNiO2 with Ni defects in the 3b sites (named "Ni defected" LiNiO2) was prepared and characterized using electrochemical calorimetry. Different from conventionally prepared "Standard" LiNiO2, "Ni defected" LiNiO2 exhibited high reversibility. The 1st coulombic efficiency was recorded to be 101% due to minimization from the Ni ion substitution at the Li 3a sites. The reversible capacity was 212 mAh g-1 in the 1st cycle with 87% capacity retention after 80 cycles because Li+ ordering and Jahn-Teller distortion during the charge and discharge cycle were suppressed by introducing the Ni defect 3b sites. The proposed simple defect design concept introduced the development of a high capacity and highly reversible LiNiO2 material without metal substitutions and without increasing the charge cut-off voltage.

  17. Correlation of the KHS Tuff of the Kibish Formation to volcanic ash layers at other sites, and the age of early Homo sapiens (Omo I and Omo II).

    PubMed

    Brown, Francis H; McDougall, Ian; Fleagle, John G

    2012-10-01

    Hominin specimens Omo I and Omo II from Member I of the Kibish Formation, Ethiopia are attributed to early Homo sapiens, and an age near 196 ka has been suggested for them. The KHS Tuff, within Member II of the Kibish Formation has not been directly dated at the site, but it is believed to have been deposited at or near the time of formation of sapropel S6 in the Mediterranean Sea. Electron microprobe analyses suggest that the KHS Tuff correlates with the WAVT (Waidedo Vitric Tuff) at Herto, Gona, and Konso (sample TA-55), and with Unit D at Kulkuletti in the Ethiopian Rift Valley. Konso sample TA-55 is older than 154 ka, and Unit D at Kulkuletti is dated at 183 ka. These correlations and ages provide strong support for the age originally suggested for the hominin remains Omo I and Omo II, and for correlation of times of deposition in the Kibish region with formation of sapropels in the Mediterranean Sea. The Aliyo Tuff in Member III of the Kibish Formation is dated at 104 ka, and correlates with Gademotta Unit 15 in the Ethiopian Rift Valley.

  18. 40Ar/(39)Ar dating of Chemeron Formation strata encompassing the site of hominid KNM-BC 1, Tugen Hills, Kenya.

    PubMed

    Deino, Alan L; Hill, Andrew

    2002-01-01

    A fossil hominid temporal bone (KNM-BC 1) from surface exposures at Baringo Paleontological Research Project site BPRP#2 in the Chemeron Formation outcropping in a tributary drainage of the Kapthurin River west of Lake Baringo, Kenya has been attributed to Homo sp. indet. K-feldspar phenocrysts from lapilli tuffs bracketing the inferred fossiliferous horizon yield single-crystal(40)Ar/(39)Ar ages of 2.456+/-0.006 and 2.393+/-0.013 Ma. These age determinations are supported by stratigraphically consistent ages on higher tuff horizons and from nearby sections. In addition, new(40)Ar/(39)Ar ages on tuffaceous units near the base and top of the formation along the Kapthurin River yield 3.19+/-0.03 and 1.60+/-0.05 Ma respectively. The base of the formation along the Kapthurin River is thus approximately 0.5 Ma younger than the uppermost Chemeron Formation strata exposed at Tabarin, 23 km to the north-northwest. The upper half of the formation along the Kapthurin River was deposited at an average rate of approximately 11 cm/ka, compared to 21-23 cm/ka at Tabarin.

  19. "Dreams Are Born on Places Like This": The Process of Interpretive Community Formation at the "Field of Dreams" Site.

    ERIC Educational Resources Information Center

    Aden, Roger C.; And Others

    1995-01-01

    Analyzes the narratives of 113 visitors to the site of the film "Field of Dreams." Develops a theory that explains how interpretive communities are formed despite theoretical writings that argue for individualized interpretations of text. Demonstrates that individuals can at once converge and diverge symbolically within the confines of…

  20. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.

    PubMed

    Itoh, Yuzuru; Bröcker, Markus J; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2014-04-17

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. New considerations on the stratigraphy and environmental context of the oldest (2.34 Ma) Lokalalei archaeological site complex of the Nachukui Formation, West Turkana, northern Kenya Rift

    NASA Astrophysics Data System (ADS)

    Tiercelin, Jean-Jacques; Schuster, Mathieu; Roche, Hélène; Brugal, Jean-Philippe; Thuo, Peter; Prat, Sandrine; Harmand, Sonia; Davtian, Gourguen; Barrat, Jean-Alix; Bohn, Marcel

    2010-09-01

    At the northwest end of the Lake Turkana Basin (northern Kenya Rift), intensive fieldwork conducted on the Plio-Pleistocene fluvio-lacustrine Nachukui Formation by the National Museums of Kenya and the West Turkana Archaeological Project (WTAP), led to the discovery of more than 50 archaeological sites aged between 2.4 and 0.7 Ma. Among them is the Lokalalei archaeological site complex, which includes the two oldest archaeological sites (2.34 Ma) found in the Kenyan segment of the East African Rift System. The environmental background of the two sites was described as a succession of ephemeral streams with floodplain palaeosols in which the archaeological sites are situated, bordering the western bank of a large axial meandering river flowing southward. The Lokalalei 1 (LA1) and Lokalalei 2C (LA2C) archaeological sites are of extreme importance in terms of knowledge of hominins' knapping activities. The stratigraphic position of the LA1 and LA2C sites as well as implications on the technical differences between the two sites have been successively discussed by Roche et al. (1999), Brown and Gathogo (2002), and Delagnes and Roche (2005). In terms of stratigraphic position, Lokalalei 2C was estimated to be slightly higher in the section (i.e. younger) than Lokalalei 1. An alternative stratigraphic correlation was proposed by Brown and Gathogo (2002), who suggested that LA2C site should have been approximately 100,000 years younger than LA1. New considerations on the stratigraphy and environmental context of the Lokalalei sites have been developed following controversy on the stratigraphic position and time interval between the LA1 and LA2C sites. High-resolution lithostratigraphic work based on bed-to-bed field correlations, facies sedimentology and tephra geochemistry confirms that the LA2C site is slightly higher in the section than the LA1 site by about 11.20 m. This represents a time interval of ˜74,000 years based on an assumed sedimentation rate of 152 mm

  2. Regeneration of nigrostriatal dopaminergic axons after transplantation of olfactory ensheathing cells and fibroblasts prevents fibrotic scar formation at the lesion site.

    PubMed

    Teng, Xichuan; Nagata, Isao; Li, Hong-Peng; Kimura-Kuroda, Junko; Sango, Kazunori; Kawamura, Koki; Raisman, Geoffrey; Kawano, Hitoshi

    2008-11-01

    The fibrotic scar formed after central nervous system injury has been considered an obstacle to axonal regeneration. The present study was designed to examine whether cell transplantation into a damaged central nervous system can reduce fibrotic scar formation and promote axonal regeneration. Nigrostriatal dopaminergic axons were unilaterally transected in rats and cultures of olfactory-ensheathing cells (OECs), and olfactory nerve fibroblasts were transplanted into the lesion site. In the absence of transplants, few tyrosine hydroxylase-immunoreactive axons extended across the lesion 2 weeks after the transection. Reactive astrocytes increased around the lesion, and a fibrotic scar containing type IV collagen deposits developed in the lesion center. The immunoreactivity of chondroitin sulfate side chains and core protein of NG2 proteoglycan increased in and around the lesion. One and 2 weeks after transection and simultaneous transplantation, dopaminergic axons regenerated across the transplanted tissues, which consisted of p75-immunoreactive OECs and fibronectin-immunoreactive fibroblasts. Reactive astrocytes and chondroitin sulfate immunoreactivity increased around the transplants, whereas the deposition of type IV collagen and fibrotic scar formation were completely prevented at the lesion site. Transplantation of meningeal fibroblasts similarly prevented the formation of the fibrotic scar, although its effect on regeneration was less potent than transplantation of OECs and olfactory nerve fibroblasts. The present results suggest that elimination of the inhibitory fibrotic scar is important for neural regeneration.

  3. Contribution of new particle formation to the total aerosol concentration at the high-altitude site Jungfraujoch (3580 m asl, Switzerland)

    NASA Astrophysics Data System (ADS)

    Tröstl, Jasmin; Herrmann, Erik; Frege, Carla; Bianchi, Federico; Molteni, Ugo; Bukowiecki, Nicolas; Hoyle, Christopher R.; Steinbacher, Martin; Weingartner, Ernest; Dommen, Josef; Gysel, Martin; Baltensperger, Urs

    2016-10-01

    Previous modeling studies hypothesized that a large fraction of cloud condensation nuclei (CCN) is attributed to new particle formation (NPF) in the free troposphere. Despite the potential importance of this process, only few long-term observations have been performed to date. Here we present the results of a 12 month campaign of NPF observations at the high-altitude site Jungfraujoch (JFJ, 3580 m above sea level (asl)). Our results show that NPF significantly adds to the total aerosol concentration at the JFJ and only occurs via previous precursor entrainment from the planetary boundary layer (PBL). Freshly nucleated particles do not directly grow to CCN size (90 nm) within observable time scales (maximum 48 h). The contribution of NPF to the CCN concentration is low within this time frame compared to other sources, such as PBL entrainment of larger particles. A multistep growth mechanism is proposed which allows previously formed Aitken mode particles to add to the CCN concentration. A parametrization is derived to explain formation rates at the JFJ, showing that precursor concentration, PBL influence, and global radiation are the key factors controlling new particle formation at the site.

  4. Improved CO Adsorption Energies, Site Preferences, and Surface Formation Energies from a Meta-Generalized Gradient Approximation Exchange-Correlation Functional, M06-L.

    PubMed

    Luo, Sijie; Zhao, Yan; Truhlar, Donald G

    2012-10-18

    A notorious failing of approximate exchange-correlation functionals when applied to problems involving catalysis has been the inability of most local functionals to predict the correct adsorption site for CO on metal surfaces or to simultaneously predict accurate surface formation energies and adsorption energies for transition metals. By adding the kinetic energy density τ to the density functional, the revTPSS density functional was shown recently to achieve a balanced description of surface energies and adsorption energies. Here, we show that the older M06-L density functional, also containing τ, provides improved surface formation energies and CO adsorption energies over revTPSS for five transition metals and correctly predicted the on-top/hollow site adsorption preferences for four of the five metals, which was not achieved by most other local functionals. Because M06-L was entirely designed on the basis of atomic and molecular energies, its very good performance is a confirmation of the reasonableness of its functional form. Two GGA functionals with an expansion in the reduced gradient that is correct through second order, namely, SOGGA and SOGGA11, were also tested and found to produce the best surface formation energies of all tested GGA functionals, although they significantly overestimate the adsorption energies.

  5. Co-doping of (Bi(0.5)Na(0.5))TiO(3): secondary phase formation and lattice site preference of Co.

    PubMed

    Schmitt, V; Staab, T E M

    2012-11-14

    Bismuth sodium titanate (Bi(0.5)Na(0.5))TiO(3) (BNT) is considered to be one of the most promising lead-free alternatives to piezoelectric lead zirconate titanate (PZT). However, the effect of dopants on the material has so far received little attention from an atomic point of view. In this study we investigated the effects of cobalt-doping on the formation of additional phases and determined the preferred lattice site of cobalt in BNT. The latter was achieved by comparing the measured x-ray absorption near-edge structure (XANES) spectra to numerically calculated spectra of cobalt on various lattice sites in BNT. (Bi(0.5)Na(0.5))TiO(3) + x mol% Co (x = 0.0, 0.5, 1.0, 2.6) was synthesized via solid state reaction. As revealed by SEM backscattering images, a secondary phase formed in all doped specimens. Using both XRD and SEM-EDX, it was identified as Co(2)TiO(4) for dopant levels >0.5 mol%. In addition, a certain amount of cobalt was incorporated into BNT, as shown by electron probe microanalysis. This amount increased with increasing dopant levels, suggesting that an equilibrium forms together with the secondary phase. The XANES experiments revealed that cobalt occupies the octahedral B-site in the BNT perovskite lattice, substituting Ti and promoting the formation of oxygen vacancies in the material.

  6. Venting formation fluids from deep-sea boreholes in a ridge flank setting: ODP Sites 1025 and 1026

    NASA Astrophysics Data System (ADS)

    Wheat, C. Geoffrey; Jannasch, Hans W.; Kastner, Miriam; Plant, Josh N.; Decarlo, Eric H.; Lebon, Geoff

    2004-08-01

    During ODP Leg 168, two of ten boreholes, ODP Holes 1025C and 1026B, were cased through the sediment section, penetrated basaltic crust that is overpressured, and sealed. In 1999 and 2000 the seals were removed, allowing crustal formation fluids to vent and be sampled. The composition of these fluids is compared to those of basal deep-sea pore waters, which have been the basis for estimating geochemical fluxes from low-temperature ridge flank hydrothermal systems. Estimates for the composition of the major ions in formation fluids based on basal pore waters are within 5% of the values measured in borehole fluids. Similar comparisons for minor and trace elements are not as good; some are reactive in the sediment section, resulting in large uncertainties in the pore water extrapolation, while others are influenced by a variety of contaminants, including steel, grease, drilling muds, and basal sediment. Evidence for contamination includes high dissolved and particulate concentrations of several metals (e.g., Fe, Cu, Co, Zn, and Pb) and measurable changes in concentration during the past four years in response to reaction with basal sediment. This new confidence in estimating the primary composition of formation fluids, coupled with advances in thermodynamic and kinetic models, reveals the possibility of anhydrite precipitation in ridge flank hydrothermal systems at temperatures of ˜70°C. Such new insights allow us to address the timing and conditions under which seawater-crustal reactions occur, leading to more accurate models of crustal evolution.

  7. Miami's Tequesta Site Yields Information That a Model For Tornado Formation Can Be Generalized To Yield Some Information About Hurricanes.

    NASA Astrophysics Data System (ADS)

    Mc Leod, David M.; Mc Leod, Roger D.

    2002-10-01

    We detect extensive blue light phenomena associated with anomalous weather at numerous sites; this is particularly so at places held sacred by Native Americans, such as Miami's Tequesta site. Our previous model for tornado generation implicates ionic flow across magnetic field lines for vortex or funnel generation. Indeed, there is a twisting motion of the entire upper part of the thunderhead depicted on televised reports of tornados. This indicates that diagonally ascending ionized air currents have to be intersecting somewhat transversely through extensive, essentially vertical components of significantly strong magnetic field lines, so that the large, upward spiraling effect of the thunderhead can be generated. It is just this aspect of extensive magnetic field emanations that seem to be transiently evident at Miami. Large masses of ionized air currents must somewhat transversely be intersecting large magnetic field emanations, which could be coupled with Earth's internal dynamo. The hurricane or typhoon is perhaps then bound to the meanderings of an internal secondary magnetic dipole.

  8. Covalent Adduct Formation between the Antihypertensive Drug Hydralazine and Abasic Sites in Double- and Single-Stranded DNA

    PubMed Central

    2015-01-01

    Hydralazine (4) is an antihypertensive agent that displays both mutagenic and epigenetic properties. Here, gel electrophoretic, mass spectroscopic, and chemical kinetics methods were used to provide evidence that medicinally relevant concentrations of 4 rapidly form covalent adducts with abasic sites in double- and single-stranded DNA under physiological conditions. These findings raise the intriguing possibility that the genotoxic properties of this clinically used drug arise via reactions with an endogenous DNA lesion rather than with the canonical structure of DNA. PMID:25405892

  9. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

    PubMed

    Sengupta, Raghuvir N; Van Schie, Sabine N S; Giambaşu, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

    2016-01-01

    Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. © 2015 Sengupta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  10. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

    PubMed Central

    Sengupta, Raghuvir N.; Van Schie, Sabine N.S.; Giambaşu, George; Dai, Qing; Yesselman, Joseph D.; York, Darrin; Piccirilli, Joseph A.; Herschlag, Daniel

    2016-01-01

    Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such “off-pathway” species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2′- and 3′-deoxy (–H) and −amino (–NH2) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3′-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2′-OH making no interaction. Upon S binding, a rearrangement occurs that allows both –OH groups to contact a different active site metal ion, termed MC, to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

  11. Day and night-time formation of organic nitrates at a forested mountain site in south-west Germany

    NASA Astrophysics Data System (ADS)

    Sobanski, Nicolas; Thieser, Jim; Schuladen, Jan; Sauvage, Carina; Song, Wei; Williams, Jonathan; Lelieveld, Jos; Crowley, John N.

    2017-03-01

    We report in situ measurements of total peroxy nitrates (ΣPNs) and total alkyl nitrates (ΣANs) in a forested-urban location at the top of the Kleiner Feldberg mountain in south-west Germany. The data, obtained using thermal dissociation cavity ring-down spectroscopy (TD-CRDS) in August-September 2011 (PARADE campaign) and July 2015 (NOTOMO campaign), represent the first detailed study of ΣPNs and ΣANs over continental Europe. We find that a significant fraction of NOx (up to 75 %) is sequestered as organics nitrates at this site. Furthermore, we also show that the night-time production of alkyl nitrates by reaction of NO3 with biogenic hydrocarbons is comparable to that from daytime OH-initiated oxidation pathways. The ΣANs / ozone ratio obtained during PARADE was used to derive an approximate average yield of organic nitrates at noon from the OH initiated oxidation of volatile organic compounds (VOCs) of ˜ 7 % at this site in 2011, which is comparable with that obtained from an analysis of VOCs measured during the campaign. A much lower AN yield, < 2 %, was observed in 2015, which may result from sampling air with different average air mass ages and thus different degrees of breakdown of assumptions used to derive the branching ratio, but it may also reflect a seasonal change in the VOC mixture at the site.

  12. Pre-injection Comparison of Methods for Sampling Formation Water and Associated Gas from a Monitoring Well at a Carbon Dioxide Injection Site, Citronelle Oil Field, Alabama

    NASA Astrophysics Data System (ADS)

    Conaway, C.; Thordsen, J. J.; Manning, M. A.; Cook, P. J.; Abedini, A. A.; Trautz, R. C.; Thomas, B.; Kharaka, Y. K.

    2012-12-01

    The chemical composition of formation water and associated gases from the lower Cretaceous Paluxy Formation was determined using four different sampling methods at a well in the Citronelle Oil Field, Alabama, a site that will be used for a carbon dioxide injection experiment. Prior to each of the two sampling periods, the well was cleaned from the drilling fluids and KCl solutions by producing at least three pore volumes of formation water. Accurate measurements of the chemical composition of groundwater or formation water, including dissolved gasses, and gas samples is essential in understanding subsurface geochemical processes occurring as a result of geologic carbon dioxide injection, which is used for enhanced oil recovery (EOR) and has been proposed as a means of carbon sequestration. In this study, formation water and gas samples for geochemical analyses were obtained from well D-9-8 #2 at Citronelle using nitrogen lift, submersible pump, U-Tube, and a downhole (Kuster) sampler. Field chemical analyses included electrical conductivity, hydrogen sulfide, alkalinity, and pH, and laboratory analyses included major, minor and trace elements by mass spectrometry and ion chromatography, dissolved carbon, organic acid anions, free and dissolved gas species. The formation water obtained from this well is a Na-Ca-Cl brine with a salinity of 160,000 and 200,000 mg/L total dissolved solids (TDS). Differences were evident between sampling methodologies, particularly in pH, Fe and alkalinity measurements. The results of the comparison demonstrate the difficulty and importance of preserving volatile analytes in samples, with the downhole sampler and U-Tube system performing most favorably in this aspect.

  13. O-O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O-O radical coupling.

    PubMed

    Shaffer, David W; Xie, Yan; Concepcion, Javier J

    2017-09-01

    In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

  14. Participation of active-site carboxylates of Escherichia coli DNA polymerase I (Klenow fragment) in the formation of a prepolymerase ternary complex.

    PubMed

    Gangurde, Rajiv; Modak, Mukund J

    2002-12-10

    We have investigated the roles of four active-site carboxylates in the formation of a prepolymerase ternary complex of Escherichia coli DNA polymerase I (Klenow fragment), containing the template-primer and dNTP. The analysis of nine mutant enzymes with conserved and nonconserved substitutions of Asp(705), Glu(710), Asp(882), and Glu(883) clearly shows that both catalytically essential aspartates, Asp(705) and Asp(882), are required for the formation of a stable ternary complex. Of the two glutamates, only Glu(710) is required for ternary complex formation, while Glu(883) does not participate in this process. This investigation also reveals two interesting properties of the Klenow fragment with regard to enzyme-template-primer binary and enzyme-template-primer-dNTP ternary complex formation. These are (a) the significant resistance of enzyme-template-primer-dNTP ternary complexes to the addition of high salt or template-primer challenge and (b) the ability of the Klenow fragment to form ternary complexes in the presence of noncatalytic divalent cations such as Ca(2+), Co(2+), Ni(2+), and Zn(2+).

  15. Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal.

    PubMed

    Jain, Rinku; Hao, Bing; Liu, Ren-Peng; Chan, Michael K

    2005-04-06

    E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.

  16. Typing of the pilus-protein-encoding FCT region and biofilm formation as novel parameters in epidemiological investigations of Streptococcus pyogenes isolates from various infection sites.

    PubMed

    Köller, Thomas; Manetti, Andrea Guido Oreste; Kreikemeyer, Bernd; Lembke, Cordula; Margarit, Immaculada; Grandi, Guido; Podbielski, Andreas

    2010-04-01

    Streptococcus pyogenes is an important human pathogen for which an association between infection site and selected epidemiological or functional markers has previously been suggested. However, the studies involved often used strains with an insufficiently defined clinical background and laboratory history. Thus, the major goal of the present study was to investigate these relationships in 183 prospectively collected, well-defined, low-passage isolates from a North-East German centre for tertiary care. For each isolate the clinical background (91 respiratory, 71 skin and 21 invasive isolates) and antibiotic-resistance pattern was recorded. All isolates were classified according to their emm type, antibiotic-resistance and PFGE pattern ( SmaI restriction analysis of genomic DNA). As novel discriminatory methods we performed a PCR-based typing of the pilus-protein-encoding FCT region (FCT) and biofilm-formation phenotyping in various culture media. Forty-one isolates were found to be resistant to at least one of the tested antibiotics. emm typing revealed emm28, emm12 , emm1, emm4, emm89 and emm2 as the most frequent types in our collection. The novel FCT typing showed isolates encoding FCT types 4 and 2 to be the most common. Overall 113 strains with unique combinations of emm and FCT types, antibiotic-resistance and PFGE patterns were identified. The majority of all isolates revealed an association of biofilm-formation capacity with growth media. Comparing all results for potential associations, no correlation could be established between the anatomical site of isolation and the emm or the FCT type. There was no relationship between biofilm formation and emm type, antibiotic-resistance or PFGE patterns. However, a novel association between biofilm formation and FCT type became obvious among strains from our collection.

  17. Field-based description of rhyolite lava flows of the Calico Hills Formation, Nevada National Security Site, Nevada

    USGS Publications Warehouse

    Sweetkind, Donald S.; Bova, Shiera C.

    2015-01-01

    In the area south of the Rainier Mesa caldera, surface and subsurface geologic data are combined to interpret the overall thickness of the Calico Hills Formation and the proportion of lava flow lithology across the study area. The formation is at least 500 meters (m) thick and contains the greatest proportion of rhyolite lava flow to the northeast of Yucca Mountain in the lower part of Fortymile Canyon. The formation thins to the south and southwest where it is between 50 and 200 m thick beneath Yucca Mountain and contains no rhyolite lavas. Geologic mapping and field-based correlation of individual lava flows allow for the interpretation of the thickness and extent of specific flows and the location of their source areas. The most extensive flows have widths from 2 to 3 kilometers (km) and lengths of at least 5–6 km. Lava flow thickness varies from 150 to 250 m above interpreted source vents to between 30 and 80 m in more distal locations. Rhyolite lavas have length-to-height ratios of 10:1 or greater and, in one instance, a length-to-width ratio of 2:1 or greater, implying a tongue-shaped geometry instead of circular domes or tabular bodies. Although geologic mapping did not identify any physical feature that could be positively identified as a vent, lava flow thickness and the size of clasts in subjacent pyroclastic deposits suggest that primary vent areas for at least some of the flows in the study area are on the east side of Fortymile Canyon, to the northeast of Yucca Mountain.

  18. Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding

    PubMed Central

    Fabbretti, Attilio; Schedlbauer, Andreas; Brandi, Letizia; Kaminishi, Tatsuya; Giuliodori, Anna Maria; Garofalo, Raffaella; Ochoa-Lizarralde, Borja; Takemoto, Chie; Yokoyama, Shigeyuki; Connell, Sean R.; Gualerzi, Claudio O.

    2016-01-01

    In prokaryotic systems, the initiation phase of protein synthesis is governed by the presence of initiation factors that guide the transition of the small ribosomal subunit (30S) from an unlocked preinitiation complex (30S preIC) to a locked initiation complex (30SIC) upon the formation of a correct codon–anticodon interaction in the peptidyl (P) site. Biochemical and structural characterization of GE81112, a translational inhibitor specific for the initiation phase, indicates that the main mechanism of action of this antibiotic is to prevent P-site decoding by stabilizing the anticodon stem loop of the initiator tRNA in a distorted conformation. This distortion stalls initiation in the unlocked 30S preIC state characterized by tighter IF3 binding and a reduced association rate for the 50S subunit. At the structural level we observe that in the presence of GE81112 the h44/h45/h24a interface, which is part of the IF3 binding site and forms ribosomal intersubunit bridges, preferentially adopts a disengaged conformation. Accordingly, the findings reveal that the dynamic equilibrium between the disengaged and engaged conformations of the h44/h45/h24a interface regulates the progression of protein synthesis, acting as a molecular switch that senses and couples the 30S P-site decoding step of translation initiation to the transition from an unlocked preIC to a locked 30SIC state. PMID:27071098

  19. Ligand binding reduces conformational flexibility in the active site of tyrosine phosphatase related to biofilm formation A (TpbA) from Pseudomonasaeruginosa.

    PubMed

    Koveal, Dorothy; Clarkson, Michael W; Wood, Thomas K; Page, Rebecca; Peti, Wolfgang

    2013-06-26

    Tyrosine phosphatase related to biofilm formation A (TpbA) is a periplasmic dual-specificity phosphatase (DUSP) that controls biofilm formation in the pathogenic bacterium Pseudomonas aeruginosa. While DUSPs are known to regulate important cellular functions in both prokaryotes and eukaryotes, very few structures of bacterial DUSPs are available. Here, we present the solution structure of TpbA in the ligand-free open conformation, along with an analysis of the structural and dynamic changes that accompany ligand/phosphate binding. While TpbA adopts a typical DUSP fold, it also possesses distinct structural features that distinguish it from eukaryotic DUSPs. These include additional secondary structural elements, β0 and α6, and unique conformations of the variable insert, the α4-α5 loop and helix α5 that impart TpbA with a flat active-site surface. In the absence of ligand, the protein tyrosine phosphatase loop is disordered and the general acid loop adopts an open conformation, placing the catalytic aspartate, Asp105, more than 11Å away from the active site. Furthermore, the loops surrounding the active site experience motions on multiple timescales, consistent with a combination of conformational heterogeneity and fast (picosecond to nanosecond) timescale dynamics, which are significantly reduced upon ligand binding. Taken together, these data structurally distinguish TpbA and possibly other bacterial DUSPs from eukaryotic DUSPs and provide a rich picture of active-site dynamics in the ligand-free state that are lost upon ligand binding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Rad54B Targeting to DNA Double-Strand Break Repair Sites Requires Complex Formation with S100A11

    PubMed Central

    Murzik, Ulrike; Hemmerich, Peter; Weidtkamp-Peters, Stefanie; Ulbricht, Tobias; Bussen, Wendy; Hentschel, Julia; von Eggeling, Ferdinand

    2008-01-01

    S100A11 is involved in a variety of intracellular activities such as growth regulation and differentiation. To gain more insight into the physiological role of endogenously expressed S100A11, we used a proteomic approach to detect and identify interacting proteins in vivo. Hereby, we were able to detect a specific interaction between S100A11 and Rad54B, which could be confirmed under in vivo conditions. Rad54B, a DNA-dependent ATPase, is described to be involved in recombinational repair of DNA damage, including DNA double-strand breaks (DSBs). Treatment with bleomycin, which induces DSBs, revealed an increase in the degree of colocalization between S100A11 and Rad54B. Furthermore, S100A11/Rad54B foci are spatially associated with sites of DNA DSB repair. Furthermore, while the expression of p21WAF1/CIP1 was increased in parallel with DNA damage, its protein level was drastically down-regulated in damaged cells after S100A11 knockdown. Down-regulation of S100A11 by RNA interference also abolished Rad54B targeting to DSBs. Additionally, S100A11 down-regulated HaCaT cells showed a restricted proliferation capacity and an increase of the apoptotic cell fraction. These observations suggest that S100A11 targets Rad54B to sites of DNA DSB repair sites and identify a novel function for S100A11 in p21-based regulation of cell cycle. PMID:18463164

  1. Biphasic β-TCP mixed with silicon increases bone formation in critical site defects in rabbit calvaria.

    PubMed

    Calvo-Guirado, José Luis; Garces, Miguel; Delgado-Ruiz, Rafael Arcesio; Ramirez Fernandez, Maria P; Ferres-Amat, Eduard; Romanos, Georgios E

    2015-08-01

    The aim of this study was to assess the bone regeneration of critical size defects in rabbit calvarias filled with β-TCP doped with silicon. Twenty-one New Zealand rabbits were used in this study. Two critical size defects were created in the parietal bones. Three experimental groups were evaluated: Test A (HA/β-TCP granules alone), Test B (HA/β-TCP granules plus 3% silicon), Control (empty defect). The animals were sacrificed at 8 and 12 weeks. Evaluation was performed by μCT analysis and histomorphometry. μCT evaluation showed higher volume reduction in Test A group compared with Test B (P < 0.05). The Test B group showed the highest values for cortical closure and bone formation around the particles, followed by Test A and controls (P < 0.05). Within the limitations of this animal study, it can be concluded that HA/β-TCP plus 3% silicon increases bone formation in critical size defects in rabbit calvarias, and the incorporation of 3% silicon reduces the resorption rate of the HA/β-TCP granules. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Heterogeneity-enhanced gas phase formation in shallow aquifers during leakage of CO2-saturated water from geologic sequestration sites

    NASA Astrophysics Data System (ADS)

    Plampin, Michael R.; Lassen, Rune N.; Sakaki, Toshihiro; Porter, Mark L.; Pawar, Rajesh J.; Jensen, Karsten H.; Illangasekare, Tissa H.

    2014-12-01

    A primary concern for geologic carbon storage is the potential for leakage of stored carbon dioxide (CO2) into the shallow subsurface where it could degrade the quality of groundwater and surface water. In order to predict and mitigate the potentially negative impacts of CO2 leakage, it is important to understand the physical processes that CO2 will undergo as it moves through naturally heterogeneous porous media formations. Previous studies have shown that heterogeneity can enhance the evolution of gas phase CO2 in some cases, but the conditions under which this occurs have not yet been quantitatively defined, nor tested through laboratory experiments. This study quantitatively investigates the effects of geologic heterogeneity on the process of gas phase CO2 evolution in shallow aquifers through an extensive set of experiments conducted in a column that was packed with layers of various test sands. Soil moisture sensors were utilized to observe the formation of gas phase near the porous media interfaces. Results indicate that the conditions under which heterogeneity controls gas phase evolution can be successfully predicted through analysis of simple parameters, including the dissolved CO2 concentration in the flowing water, the distance between the heterogeneity and the leakage location, and some fundamental properties of the porous media. Results also show that interfaces where a less permeable material overlies a more permeable material affect gas phase evolution more significantly than interfaces with the opposite layering.

  3. A dynamic flow simulation code benchmark study addressing the highly heterogeneous properties of the Stuttgart formation at the Ketzin pilot site

    NASA Astrophysics Data System (ADS)

    Kempka, Thomas; Class, Holger; Görke, Uwe-Jens; Norden, Ben; Kolditz, Olaf; Kühn, Michael; Walter, Lena; Wang, Wenqing; Zehner, Björn

    2013-04-01

    CO2 injection at the Ketzin pilot site located in Eastern Germany (Brandenburg) about 25 km west of Berlin is undertaken since June 2008 with a scheduled total amount of about 70,000 t CO2 to be injected into the saline aquifer represented by the Stuttgart Formation at a depth of 630 m to 650 m until the end of August 2013. The Stuttgart Formation is of fluvial origin determined by high-permeablity sandstone channels embedded in a floodplain facies of low permeability indicating a highly heterogeneous distribution of reservoir properties as facies distribution, porosity and permeability relevant for dynamic flow simulations. Following the dynamic modelling activities discussed by Kempka et al. (2010), a revised geological model allowed us to history match CO2 arrival times in the observation wells and reservoir pressure with a good agreement (Martens et al., 2012). Consequently, the validated reservoir model of the Stuttgart Formation at the Ketzin pilot site enabled us to predict the development of reservoir pressure and the CO2 plume migration in the storage formation by dynamic flow simulations. A benchmark study of industrial (ECLIPSE 100 as well as ECLIPSE 300 CO2STORE and GASWAT) and scientific dynamic flow simulations codes (TOUGH2-MP/ECO2N, OpenGeoSys and DuMuX) was initiated to address and compare the simulator capabilities considering a highly complex reservoir model. Hence, our dynamic flow simulations take into account different properties of the geological model such as significant variation of porosity and permeability in the Stuttgart Formation as well as structural geological features implemented in the geological model such as seven major faults located at the top of the Ketzin anticline. Integration of the geological model into reservoir models suitable for the different dynamic flow simulators applied demonstrated that a direct conversion of reservoir model discretization between Finite Volume and Finite Element flow simulators is not feasible

  4. Chimerism reveals a role for the streptokinase Beta -domain in nonproteolytic active site formation, substrate, and inhibitor interactions.

    PubMed

    Gladysheva, Inna P; Sazonova, Irina Y; Chowdhry, Shakeel A; Liu, Lin; Turner, Ryan B; Reed, Guy L

    2002-07-26

    Streptokinase (SK) and staphylokinase form cofactor-enzyme complexes that promote the degradation of fibrin thrombi by activating human plasminogen. The unique abilities of streptokinase to nonproteolytically activate plasminogen or to alter the interactions of plasmin with substrates and inhibitors may be the result of high affinity binding mediated by the streptokinase beta-domain. To examine this hypothesis, a chimeric streptokinase, SKbetaswap, was created by swapping the SK beta-domain with the homologous beta-domain of Streptococcus uberis Pg activator (SUPA or PauA, SK uberis), a streptokinase that cannot activate human plasminogen. SKbetaswap formed a tight complex with microplasminogen with an affinity comparable with streptokinase. The SKbetaswap-plasmin complex also activated human plasminogen with catalytic efficiencies (k(cat)/K(m) = 16.8 versus 15.2 microm(-1) min(-1)) comparable with streptokinase. However, SKbetaswap was incapable of nonproteolytic active site generation and activated plasminogen by a staphylokinase mechanism. When compared with streptokinase complexes, SKbetaswap-plasmin and SKbetaswap-microplasmin complexes had altered affinities for low molecular weight substrates. The SKbetaswap-plasmin complex also was less resistant than the streptokinase-plasmin complex to inhibition by alpha(2)-antiplasmin and was readily inhibited by soybean trypsin inhibitor. Thus, in addition to mediating high affinity binding to plasmin(ogen), the streptokinase beta-domain is required for nonproteolytic active site generation and specifically modulates the interactions of the complex with substrates and inhibitors.

  5. A Threonine on the Active Site Loop Controls Transition State Formation in Escherichia Coli Respiratory Complex II

    SciTech Connect

    Tomasiak, T.M.; Maklashina, E.; Cecchini, G.; Iverson, T.M.

    2009-05-26

    In Escherichia coli, the complex II superfamily members succinate:ubiquinone oxidoreductase (SQR) and quinol:fumarate reductase (QFR) participate in aerobic and anaerobic respiration, respectively. Complex II enzymes catalyze succinate and fumarate interconversion at the interface of two domains of the soluble flavoprotein subunit, the FAD binding domain and the capping domain. An 11-amino acid loop in the capping domain (Thr-A234 to Thr-A244 in quinol:fumarate reductase) begins at the interdomain hinge and covers the active site. Amino acids of this loop interact with both the substrate and a proton shuttle, potentially coordinating substrate binding and the proton shuttle protonation state. To assess the loop's role in catalysis, two threonine residues were mutated to alanine: QFR Thr-A244 (act-T; Thr-A254 in SQR), which hydrogen-bonds to the substrate at the active site, and QFR Thr-A234 (hinge-T; Thr-A244 in SQR), which is located at the hinge and hydrogen-bonds the proton shuttle. Both mutations impair catalysis and decrease substrate binding. The crystal structure of the hinge-T mutation reveals a reorientation between the FAD-binding and capping domains that accompanies proton shuttle alteration. Taken together, hydrogen bonding from act-T to substrate may coordinate with interdomain motions to twist the double bond of fumarate and introduce the strain important for attaining the transition state.

  6. Observation of aerosol number size distribution and new particle formation at a mountainous site in Southeast China.

    PubMed

    Zhang, Xiaoru; Yin, Yan; Lin, Zhenyi; Han, Yongxiang; Hao, Jian; Yuan, Liang; Chen, Kui; Chen, Jinghua; Kong, Shaofei; Shan, Yunpeng; Xiao, Hui; Tan, Wen

    2017-01-01

    To quantify the physical/chemical properties, and the formation and growth processes of aerosol particles on mountainous regions in Southeast China, an intensive field campaign was conducted from April to July 2008 on the top of Mt. Huang (1840m above mean sea level). The average particle number concentration was 2.35×10(3)cm(-3), and the ultrafine particles (<0.1μm) represented 70.5% of the total particle number concentration. Excluding the accumulation mode particles, the average daytime particle number concentrations were prominently higher than those measured at nighttime, suggesting there was a diurnal pattern of changes between planetary boundary layer and free troposphere air. The aerosol spectra were classified into two categories: the first category (FCS) exhibited a clear diurnal cycle, with relatively higher number concentration (3.19×10(3)cm(-3)), smaller sizes and air masses from the inland; the second category (SCS) presented less obvious diurnal cycle, with lower number concentration (1.88×10(3)cm(-3)), larger sizes and air masses from coastal regions. Air mass sources, weather conditions, and new particle formation (NPF) events were responsible for the differences of these two particle spectra. Six NPF events were identified, which usually began at 10:00-11:00 LT, with the estimated formation rate J10 in the range of 0.09-0.30cm(-3)s(-1) and the growth rate at 1.42-4.53nmh(-1). Wind speed, sulfur dioxide and ozone concentrations were higher on NPF days than those on non-NPF days, whereas temperature, relative humidity, concentrations of nitrogen oxide and carbonic oxide were lower on NPF days. Sulfur dioxide and ozone might be main potentially precursor gases for those NPF events. The NPF events at Mt. Huang corresponded closely to a southwest winds. These results are useful for improving our understanding of the main factors controlling the variation of aerosol size distribution and NPF events in this region. Copyright © 2016 Elsevier B.V. All

  7. Site specific isolated nanostructure array formation on a large area by broad ion beam without any mask and resist

    SciTech Connect

    Karmakar, Prasanta

    2014-06-09

    We report the formation of isolated nanostructure arrays on a large area via broad ion beam implantation without the aid of any mask or resist. Desired ions have been implanted at specific locations of the prefabricated silicon ripple or triangular structures by exploiting the variation of local ion impact angles. We have shown that the implantation of Fe ions on an O{sup +} ions induced pre fabricated triangular shaped patterned Si surface results in a self-organized periodic array of striped magnetic nanostructures having several micron length and about 50 nm width arranged with a spacial separation of ∼200 nm. The morphology, composition, crystalline structure, and magnetic property of these nanopatterns have been analyzed using high-resolution cross-sectional transmission electron microscopy and atomic force microscopy. A geometrical model has been proposed to explain the fundamental features of such ion-induced nanopattern structures.

  8. The Lindi Formation (upper Albian-Coniacian) and Tanzania Drilling Project Sites 36-40 (Lower Cretaceous to Paleogene): Lithostratigraphy, biostratigraphy and chemostratigraphy

    NASA Astrophysics Data System (ADS)

    Jiménez Berrocoso, Álvaro; Huber, Brian T.; MacLeod, Kenneth G.; Petrizzo, Maria Rose; Lees, Jacqueline A.; Wendler, Ines; Coxall, Helen; Mweneinda, Amina K.; Falzoni, Francesca; Birch, Heather; Haynes, Shannon J.; Bown, Paul R.; Robinson, Stuart A.; Singano, Joyce M.

    2015-01-01

    The 2009 Tanzania Drilling Project (TDP) expedition to southeastern Tanzania cored a total of 572.3 m of sediments at six new mid-Cretaceous to mid-Paleocene boreholes (TDP Sites 36, 37, 38, 39, 40A, 40B). Added to the sites drilled in 2007 and 2008, the new boreholes confirm the common excellent preservation of planktonic and benthic foraminifera and calcareous nannofossils from core samples that will be used for biostratigraphy, evolutionary studies, paleoceanography and climatic reconstructions from the Tanzanian margin, with implications elsewhere. The new sites verify the presence of a relatively expanded Upper Cretaceous succession in the region that has allowed a new stratigraphic unit, named here as the Lindi Formation (Fm), to be formally defined. The Lindi Fm (upper Albian to Coniacian), extending ∼120 km between Kilwa and Lindi, comprises a 335-m-thick, outer-shelf to upper-slope unit, consisting of dark gray claystone and siltstone interbeds, common finely-laminated intervals, minor cm-thick sandstones and up to 2.6% organic carbon in the Turonian. A subsurface, composite stratotype section is proposed for the Lindi Fm, with a gradational top boundary with the overlying Nangurukuru Fm (Santonian to Maastrichtian) and a sharp bottom contact with underlying upper Albian sandstones. The section cored at TDP Sites 36 and 38 belongs to the Lindi Fm and are of lower to middle Turonian age (planktonic foraminifera Whiteinella archaeocretacea to Helvetoglobotruncana helvetica Zones and nannofossils subzones UC6b ± UC7). The lower portion of TDP Site 39 (uppermost part of the Lindi Fm) is assigned to the lower to upper Coniacian (planktonic foraminifera Dicarinella concavata Zone and nannofossils zone UC 10), while the remaining part of this site is attributed to the Coniacian-Santonian transition and younger Santonian (planktonic foraminifera D. asymetrica Zone and upper part of nannofossils zone UC10). TDP Site 37 recovered relatively expanded (150 m thick

  9. Site-specific effect of thymine dimer formation of dA sub n ter dot dT sub n tract bending and its biological implications

    SciTech Connect

    Wang, C.I.; Taylor, J.S. )

    1991-10-15

    dA{sub n}{center dot}dT{sub n} sequences, otherwise known as A tracts, are hotspots for cis-syn thymine dimer formation and deletion mutations induced by UV light. Such A tracts are also known to bend DNA, suggesting that some biological effects of UV light might be related to the distinctive structure and properties of cis-syn dimer-containing A tracts. To investigate the effect of thymine dimer formation on A-tract bending multimers of all possible dimer monoadducts of a dA{sub 6}{center dot}dT{sub 6}-containing decamer known to bend DNA were prepared along with multimers of a dimer-containing 21-mer of heterogeneous sequence. The characteristic anomalous electrophoretic behavior of the phased A-tract multimers was essentially abolished by dimer formation at the center of the A tract and was only slightly reduced by dimer formation at the ends. These effects are attributed to disruption of the A-tract structure at the site of the dimer, resulting in intact A tracts of reduced length and, hence, reduced bending. This model was suggested by the ability to formulate the estimated bend angles of the dimer-containing A tracts as approximately equal to the sum of the bend angels induced by the dimer and the remaining intact portion of the A tract. Contrary to a previous experimental study that concluded that the thymine dimer bends DNA by {approx} 30{degree}, the dimer was determined to bend DNA by only {approx} 7{degree}. Reduction of the bending of a DNA sequence by dimer formation may have a number of unpredicted and important biological consequences.

  10. Site-directed mutagenesis reveals regions implicated in the stability and fiber formation of human λ3r light chains.

    PubMed

    Villalba, Miryam I; Canul-Tec, Juan C; Luna-Martínez, Oscar D; Sánchez-Alcalá, Rosalba; Olamendi-Portugal, Timoteo; Rudiño-Piñera, Enrique; Rojas, Sonia; Sánchez-López, Rosana; Fernández-Velasco, Daniel A; Becerril, Baltazar

    2015-01-30

    Light chain amyloidosis (AL) is a disease that affects vital organs by the fibrillar aggregation of monoclonal light chains. λ3r germ line is significantly implicated in this disease. In this work, we contrasted the thermodynamic stability and aggregation propensity of 3mJL2 (nonamyloidogenic) and 3rJL2 (amyloidogenic) λ3 germ lines. Because of an inherent limitation (extremely low expression), Cys at position 34 of the 3r germ line was replaced by Tyr reaching a good expression yield. A second substitution (W91A) was introduced in 3r to obtain a better template to incorporate additional mutations. Although the single mutant (C34Y) was not fibrillogenic, the second mutation located at CDR3 (W91A) induced fibrillogenesis. We propose, for the first time, that CDR3 (position 91) affects the stability and fiber formation of human λ3r light chains. Using the double mutant (3rJL2/YA) as template, other variants were constructed to evaluate the importance of those substitutions into the stability and aggregation propensity of λ3 light chains. A change in position 7 (P7D) boosted 3rJL2/YA fibrillogenic properties. Modification of position 48 (I48M) partially reverted 3rJL2/YA fibril aggregation. Finally, changes at positions 8 (P8S) or 40 (P40S) completely reverted fibril formation. These results confirm the influential roles of N-terminal region (positions 7 and 8) and the loop 40-60 (positions 40 and 48) on AL. X-ray crystallography revealed that the three-dimensional topology of the single and double λ3r mutants was not significantly altered. This mutagenic approach helped to identify key regions implicated in λ3 AL.

  11. Site-directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human λ3r Light Chains*

    PubMed Central

    Villalba, Miryam I.; Canul-Tec, Juan C.; Luna-Martínez, Oscar D.; Sánchez-Alcalá, Rosalba; Olamendi-Portugal, Timoteo; Rudiño-Piñera, Enrique; Rojas, Sonia; Sánchez-López, Rosana; Fernández-Velasco, Daniel A.; Becerril, Baltazar

    2015-01-01

    Light chain amyloidosis (AL) is a disease that affects vital organs by the fibrillar aggregation of monoclonal light chains. λ3r germ line is significantly implicated in this disease. In this work, we contrasted the thermodynamic stability and aggregation propensity of 3mJL2 (nonamyloidogenic) and 3rJL2 (amyloidogenic) λ3 germ lines. Because of an inherent limitation (extremely low expression), Cys at position 34 of the 3r germ line was replaced by Tyr reaching a good expression yield. A second substitution (W91A) was introduced in 3r to obtain a better template to incorporate additional mutations. Although the single mutant (C34Y) was not fibrillogenic, the second mutation located at CDR3 (W91A) induced fibrillogenesis. We propose, for the first time, that CDR3 (position 91) affects the stability and fiber formation of human λ3r light chains. Using the double mutant (3rJL2/YA) as template, other variants were constructed to evaluate the importance of those substitutions into the stability and aggregation propensity of λ3 light chains. A change in position 7 (P7D) boosted 3rJL2/YA fibrillogenic properties. Modification of position 48 (I48M) partially reverted 3rJL2/YA fibril aggregation. Finally, changes at positions 8 (P8S) or 40 (P40S) completely reverted fibril formation. These results confirm the influential roles of N-terminal region (positions 7 and 8) and the loop 40–60 (positions 40 and 48) on AL. X-ray crystallography revealed that the three-dimensional topology of the single and double λ3r mutants was not significantly altered. This mutagenic approach helped to identify key regions implicated in λ3 AL. PMID:25505244

  12. Site-directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human λ3r Light Chains

    SciTech Connect

    Villalba, Miryam I.; Canul-Tec, Juan C.; Luna-Martínez, Oscar D.; Sánchez-Alcalá, Rosalba; Olamendi-Portugal, Timoteo; Rudiño-Piñera, Enrique; Rojas, Sonia; Sánchez-López, Rosana; Fernández-Velasco, Daniel A.; Becerril, Baltazar

    2014-12-11

    Light chain amyloidosis (AL) is a disease that affects vital organs by the fibrillar aggregation of monoclonal light chains. λ3r germ line is significantly implicated in this disease. In this paper, we contrasted the thermodynamic stability and aggregation propensity of 3mJL2 (nonamyloidogenic) and 3rJL2 (amyloidogenic) λ3 germ lines. Because of an inherent limitation (extremely low expression), Cys at position 34 of the 3r germ line was replaced by Tyr reaching a good expression yield. A second substitution (W91A) was introduced in 3r to obtain a better template to incorporate additional mutations. Although the single mutant (C34Y) was not fibrillogenic, the second mutation located at CDR3 (W91A) induced fibrillogenesis. We propose, for the first time, that CDR3 (position 91) affects the stability and fiber formation of human λ3r light chains. Using the double mutant (3rJL2/YA) as template, other variants were constructed to evaluate the importance of those substitutions into the stability and aggregation propensity of λ3 light chains. A change in position 7 (P7D) boosted 3rJL2/YA fibrillogenic properties. Modification of position 48 (I48M) partially reverted 3rJL2/YA fibril aggregation. Finally, changes at positions 8 (P8S) or 40 (P40S) completely reverted fibril formation. These results confirm the influential roles of N-terminal region (positions 7 and 8) and the loop 40–60 (positions 40 and 48) on AL. X-ray crystallography revealed that the three-dimensional topology of the single and double λ3r mutants was not significantly altered. Finally, this mutagenic approach helped to identify key regions implicated in λ3 AL.

  13. Site-directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human λ3r Light Chains

    DOE PAGES

    Villalba, Miryam I.; Canul-Tec, Juan C.; Luna-Martínez, Oscar D.; ...

    2014-12-11

    Light chain amyloidosis (AL) is a disease that affects vital organs by the fibrillar aggregation of monoclonal light chains. λ3r germ line is significantly implicated in this disease. In this paper, we contrasted the thermodynamic stability and aggregation propensity of 3mJL2 (nonamyloidogenic) and 3rJL2 (amyloidogenic) λ3 germ lines. Because of an inherent limitation (extremely low expression), Cys at position 34 of the 3r germ line was replaced by Tyr reaching a good expression yield. A second substitution (W91A) was introduced in 3r to obtain a better template to incorporate additional mutations. Although the single mutant (C34Y) was not fibrillogenic, themore » second mutation located at CDR3 (W91A) induced fibrillogenesis. We propose, for the first time, that CDR3 (position 91) affects the stability and fiber formation of human λ3r light chains. Using the double mutant (3rJL2/YA) as template, other variants were constructed to evaluate the importance of those substitutions into the stability and aggregation propensity of λ3 light chains. A change in position 7 (P7D) boosted 3rJL2/YA fibrillogenic properties. Modification of position 48 (I48M) partially reverted 3rJL2/YA fibril aggregation. Finally, changes at positions 8 (P8S) or 40 (P40S) completely reverted fibril formation. These results confirm the influential roles of N-terminal region (positions 7 and 8) and the loop 40–60 (positions 40 and 48) on AL. X-ray crystallography revealed that the three-dimensional topology of the single and double λ3r mutants was not significantly altered. Finally, this mutagenic approach helped to identify key regions implicated in λ3 AL.« less

  14. Surface and subsurface features of the upper Pleistocene Beaumont Formation as studied in a proposed super collider site in Liberty and Hardin counties, southeastern Texas

    SciTech Connect

    Aronow, S.

    1994-12-31

    In 1987 an area in Hardin and Libery Counties in southeastern Texas was a much-studied candidate site for the ill-fated Superconducting Super Collider. The site is on the outcrop of the upper Pleistocene Beaumont Formation, which locally was deposited by a sequence of meandering, avulsing, suspended-load, paleo-Trinity River courses, now preserved as a well-defined to poorly defined depositional topography. Test holes in meanderbelt ridges showed that channel and point-bar silty fine to very fine sands are almost everywhere covered by approximately 10 to 40 ft ({approximately}3 to 12 m) of CH and CL overbank clays. Where completely penetrated, sand bodies are approximately 20 to 50 ft ({approximately}6 to 15 m) thick. Pedogenic calcareous deposits and slickensides at depths well below any influence from present-day surface processes are probably parts of lower horizons of truncated now-buried soils generated during the accumulation of the Beaumont, or on the surface of the underlying Lissie Formation. The relationship of one of the paleo-meanderbelts to the uplifted topographic surface of the Hull salt dome suggests that the rise of the surface postdated deposition of the Beaumont.

  15. Analysis of Dose at the Site of Second Tumor Formation After Radiotherapy to the Central Nervous System

    SciTech Connect

    Galloway, Thomas J.; Indelicato, Daniel J.; Amdur, Robert J.; Morris, Christopher G.; Swanson, Erika L.; Marcus, Robert B.

    2012-01-01

    Purpose: Second tumors are an uncommon complication of multimodality treatment of childhood cancer. The present analysis attempted to correlate the dose received as a component of primary treatment and the site of the eventual development of a second tumor. Methods and Materials: We retrospectively identified 16 patients who had received radiotherapy to sites in the craniospinal axis and subsequently developed a second tumor. We compared the historical fields and port films of the primary treatment with the modern imaging of the second tumor locations. We classified the location of the second tumors as follows: in the boost field; marginal to the boost field, but in a whole-brain field; in a whole-brain field; marginal to the whole brain/primary treatment field; and distant to the field. We divided the dose received into 3 broad categories: high dose (>45 Gy), moderate dose (20-36 Gy), and low dose (<20 Gy). Results: The most common location of the second tumor was in the whole brain field (57%) and in the moderate-dose range (81%). Conclusions: Our data contradict previous publications that suggested that most second tumors develop in tissues that receive a low radiation dose. Almost all the second tumors in our series occurred in tissue within a target volume in the cranium that had received a moderate dose (20-36 Gy). These findings suggest that a major decrease in the brain volume that receives a moderate radiation dose is the only way to substantially decrease the second tumor rate after central nervous system radiotherapy.

  16. Site Formation Processes and Hunter-Gatherers Use of Space in a Tropical Environment: A Geo-Ethnoarchaeological Approach from South India.

    PubMed

    Friesem, David E; Lavi, Noa; Madella, Marco; Ajithprasad, P; French, Charles

    2016-01-01

    Hunter-gatherer societies have distinct social perceptions and practices which are expressed in unique use of space and material deposition patterns. However, the identification of archaeological evidence associated with hunter-gatherer activity is often challenging, especially in tropical environments such as rainforests. We present an integrated study combining ethnoarchaeology and geoarchaeology in order to study archaeological site formation processes related to hunter-gatherers' ways of living in tropical forests. Ethnographic data was collected from an habitation site of contemporary hunter-gatherers in the forests of South India, aimed at studying how everyday activities and way of living dictate patterns of material deposition. Ethnoarchaeological excavations of abandoned open-air sites and a rock-shelter of the same group located deep in the forests, involved field observations and sampling of sediments from the abandoned sites and the contemporary site. Laboratory analyses included geochemical analysis (i.e., FTIR, ICP-AES), phytolith concentration analysis and soil micromorphology. The results present a dynamic spatial deposition pattern of macroscopic, microscopic and chemical materials, which stem from the distinctive ways of living and use of space by hunter-gatherers. This study shows that post-depositional processes in tropical forests result in poor preservation of archaeological materials due to acidic conditions and intensive biological activity within the sediments. Yet, the multiple laboratory-based analyses were able to trace evidence for activity surfaces and their maintenance practices as well as localized concentrations of activity remains such as the use of plants, metals, hearths and construction materials.

  17. Site Formation Processes and Hunter-Gatherers Use of Space in a Tropical Environment: A Geo-Ethnoarchaeological Approach from South India

    PubMed Central

    Friesem, David E.; Lavi, Noa; Madella, Marco; Ajithprasad, P.; French, Charles

    2016-01-01

    Hunter-gatherer societies have distinct social perceptions and practices which are expressed in unique use of space and material deposition patterns. However, the identification of archaeological evidence associated with hunter-gatherer activity is often challenging, especially in tropical environments such as rainforests. We present an integrated study combining ethnoarchaeology and geoarchaeology in order to study archaeological site formation processes related to hunter-gatherers’ ways of living in tropical forests. Ethnographic data was collected from an habitation site of contemporary hunter-gatherers in the forests of South India, aimed at studying how everyday activities and way of living dictate patterns of material deposition. Ethnoarchaeological excavations of abandoned open-air sites and a rock-shelter of the same group located deep in the forests, involved field observations and sampling of sediments from the abandoned sites and the contemporary site. Laboratory analyses included geochemical analysis (i.e., FTIR, ICP-AES), phytolith concentration analysis and soil micromorphology. The results present a dynamic spatial deposition pattern of macroscopic, microscopic and chemical materials, which stem from the distinctive ways of living and use of space by hunter-gatherers. This study shows that post-depositional processes in tropical forests result in poor preservation of archaeological materials due to acidic conditions and intensive biological activity within the sediments. Yet, the multiple laboratory-based analyses were able to trace evidence for activity surfaces and their maintenance practices as well as localized concentrations of activity remains such as the use of plants, metals, hearths and construction materials. PMID:27783683

  18. Comparison of particle number size distributions and new particle formation between the urban and rural sites in the PRD region, China

    NASA Astrophysics Data System (ADS)

    Yue, D. L.; Hu, M.; Wang, Z. B.; Wen, M. T.; Guo, S.; Zhong, L. J.; Wiedensohler, A.; Zhang, Y. H.

    2013-09-01

    Particle number size distributions were simultaneously measured at the Guangzhou (GZ) urban site (23.13°N, 113.26°E) and the Back-garden (BG) rural site (23.5°N, 113.03°E) in the Pearl River Delta (PRD) region in July, 2006. It provided new findings into the evolution of particle number size distribution and new particle formation (NPF) in two different environments. Number concentration of particles (20 nm-10 μm diameter) at GZ was about 70% higher than at BG and significantly affected by traffic emission. However, number concentrations of the regional aerosols (100-660 nm) were (6 ± 3) × 103 cm-3 at both sites. At BG, the diurnal variation of particle number size distributions showed an obvious particle growth process beginning at about 9:00 (LT), probably caused by NPF. In contrast, particle number concentrations in the size rages of 20-45 nm, 45-100 nm, and 100-660 nm showed similar trends with two main peaks at about 12:00 (LT) and 19:00 (LT) at GZ. NPF events were observed at both sites, but the occurrence frequency at GZ was about 50% lower than at BG. Regional NPF events at both sites probably in the same air mass were simultaneously observed with similar growth rates, concentrations and production rates of the condensable vapors, and condensational sinks on July 6. On the whole, deceasing traffic emission will improve air quality efficiently in the aspect of particle number concentration and fine particulate pollution in the summer of PRD should be controlled in a regional scale, especially with stagnant air mass from South China Sea.

  19. Tianeptine: 5-HT uptake sites and 5-HT(1-7) receptors modulate memory formation in an autoshaping Pavlovian/instrumental task.

    PubMed

    Meneses, Alfredo

    2002-05-01

    Recent studies using invertebrate and mammal species have revealed that, endogenous serotonin (5-hydroxytryptamine, 5-HT) modulates cognitive processes, particularly learning and memory, though, at present, it is unclear the manner, where, and how long 5-HT systems are involved. Hence in this work, an attempt was made to study the effects of 5-HT endogenous on memory formation, using a 5-HT uptake facilitator (tianeptine) and, selective 5-HT(1-7) receptor antagonists to determine whether 5-HT uptake sites and which 5-HT receptors are involved, respectively. Results showed that post-training tianeptine injection enhanced memory consolidation in an autoshaping Pavlovian/instrumental learning task, which has been useful to detect changes on memory formation elicited by drugs or aging. On interaction experiments, ketanserin (5-HT(1D/2A/2C) antagonist) slightly enhanced tianeptine effects, while WAY 100635 (5-HT(1A) antagonist), SB-224289 (5-HT(1B) inverse agonist), SB-200646 (5-HT(2B/2C) antagonist), ondansetron (5-HT(3) antagonist), GR 127487 (5-HT(4) antagonist), Ro 04-6790 (5-HT(6) antagonist), DR 4004 (5-HT(7) antagonist), or fluoxetine (an inhibitor of 5-HT reuptake) blocked the facilitatory tianeptine effect. Notably, together tianeptine and Ro 04-6790 impaired learning consolidation. Moreover, 5-HT depletion completely reversed the tianeptine effect. Tianeptine also normalized an impaired memory elicited by scopolamine (an antimuscarinic) or dizocilpine (non-competitive glutamatergic antagonist), while partially reversed that induced by TFMPP (5-HT(1B/1D/2A-2C/7) agonist/antagonist). Finally, tianeptine-fluoxetine coadministration had no effect on learning consolidation; nevertheless, administration of an acetylcholinesterase inhibitor, phenserine, potentiated subeffective tianeptine or fluoxetine doses. Collectively, these data confirmed that endogenously 5-HT modulates, via uptake sites and 5-HT(1-7) receptors, memory consolidation, and are consistent with the

  20. Dislocation pile-ups as sites for formation of electromigration-induced transgranular slit-like voids in Al interconnects

    SciTech Connect

    Srikar, V.T.; Thompson, C.V.

    1999-12-17

    Electromigration-induced voiding in metal interconnects in Si integrated circuits is a serious reliability concern. The microstructure of narrow interconnects subject to post-pattern anneal is expected to be bamboo-like in character. These structures are best described as chains of single crystals, with grain boundaries perpendicular to the interconnect axis. In these microstructures, two distinct types of void morphologies have been reported in Al-alloy interconnects: large, wedge shaped erosion voids (E-voids), and narrow slit-like voids (S-voids). A summarized below, electromigration experiments conducted on single-crystal Al interconnects have clearly shown that the transition of erosion voids to slit-like voids is very strongly dependent on the crystallography of the interconnect, and also that there is some inhomogeneously distributed feature which triggers S-void formation, even in single-crystal interconnects. In summary, the authors feel that the strong crystallographic dependence of the S-voids, the possible effects of the enormous mechanical stresses (in excess of 1 GPa in some cases) which can exist in such interconnects, and the stochastic nature of the development of slit-like features, have not been adequately captured in the existing models. In what follows, the authors present a model for a role that dislocation pile-ups may play in reducing the energy of transition of E-voids to S-voids, and for controlling the location of this transition.

  1. Effects of CO2 on mechanical variability and constitutive behavior of the Lower Tuscaloosa formation, Cranfield Injection Site, USA

    DOE PAGES

    Rinehart, Alex J.; Dewers, Thomas A.; Broome, Scott T.; ...

    2016-08-25

    We characterize geomechanical constitutive behavior of reservoir sandstones at conditions simulating the “Cranfield” Southeast Regional Carbon Sequestration Partnership injection program. From two cores of Lower Tuscaloosa Formation, three sandstone lithofacies were identified for mechanical testing based on permeability and lithology. These include: chlorite-cemented conglomeratic sandstone (Facies A); quartz-cemented fine sandstone (Facies B); and quartz- and calcite-cemented very fine sandstone (Facies C). We performed a suite of compression tests for each lithofacies at 100 °C and pore pressure of 30 MPa, including hydrostatic compression and triaxial tests at several confining pressures. Plugs were saturated with supercritical CO2-saturated brine. Chemical environment affectedmore » the mechanical response of all three lithofacies, which experience initial plastic yielding at stresses far below estimated in situ stress. Measured elastic moduli degradation defines a secondary yield surface coinciding with in situ stress for Facies B and C. Facies A shows measurable volumetric creep strain and a failure envelope below estimates of in situ stress, linked to damage of chlorite cements by acidic pore solutions. Furthermore, the substantial weakening of a particular lithofacies by CO2 demonstrates a possible chemical-mechanical coupling during injection at Cranfield with implications for CO2 injection, reservoir permeability stimulation, and enhanced oil recovery.« less

  2. Effects of CO2 on mechanical variability and constitutive behavior of the Lower Tuscaloosa formation, Cranfield Injection Site, USA

    DOE PAGES

    Rinehart, Alex J.; Dewers, Thomas A.; Broome, Scott T.; ...

    2016-08-25

    We characterize geomechanical constitutive behavior of reservoir sandstones at conditions simulating the “Cranfield” Southeast Regional Carbon Sequestration Partnership injection program. From two cores of Lower Tuscaloosa Formation, three sandstone lithofacies were identified for mechanical testing based on permeability and lithology. These include: chlorite-cemented conglomeratic sandstone (Facies A); quartz-cemented fine sandstone (Facies B); and quartz- and calcite-cemented very fine sandstone (Facies C). We performed a suite of compression tests for each lithofacies at 100 °C and pore pressure of 30 MPa, including hydrostatic compression and triaxial tests at several confining pressures. Plugs were saturated with supercritical CO2-saturated brine. Chemical environment affectedmore » the mechanical response of all three lithofacies, which experience initial plastic yielding at stresses far below estimated in situ stress. Measured elastic moduli degradation defines a secondary yield surface coinciding with in situ stress for Facies B and C. Facies A shows measurable volumetric creep strain and a failure envelope below estimates of in situ stress, linked to damage of chlorite cements by acidic pore solutions. Furthermore, the substantial weakening of a particular lithofacies by CO2 demonstrates a possible chemical-mechanical coupling during injection at Cranfield with implications for CO2 injection, reservoir permeability stimulation, and enhanced oil recovery.« less

  3. Formation and Persistence of Brine on Mars: Experimental Simulations throughout the Diurnal Cycle at the Phoenix Landing Site

    NASA Astrophysics Data System (ADS)

    Fischer, E.; Martínez, G. M.; Rennó, N. O.

    2016-12-01

    In the last few years, water ice and salts capable of melting this ice and producing liquid saline water (brine) have been detected on Mars. Moreover, indirect evidence for brine has been found in multiple areas of the planet. Here, we simulate full diurnal cycles of temperature and atmospheric water vapor content at the Phoenix landing site for the first time and show experimentally that, in spite of the low Mars-like chamber temperature, brine forms minutes after the ground temperature exceeds the eutectic temperature of salts in contact with water ice. Moreover, we show that the brine stays liquid for most of the diurnal cycle when enough water ice is available to compensate for evaporation. This is predicted to occur seasonally in areas of the polar region where the temperature exceeds the eutectic value and frost or snow is deposited on saline soils, or where water ice and salts coexist in the shallow subsurface. This is important because the existence of liquid water is a key requirement for habitability.

  4. Formation and Persistence of Brine on Mars: Experimental Simulations throughout the Diurnal Cycle at the Phoenix Landing Site.

    PubMed

    Fischer, E; Martínez, G M; Rennó, N O

    2016-12-01

    In the last few years, water ice and salts capable of melting this ice and producing liquid saline water (brine) have been detected on Mars. Moreover, indirect evidence for brine has been found in multiple areas of the planet. Here, we simulate full diurnal cycles of temperature and atmospheric water vapor content at the Phoenix landing site for the first time and show experimentally that, in spite of the low Mars-like chamber temperature, brine forms minutes after the ground temperature exceeds the eutectic temperature of salts in contact with water ice. Moreover, we show that the brine stays liquid for most of the diurnal cycle when enough water ice is available to compensate for evaporation. This is predicted to occur seasonally in areas of the polar region where the temperature exceeds the eutectic value and frost or snow is deposited on saline soils, or where water ice and salts coexist in the shallow subsurface. This is important because the existence of liquid water is a key requirement for habitability. Key Words: Mars-Ice-Perchlorates-Brine-Water-Raman spectroscopy. Astrobiology 16, 937-948.

  5. Formation and Persistence of Brine on Mars: Experimental Simulations throughout the Diurnal Cycle at the Phoenix Landing Site

    PubMed Central

    Martínez, G.M.; Rennó, N.O.

    2016-01-01

    Abstract In the last few years, water ice and salts capable of melting this ice and producing liquid saline water (brine) have been detected on Mars. Moreover, indirect evidence for brine has been found in multiple areas of the planet. Here, we simulate full diurnal cycles of temperature and atmospheric water vapor content at the Phoenix landing site for the first time and show experimentally that, in spite of the low Mars-like chamber temperature, brine forms minutes after the ground temperature exceeds the eutectic temperature of salts in contact with water ice. Moreover, we show that the brine stays liquid for most of the diurnal cycle when enough water ice is available to compensate for evaporation. This is predicted to occur seasonally in areas of the polar region where the temperature exceeds the eutectic value and frost or snow is deposited on saline soils, or where water ice and salts coexist in the shallow subsurface. This is important because the existence of liquid water is a key requirement for habitability. Key Words: Mars—Ice—Perchlorates—Brine—Water—Raman spectroscopy. Astrobiology 16, 937–948. PMID:27912028

  6. Site-1 protease-activated formation of lysosomal targeting motifs is independent of the lipogenic transcription control[S

    PubMed Central

    Klünder, Sarah; Heeren, Jörg; Markmann, Sandra; Santer, René; Braulke, Thomas; Pohl, Sandra

    2015-01-01

    Site-1 protease (S1P) cleaves membrane-bound lipogenic sterol regulatory element-binding proteins (SREBPs) and the α/β-subunit precursor protein of the N-acetylglucosamine-1-phosphotransferase forming mannose 6-phosphate (M6P) targeting markers on lysosomal enzymes. The translocation of SREBPs from the endoplasmic reticulum (ER) to the Golgi-resident S1P depends on the intracellular sterol content, but it is unknown whether the ER exit of the α/β-subunit precursor is regulated. Here, we investigated the effect of cholesterol depletion (atorvastatin treatment) and elevation (LDL overload) on ER-Golgi transport, S1P-mediated cleavage of the α/β-subunit precursor, and the subsequent targeting of lysosomal enzymes along the biosynthetic and endocytic pathway to lysosomes. The data showed that the proteolytic cleavage of the α/β-subunit precursor into mature and enzymatically active subunits does not depend on the cholesterol content. In either treatment, lysosomal enzymes are normally decorated with M6P residues, allowing the proper sorting to lysosomes. In addition, we found that, in fibroblasts of mucolipidosis type II mice and Niemann-Pick type C patients characterized by aberrant cholesterol accumulation, the proteolytic cleavage of the α/β-subunit precursor was not impaired. We conclude that S1P substrate-dependent regulatory mechanisms for lipid synthesis and biogenesis of lysosomes are different. PMID:26108224

  7. The effect of animal health products on the formation of injection site lesions in subprimals of experimentally injected beef calves.

    PubMed Central

    Van Donkersgoed, J; Dubeski, P L; VanderKop, M; Aalhus, J L; Bygrove, S; Starr, W N

    2000-01-01

    Two hundred and twenty beef calves were used in an experimental study to determine the occurrence of injection site lesions at slaughter (15 to 18 months of age) following subcutaneous and intramuscular injection of various products into the top hip (top butt), thigh (round), and neck or rib of calves at birth, branding, or weaning. Products tested were: 2 different preparations of selenium; a 2-way, a 7-way, and an 8-way clostridial bacterin; 2 combination 7-way clostridial and Haemophilus somnus bacterins; 2 H. somnus bacterins; 2 different 4-way modified-live viral respiratory vaccines; a 4-way killed viral and H. somnus vaccine; and penicillin, florfenicol, ceftiofur, trimethoprim-sulfa, and tilmicosin. The occurrence of lesions, number of steaks affected with lesions, the trim weight of lesions, the histological class of lesions, and the estimated economic losses are described. Generally, products administered subcutaneously in the neck produced minimal tissue damage and economic losses. Images Figure 1. Figure 2. Figure 3. PMID:10945127

  8. Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA.

    PubMed Central

    Weitzman, M D; Kyöstiö, S R; Kotin, R M; Owens, R A

    1994-01-01

    AAV is unique among eukaryotic viruses in the ability of its DNA to integrate preferentially into a specific region of the human genome. Understanding AAV integration may aid in developing gene therapy systems with predictable integration sites. Using a gel mobility-shift assay, we have identified a DNA sequence within the AAV integration locus on human chromosome 19 which is specifically bound by the AAV Rep78 and Rep68 proteins. This Rep recognition sequence is a GCTC repeating motif very similar to sequences within the inverted terminal repeats of the AAV genome which are also bound by Rep78 and Rep68. Cloned oligonucleotides containing the recognition sequence can direct specific binding by Rep proteins. Binding assays with mutant Rep proteins show that the amino-terminal portion of Rep78 and Rep68 can direct binding to either the AAV terminal repeat hairpin DNA or chromosome 19. This human genomic DNA can be complexed with AAV DNA by Rep proteins as demonstrated by a dual-label (32P/biotin) assay. These results suggest a role for Rep in targeting viral integration. Images PMID:8016070

  9. Formation of nanostructured porous Cu-Au surfaces: the influence of cationic sites on (electro)-catalysis

    NASA Astrophysics Data System (ADS)

    Najdovski, Ilija; Selvakannan, Pr.; Bhargava, Suresh K.; O'Mullane, Anthony P.

    2012-09-01

    The fabrication of nanostructured bimetallic materials through electrochemical routes offers the ability to control the composition and shape of the final material that can then be effectively applied as (electro)-catalysts. In this work a clean and transitory hydrogen bubble templating method is employed to generate porous Cu-Au materials with a highly anisotropic nanostructured interior. Significantly, the co-electrodeposition of copper and gold promotes the formation of a mixed bimetallic oxide surface which does not occur at the individually electrodeposited materials. Interestingly, the surface is dominated by Au(i) oxide species incorporated within a Cu2O matrix which is extremely effective for the industrially important (electro)-catalytic reduction of 4-nitrophenol. It is proposed that an aurophilic type of interaction takes place between both oxidized gold and copper species which stabilizes the surface against further oxidation and facilitates the binding of 4-nitrophenol to the surface and increases the rate of reaction. An added benefit is that very low gold loadings are required typically less than 2 wt% for a significant enhancement in performance to be observed. Therefore the ability to create a partially oxidized Cu-Au surface through a facile electrochemical route that uses a clean template consisting of only hydrogen bubbles should be of benefit for many more important reactions.The fabrication of nanostructured bimetallic materials through electrochemical routes offers the ability to control the composition and shape of the final material that can then be effectively applied as (electro)-catalysts. In this work a clean and transitory hydrogen bubble templating method is employed to generate porous Cu-Au materials with a highly anisotropic nanostructured interior. Significantly, the co-electrodeposition of copper and gold promotes the formation of a mixed bimetallic oxide surface which does not occur at the individually electrodeposited materials

  10. Remobilization causes site-specific cyst formation in immobilization-induced knee cartilage degeneration in an immobilized rat model.

    PubMed

    Nagai, Momoko; Ito, Akira; Tajino, Junichi; Iijima, Hirotaka; Yamaguchi, Shoki; Zhang, Xiangkai; Aoyama, Tomoki; Kuroki, Hiroshi

    2016-06-01

    An understanding of the articular cartilage degenerative process is necessary for the prevention and treatment of joint disease. The present study aimed to examine how long-term immobilization-induced cartilage degeneration is aggravated by remobilization. Sixty 8-week-old male Wistar rats were used in this study. The unilateral knee joint was immobilized using an external fixator for 8 weeks. The rats were killed at 0 and 3 days, and at 1, 2, 4 and 8 weeks after removing the fixator. After the rats were killed, the maximum knee extension angles were measured. Histological sections at the medial mid-condylar region (non-contact, transitional and contact regions of the femur and tibia) were prepared and scored. The cartilage thickness and number of chondrocytes were measured, and CD44 and Col2-3/4c expression levels were assessed immunohistochemically. The histological assessment revealed progressive aggravation of cartilage degeneration in the transitional region, with a decreased number of chondrocytes and CD44-positive chondrocytes as well as poor scoring over time, particularly in the tibia. Cyst formation was confirmed in the transitional region of the tibia at 8 weeks post-remobilization. The cartilage thickness in the transitional region was thicker than that in the contact region, particularly in the tibia. Col2-3/4c expression was observed in the non-contact and transitional regions, and the knee extension angle was recovered. In conclusion, immobilization-induced cartilage degeneration was aggravated by remobilization over time in the transitional region, followed by observations of a decreased number of chondrocytes and morphological disparity between different cartilage regions. © 2016 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

  11. Histone H1 plays a role in heterochromatin formation and VSG expression site silencing in Trypanosoma brucei.

    PubMed

    Povelones, Megan L; Gluenz, Eva; Dembek, Marcin; Gull, Keith; Rudenko, Gloria

    2012-01-01

    The African sleeping sickness parasite Trypanosoma brucei evades the host immune system through antigenic variation of its variant surface glycoprotein (VSG) coat. Although the T. brucei genome contains ∼1500 VSGs, only one VSG is expressed at a time from one of about 15 subtelomeric VSG expression sites (ESs). For antigenic variation to work, not only must the vast VSG repertoire be kept silent in a genome that is mainly constitutively transcribed, but the frequency of VSG switching must be strictly controlled. Recently it has become clear that chromatin plays a key role in silencing inactive ESs, thereby ensuring monoallelic expression of VSG. We investigated the role of the linker histone H1 in chromatin organization and ES regulation in T. brucei. T. brucei histone H1 proteins have a different domain structure to H1 proteins in higher eukaryotes. However, we show that they play a key role in the maintenance of higher order chromatin structure in bloodstream form T. brucei as visualised by electron microscopy. In addition, depletion of histone H1 results in chromatin becoming generally more accessible to endonucleases in bloodstream but not in insect form T. brucei. The effect on chromatin following H1 knock-down in bloodstream form T. brucei is particularly evident at transcriptionally silent ES promoters, leading to 6-8 fold derepression of these promoters. T. brucei histone H1 therefore appears to be important for the maintenance of repressed chromatin in bloodstream form T. brucei. In particular H1 plays a role in downregulating silent ESs, arguing that H1-mediated chromatin functions in antigenic variation in T. brucei.

  12. Enhanced formation of fine particulate nitrate at a rural site on the North China Plain in summer: The important roles of ammonia and ozone

    NASA Astrophysics Data System (ADS)

    Wen, Liang; Chen, Jianmin; Yang, Lingxiao; Wang, Xinfeng; Xu, Caihong; Sui, Xiao; Yao, Lan; Zhu, Yanhong; Zhang, Junmei; Zhu, Tong; Wang, Wenxing

    2015-01-01

    Severe PM2.5 pollution was observed frequently on the North China Plain, and nitrate contributed a large fraction of the elevated PM2.5 concentrations. To obtain a comprehensive understanding of the formation pathways of these fine particulate nitrate and the key factors that affect these pathways, field measurements of fine particulate nitrate and related air pollutants were made at a rural site on the North China Plain in the summer of 2013. Extremely high concentrations of fine particulate nitrate were frequently observed at night and in the early morning. The maximum hourly concentration of fine particulate nitrate reached 87.2 μg m-3. This concentration accounted for 29.9% of the PM2.5. The very high NH3 concentration in the early morning significantly accelerated the formation of fine particulate nitrate, as indicated by the concurrent appearance of NH3 and NO3- concentration peaks and a rising neutralization ratio (the equivalent ratio of NH4+ to the sum of SO42- and NO3-). On a number of other episode days, strong photochemical activity during daytime led to high concentrations of O3 at night. The fast secondary formation of fine particulate nitrate was mainly attributed to the hydrolysis of N2O5, which was produced from O3 and NO2. Considering the important roles of NH3 and O3 in fine particulate nitrate formation, we suggest the control of NH3 emissions and photochemical pollution to address the high levels of fine particulate nitrate and the severe PM2.5 pollution on the North China Plain.

  13. Is G84.0+0.8 a high mass star formation site near the edge of the Pelican nebula?

    NASA Astrophysics Data System (ADS)

    Comerón, F.; Pasquali, A.; Torra, J.

    2005-09-01

    We present visible and near-infrared observations of the G84.0+0.8 HII region, a bright compact knot projected within the boundaries of the W80 complex dominated by the North America and Pelican nebulae. The spectrum of the nebula indicates a temperature of the ionizing stellar spectrum T* ≃ 40 000{-}45 000 K (corresponding to a O7-O5 star) and a density of the HII region n ≃ 460 cm-3, with a foreground extinction of AV ≃ 5.9 mag. A comparison of narrow-band near-infrared images through the Brγ and the H2 S(1) v=1 → 0 filters shows that G84.0+0.8 consists of a fan-shaped cavity in a molecular cloud at least partly bounded by a photodissociation region, filled with Brγ-emitting ionized gas, and with a compact cluster at the tip of the fan. The brightest star at the position of the cluster is found to be a late G-type interloper. While membership of G84.0+0.8 in the local arm is well established from existing radial velocity measurements of the ionized gas, we find that the ionizing flux estimated from the size and density of the nebula on the one hand, and the radio continuum properties of the nebula on the other hand, are well below the expected ionizing flux of a mid, or even late, O-type star. We consider the possibility that G84.0+0.8 might be externally ionized by a nearby mid-O star. Currently available observations do not definitely confirm or reject the membership of G84.0+0.8 in the W80 complex, although a larger distance seems favored by the available data. Nevertheless, we can firmly rule out the possibility that it represents a massive star forming site in that complex, as its appearance as a compact HII region containing an embedded cluster may lead one to think.

  14. Evaluation of Radionuclide Mobilization and Redistribution during Playa Lake Formation on the Frenchman Flat Playa, Nevada Nuclear Security Site

    NASA Astrophysics Data System (ADS)

    LeFebre, K.; Hershey, R. L.; Decker, D.

    2011-12-01

    An array of programs has been investigating the environmental impacts of nuclear testing at the Nevada National Security Site since 1973. Because of above-ground testing in the 1950s, ground surface contamination on surface soils and neutron activation of nearby soil and materials has occurred from atmospheric deposition. Other concerns include redistribution of surface-deposited radionuclides by runoff, infiltration, wind, and other mechanical means. The goal of this study is to identify the potential for radionuclide mobilization and redistribution by chemical reactions during sporadic flooding of the Frenchman Flat Playa. Radionuclide mobility is dependent on a number of factors and might occur when the playa becomes flooded. Several geochemical processes that could mobilize and redistribute radionuclides include dissolution of playa minerals, precipitation of new minerals in different locations, sorption of radionuclides onto suspended or colloidal materials, and infiltration of soluble radionuclides to the subsurface environment. Following the heavy winter precipitation that flooded the playa in 2010 and 2011, playa-lake water samples were collected from easily accessed locations and analyzed for major ions, TDS, hydrogen and oxygen isotopes and radionuclides; suspended/precipitated materials were characterized by XRD; and, water-soil geochemical reactions were modeled. The geochemical software PHREEQC was used to model the soil-water evolution of the playa-lake water over time. Inputs to model simulations include precipitation chemistry, major-ion chemistry from water samples, mineralogy from XRD analysis of sediments, and radionuclides from spectroscopic measurements or literature values. Model simulations were constructed in a series of steps so that important water-soil chemical reactions could be determined and the changes in the playa water chemistry quantified as a result of these reactions. As the sequence of steps is taken, the simulations become

  15. Radiolytic bubble formation and level changes in simulated high-level waste salts and sludges -- application to Savannah River Site and Hanford Storage tanks

    SciTech Connect

    Walker, D.D.; Crawford, C.L.; Bibler, N.E.

    1993-12-31

    Radiolytically-produced bubbles of trapped gas are observed in simulated high-level waste (HLW) damp salt cake exposed to Co-60 gamma radiation. As the damp salt cake is irradiated, its volume increases due to the formation of trapped gas bubbles. Based on the increase in volume, the rate of trapped gas generation varies between 0.04 and 0.2 molecules/100 eV of energy deposited in the damp salt cake. The maximum volume of trapped gas observed in experiments is in the range 21--26 vol %. After reaching these volumes, the gas bubbles begin to escape. The generated gas includes hydrogen, oxygen, and nitrous oxide. The ratio in which these components are produced depends on the composition of the waste. Nitrous oxide production increases with the amount of sodium nitrite. Gases trapped by this mechanism may account for some of the observed level changes in Savannah River Site and Hanford waste tanks.

  16. Evidence for the coupling of Gq protein to D1-like dopamine sites in rat striatum: possible role in dopamine-mediated inositol phosphate formation.

    PubMed

    Wang, H Y; Undie, A S; Friedman, E

    1995-12-01

    The role of G proteins in mediating the coupling of D1 dopamine receptors to inositol phosphate formation was investigated in rat brain striatum. Pertussis toxin-activated ADP-ribosylation ( > or = 95%) did not affect the ability of the D1 agonist SKF38393 to stimulate the generation of inositol phosphates in striatal slices. Stimulation of striatal membranes with dopamine in the presence of [35S]GTP gamma S or [alpha-32P]GTP increased guanine nucleotide binding to G alpha s, G alpha i, and G alpha q in a concentration-dependent fashion. The activation of G alpha s and G alpha q was mimicked by the D1 agonist SKF38393 and blocked by the D1 antagonist SCH23390. In contrast, the D2/3 dopamine receptor agonist quinpirole stimulated guanine nucleotide binding to G alpha i, and dopamine-stimulated activation of G alpha i was attenuated by the D2 antagonist I-sulpiride. Furthermore, antisera directed against G alpha s or G alpha q but not G alpha i, G alpha o, or G alpha z precipitated specific D1-like binding sites labeled with [3H]SCH23390. The D1-like receptors that coprecipitated with G alpha s-but not with G alpha q can be recognized by a specific D1 dopamine receptor antibody. The data provide evidence to suggest that in addition to coupling to Gs/adenylyl cyclase, D1-like dopamine sites that couple to Gq may mediate dopamine-stimulated formation of inositol phosphates in the rat striatum.

  17. Inactivation of the Lactobacillus leichmannii ribonucleoside triphosphate reductase by 2'-chloro-2'-deoxyuridine 5'-triphosphate: stoichiometry of inactivation, site of inactivation, and mechanism of the protein chromophore formation

    SciTech Connect

    Ashley, G.W.; Harris, G.; Stubbe, J.A.

    1988-06-14

    The ribonucleoside triphosphate reductase (RTPR) of Lactobacillus leichmannii is inactivated by the substrate analogue 2'-chloro-2'-deoxyuridine 5'-triphosphate (ClUTP). Inactivation is due to alkylation by 2-methylene-3(2H)-furanone, a decomposition product of the enzymic product 3'-keto-2'-deoxyuridine triphosphate. The former has been unambiguously identified as 2-((ethylthio)methyl)-3(2H)-furanone, an ethanethiol trapped adduct, which is identical by /sup 1/H NMR spectroscopy with material synthesized chemically. Subsequent to rapid inactivation, a slow process occurs that results in formation of a new protein-associated chromophore absorbing maximally near 320 nm. The terminal stages of the inactivation have now been investigated in detail. The alkylation and inactivation stoichiometries were studied as a function of the ratio of ClUTP to enzyme. The amount of labeling of RTPR increased with increasing ClUTP concentration up to the maximum of approximately 4 labels/RTPR, yet the degree of inactivation did not increase proportionally. This suggests that (1) RTPR may be inactivated by alkylation of a single site and (2) decomposition of 3'-keto-dUTP is not necessarily enzyme catalyzed. The formation of the new protein chromophore was also monitored during inactivation and found to reach its full extent upon the first alkylation . Thus, out of four alkylation sites, only one appears capable of undergoing the subsequent reaction to form the new chromophore. Model studies suggest that the new chromophore is due to addition of an amino group to the 5-position of enzyme-bound furanone, followed by ring opening and tautomerization to give a ..beta..-aminoenone structure.

  18. Formation of lipid bilayer membrane in a poly(dimethylsiloxane) microchip integrated with a stacked polycarbonate membrane support and an on-site nanoinjector.

    PubMed

    Teng, Wei; Ban, Changill; Hahn, Jong Hoon

    2015-03-01

    This paper describes a new and facile approach for the formation of pore-spanning bilayer lipid membranes (BLMs) within a poly(dimethylsiloxane) (PDMS) microfluidic device. Commercially, readily available polycarbonate (PC) membranes are employed for the support of BLMs. PC sheets with 5 μm, 2 μm, and 0.4 μm pore diameters, respectively, are thermally bonded into a multilayer-stack, reducing the pore density of 0.4 μm-pore PC by a factor of 200. The BLMs on this support are considerably stable (a mean lifetime: 17 h). This multilayer-stack PC (MSPC) membrane is integrated into the PDMS chip by an epoxy bonding method developed to secure durable bonding under the use of organic solvents. The microchip has a special channel for guiding a micropipette in the proximity of the MSPC support. With this on-site injection technique, tens to hundreds of nanoliters of solutions can be directly dispensed to the support. Incorporating gramicidin ion channels into BLMs on the MSPC support has confirmed the formation of single BLMs, which is based on the observation from current signals of 20 pS conductance that is typical to single channel opening. Based on the bilayer capacitance (1.4 pF), about 15% of through pores across the MSPC membrane are estimated to be covered with BLMs.

  19. Development of a magnetic method for reconstructing the paleoclimate of the rock formation time: A case study of the Paleolithic Kostenki-12 site section (the Voronezh region)

    NASA Astrophysics Data System (ADS)

    Pospelova, G. A.; Anikovich, M. V.; Hoffecker, J. F.; Kadzialko-Hofmokl, M.

    2007-12-01

    A magnetic method is proposed for reconstructing the paleoclimate existing at the formation time of rocks of the Paleolithic Kostenki-12 site section. Results obtained from an experimental study of scalar magnetic characteristics (SMCs) of the rocks (magnetic susceptibility, anhysteretic remanent magnetization, and saturation isothermal remanent magnetization) are presented. These results indicate complex along-section SMC behavior distinguished by alternating larger and smaller values of the parameters. The magnetic minerals of the section are mainly represented by pseudo-single-domain magnetite grains. The size of the magnetite grains in the pseudo-single-domain range varies along the section, increasing in its lower half. The SMCs values plotted on different scales for the upper and lower halves of the section clearly revealed 12 magnetic zones (MZs). Comparison of the MZs with palynological zones obtained in a parallel section showed, on the whole, a convergence of data: MZs with larger (smaller) SMC values correlate with thermomers (cryomers). Comparison of along-section SMC variations with the GRIP (Greenland Ice Core Project) curve of the time dependence of paleotemperatures confirmed or refined the ages of lithologic horizons. As a result, it is established that constraints on paleoclimatic changes in the rock formation time can be gained from SMC variations if the main carriers of magnetization in rocks are pseudo-single-domain magnetite grains even with magnetic grain size varying along the section.

  20. Formation of lipid bilayer membrane in a poly(dimethylsiloxane) microchip integrated with a stacked polycarbonate membrane support and an on-site nanoinjector

    PubMed Central

    Teng, Wei; Ban, Changill; Hahn, Jong Hoon

    2015-01-01

    This paper describes a new and facile approach for the formation of pore-spanning bilayer lipid membranes (BLMs) within a poly(dimethylsiloxane) (PDMS) microfluidic device. Commercially, readily available polycarbonate (PC) membranes are employed for the support of BLMs. PC sheets with 5 μm, 2 μm, and 0.4 μm pore diameters, respectively, are thermally bonded into a multilayer-stack, reducing the pore density of 0.4 μm-pore PC by a factor of 200. The BLMs on this support are considerably stable (a mean lifetime: 17 h). This multilayer-stack PC (MSPC) membrane is integrated into the PDMS chip by an epoxy bonding method developed to secure durable bonding under the use of organic solvents. The microchip has a special channel for guiding a micropipette in the proximity of the MSPC support. With this on-site injection technique, tens to hundreds of nanoliters of solutions can be directly dispensed to the support. Incorporating gramicidin ion channels into BLMs on the MSPC support has confirmed the formation of single BLMs, which is based on the observation from current signals of 20 pS conductance that is typical to single channel opening. Based on the bilayer capacitance (1.4 pF), about 15% of through pores across the MSPC membrane are estimated to be covered with BLMs. PMID:26015832

  1. Self-expression and relationship formation in high relational mobility environments: A study of dual users of American and Japanese social networking sites.

    PubMed

    Takemura, Kosuke; Suzuki, Satoko

    2015-09-03

    This study proposes that self-expression motivation, an aspect of independent/individualistic psychological tendencies, aids in the formation of social relationships when social relationships are open and mobile. In societies characterised by high relational mobility (e.g., North America), which creates market-like competition in social relationships, individuals must express their uniqueness and worthiness to form new social relationships. Self-expression motivation has a relatively weak effect on relationship formation in low relational mobility societies (e.g., Japan), where social relationships are generally predetermined. This hypothesis was examined and supported through a study on dual users of two social networking sites-Facebook and Mixi (the "Facebook of Japan"). As expected, relational mobility was higher on Facebook than on Mixi. Moreover, the association between self-expression motivation and the number of new friends met on Facebook/Mixi was more positive for Facebook than it was for Mixi. The social functionality of independent tendencies is then discussed.

  2. The formation conditions of the burial site of Late Cretaceous dinosaurs and plants in the Kakanaut River basin (Koryak Highlands, Northeastern Asia)

    NASA Astrophysics Data System (ADS)

    Shczepetov, S. V.; Herman, A. B.

    2017-07-01

    The stratigraphic position of layers containing plant and animal remains in the Koryak Highlands (Northeast Asia) is under discussion. Their age is defined as late Campanian-early Maastrichtian. Plant-bearing and bone-bearing rocks represent cemented basaltic tephra. The former contain a small amount of xenogenic material and slightly rounded volcaniclastic material, which indicates its insignificant transportation. Ash particles in bone-bearing rocks are even less rounded. Among them, there are no rock fragments of other composition. Large bones and their fragments, as xenoliths, are chaotically distributed in the rock matrix as if floating in mass of ash material. This burial site was probably formed in a continental environment as a result of the gravitational and eolian transportation of the terrigenous material. The burial of small dinosaur bones and teeth occurred during the deposition of a small stream of a semiliquid water-ash mixture. This work presents a possible mechanism of the formation of burial sites, taking into consideration proposed conditions of the life and reproduction of dinosaurs in the Late Mesozoic Arctic.

  3. Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from DFT Studies

    SciTech Connect

    Das, Ujjal; Zhang, Guanghui; Hu, Bo; Hock, Adam S.; Redfern, Paul C.; Miller, Jeffrey T.; Curtiss, Larry A.

    2015-12-01

    Amorphous silica (SiO2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure and activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. The molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.

  4. Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from Density Functional Theory (DFT) Studies

    DOE PAGES

    Das, Ujjal; Zhang, Guanghui; Hu, Bo; ...

    2015-10-28

    Amorphous silica (SiO2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure and activitymore » of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. In conclusion, the molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.« less

  5. Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from Density Functional Theory (DFT) Studies

    SciTech Connect

    Das, Ujjal; Zhang, Guanghui; Hu, Bo; Hock, Adam S.; Redfern, Paul C.; Miller, Jeffrey T.; Curtiss, Larry A.

    2015-10-28

    Amorphous silica (SiO2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure and activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. In conclusion, the molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.

  6. Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda.

    PubMed

    Piekarska, B; Konieczny, L; Rybarska, J; Stopa, B; Zemanek, G; Szneler, E; Król, M; Nowak, M; Roterman, I

    2001-11-01

    Moderate heating (40-50 degrees C) of immunoglobulins makes them accessible for binding with Congo Red and some related highly associated dyes. The binding is specific and involves supramolecular dye ligands presenting ribbon-like micellar bodies. The L chain lambda dimer, which upon heating disclosed the same binding requirement with respect to supramolecular dye ligands, was used in this work to identify the site of their attachment. Two clearly defined dye-protein (L lambda chain) complexes arise upon heating, here called complex I and complex II. The first is formed at low temperatures (up to 40-45 degrees C) and hence by a still native protein, while the formation of the second one is associated with domain melting above 55 degrees C. They contain 4 and 8 dye molecules bound per L chain monomer, respectively. Complex I also forms efficiently at high dye concentration even at ambient temperature. Complex I and its formation was the object of the present studies. Three structural events that could make the protein accessible to penetration by the large dye ligand were considered to occur in L chains upon heating: local polypeptide chain destabilization, VL-VL domain incoherence, and protein melting. Of these three possibilities, local low-energy structural alteration was found to correlate best with the formation of complex I. It was identified as decreased packing stability of the N-terminal polypeptide chain fragment, which as a result made the V domain accessible for dye penetration. The 19-amino acid N-terminal fragment becomes susceptible to proteolytic cleavage after being replaced by the dye at its packing locus. Its splitting from the dye-protein complex was proved by amino acid sequence analysis. The emptied packing locus, which becomes the site that holds the dye, is bordered by strands of amino acids numbered 74-80 and 105-110, as shown by model analysis. The character of the temperature-induced local polypeptide chain destabilization and its possible

  7. Repeated occurrences of methanogenic zones, diagenetic dolomite formation and linked silicate alteration in southern Bering Sea sediments (Bowers Ridge, IODP Exp. 323 Site U1341)

    NASA Astrophysics Data System (ADS)

    Wehrmann, L. M.; Ockert, C.; Mix, A. C.; Gussone, N.; Teichert, B. M. A.; Meister, P.

    2016-03-01

    porewater calcium was also influenced by ammonium-calcium exchange on clay minerals and carbonate recrystallization. Our study elucidates the response of porewater element concentrations and isotopic profiles interlinked with the formation of diagenetic carbonates to changes in the deposition of organic carbon in sediments of deeper water sites (>2000 m water depth) over prolonged timescales. It shows that variations in biogeochemical processes in response to changes in oceanographic conditions and a dynamic subseafloor biogeochemical zonation have to also be taken into account at these deep water sites for a global assessment of organic carbon burial fluxes and remineralization.

  8. Importance of Highly Conserved Peptide Sites of Human Cytomegalovirus gO for Formation of the gH/gL/gO Complex

    PubMed Central

    Stegmann, Cora; Abdellatif, Mohamed E. A.; Laib Sampaio, Kerstin; Walther, Paul

    2016-01-01

    ABSTRACT The glycoprotein O (gO) is betaherpesvirus specific. Together with the viral glycoproteins H and L, gO forms a covalent trimeric complex that is part of the viral envelope. This trimer is crucial for cell-free infectivity of human cytomegalovirus (HCMV) but dispensable for cell-associated spread. We hypothesized that the amino acids that are conserved among gOs of different cytomegaloviruses are important for the formation of the trimeric complex and hence for efficient virus spread. In a mutational approach, nine peptide sites, containing all 13 highly conserved amino acids, were analyzed in the context of HCMV strain TB40-BAC4 with regard to infection efficiency and formation of the gH/gL/gO complex. Mutation of amino acids (aa) 181 to 186 or aa 193 to 198 resulted in the loss of the trimer and a complete small-plaque phenotype, whereas mutation of aa 108 or aa 249 to 254 caused an intermediate phenotype. While individual mutations of the five conserved cysteines had little impact, their relevance was revealed in a combined mutation, which abrogated both complex formation and cell-free infectivity. C343 was unique, as it was sufficient and necessary for covalent binding of gO to gH/gL. Remarkably, however, C218 together with C167 rescued infectivity in the absence of detectable covalent complex formation. We conclude that all highly conserved amino acids contribute to the function of gO to some extent but that aa 181 to 198 and cysteines 343, 218, and 167 are particularly relevant. Surprisingly, covalent binding of gO to gH/gL is required neither for its incorporation into virions nor for proper function in cell-free infection. IMPORTANCE Like all herpesviruses, the widespread human pathogen HCMV depends on glycoproteins gB, gH, and gL for entry into target cells. Additionally, gH and gL have to bind gO in a trimeric complex for efficient cell-free infection. Homologs of gO are shared by all cytomegaloviruses, with 13 amino acids being highly conserved

  9. Importance of Highly Conserved Peptide Sites of Human Cytomegalovirus gO for Formation of the gH/gL/gO Complex.

    PubMed

    Stegmann, Cora; Abdellatif, Mohamed E A; Laib Sampaio, Kerstin; Walther, Paul; Sinzger, Christian

    2017-01-01

    The glycoprotein O (gO) is betaherpesvirus specific. Together with the viral glycoproteins H and L, gO forms a covalent trimeric complex that is part of the viral envelope. This trimer is crucial for cell-free infectivity of human cytomegalovirus (HCMV) but dispensable for cell-associated spread. We hypothesized that the amino acids that are conserved among gOs of different cytomegaloviruses are important for the formation of the trimeric complex and hence for efficient virus spread. In a mutational approach, nine peptide sites, containing all 13 highly conserved amino acids, were analyzed in the context of HCMV strain TB40-BAC4 with regard to infection efficiency and formation of the gH/gL/gO complex. Mutation of amino acids (aa) 181 to 186 or aa 193 to 198 resulted in the loss of the trimer and a complete small-plaque phenotype, whereas mutation of aa 108 or aa 249 to 254 caused an intermediate phenotype. While individual mutations of the five conserved cysteines had little impact, their relevance was revealed in a combined mutation, which abrogated both complex formation and cell-free infectivity. C343 was unique, as it was sufficient and necessary for covalent binding of gO to gH/gL. Remarkably, however, C218 together with C167 rescued infectivity in the absence of detectable covalent complex formation. We conclude that all highly conserved amino acids contribute to the function of gO to some extent but that aa 181 to 198 and cysteines 343, 218, and 167 are particularly relevant. Surprisingly, covalent binding of gO to gH/gL is required neither for its incorporation into virions nor for proper function in cell-free infection. Like all herpesviruses, the widespread human pathogen HCMV depends on glycoproteins gB, gH, and gL for entry into target cells. Additionally, gH and gL have to bind gO in a trimeric complex for efficient cell-free infection. Homologs of gO are shared by all cytomegaloviruses, with 13 amino acids being highly conserved. In a mutational

  10. The mechanism of formation of the seafloor massive sulfide ore body beneath the seafloor at HAKUREI Site in Izena Caldera, Middle Okinawa Trough

    NASA Astrophysics Data System (ADS)

    Yoshizumi, R.; Urabe, T.

    2012-12-01

    dominant at lower of the ore, relatively. The existence of "Black ore (sphalerite-galena ore)" at upper part and "Yellow ore (chalcopyrite-pyrite ore)" at lower part of the Lower ore indicate that the SMS ore beneath the seafloor has already the characteristic mineral assemblage of Kuroko ore deposit at the time of formation. Fe content in Sphalerite is over 6wt% in the Upper ore and under 1wt% in the Lower ore, respectively, which shows that the Lower ore is formed under high Sulfur and Oxygen fugacity than Upper ore if the temperature of formation is not very different each other. Barite occurs not only in the Upper ore, but also in the Lower ore and the crystal size becomes coarser downwards. These lines of evidence imply that the existence of the Lower ore indicates that the mineralization has been repeated in the HAKUREI site. This study is a part of "TAIGA" project funded by Grant-in-Aid program by Monbusho.t; t;

  11. The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences.

    PubMed

    Raj, Isha; Kumar, Sudhir; Gourinath, Samudrala

    2012-08-01

    Cysteine is a crucial substrate for the synthesis of glutathione and trypanothione, which in turn maintain intracellular redox homeostasis and defend against oxidative stress in the pathogen Leishmania donovani. Here, the identification, sequencing, characterization and crystal structure at 1.79 Å resolution of O-acetylserine sulfhydrylase (OASS), a cysteine-biosynthetic pathway enzyme from L. donovani (LdOASS), are reported. It shows binding to the serine acetyltransferase (SAT) C-terminal peptide, indicating that OASS and SAT interact with each other to form a cysteine synthase complex, further confirmed by the structure of LdOASS in complex with SAT C-terminal octapeptide at 1.68 Å resolution. Docking and fluorescence binding studies show that almost all SAT C-terminus mimicking tetrapeptides can bind to LdOASS. Some peptides had a higher binding affinity than the native peptide, indicating that SAT-OASS interactions are not sequence-specific. The structure of LdOASS with a designed peptide (DWSI) revealed that LdOASS makes more interactions with the designed peptide than with the native peptide. In almost all known SAT-OASS interactions the SAT C-terminal sequence was shown to contain amino acids with large side chains. Structural comparison with other OASSs revealed that LdOASS has a relatively less open active-site cleft, which may be responsible for its interaction with the smaller-amino-acid-containing C-terminal LdSAT peptide. Biochemical studies confirmed that LdOASS interacts with SATs from Entamoeba histolytica and Brucella abortus, further displaying its sequence-independent and versatile mode of interaction with SATs. This implicates a critical role of the size of the active-site cleft opening in OASS for SAT-OASS interaction and thus cysteine synthase complex formation.

  12. Overburden characterization and post-burn study at the Hanna, Wyoming underground coal gasification site: stratigraphy, depositional environments and mineralogy, Hanna Formation

    SciTech Connect

    Craig, G.N. II; Burns, L.K.; Ethridge, F.G.; Laughter, T.; Youngberg, A.D.

    1982-03-01

    Several underground coal gasification (UCG) experiments have been conducted in the Hanna No. 1 coal seam. During the fall of 1980 the Laramie Energy Technology Center performed a post-burn field study of the Hanna II, Phases 2 and 3 experiment at the Hanna UCG site. The field work consisted of high resolution seismic, drilling, coring, and geophysical logging. The Department of Earth Resources, Colorado State University, contributed to the post-burn study by doing laboratory work on the cores and geophysical logs. The purpose of the laboratory work was to provide an estimate of the temperatures and chemical conditions reached during the conversion experiment by studying the mineralogical and textural characteristics of thermally altered and ulaltered overburden. In the vicinity of the burn cavity, overburden rocks have been subjected to high temperature pyrometamorphism during the Hanna II Phases 2 and 3 UCG experiments. Paralava rocks, buchites and paralava breccias containing glass and various high temperature minerals such as oligoclase, clinopyroxene, ferrocordierite, mullite, cristobalite, magnetite, and tridymite formed. Textures of some of these minerals suggest crystallization directly from a melt. Mineralogy and melting relations of the paralavas, ash fusion temperatures, and thermocouple measurements made during the experiment suggest that tempratures in excess of 1200/sup 0/C were attained. Rock color and the presence of reduced iron bearing minerals and blebs of native iron indicate that the experimental burn and the product gases in the area of paralava formation were reducing.

  13. CO2–rock–brine interactions in Lower Tuscaloosa Formation at Cranfield CO2 sequestration site, Mississippi, U.S.A.

    USGS Publications Warehouse

    Lu, Jiemin; Kharaka, Yousif K.; Thordsen, James J.; Horita, Juske; Karamalidis, Athanasios; Griffith, Craig; Hakala, J. Alexandra; Ambats, Gil; Cole, David R.; Phelps, Tommy J.; Manning, Michael A.; Cook, Paul J.; Hovorka, Susan D.

    2012-01-01

    A highly integrated geochemical program was conducted at the Cranfield CO2-enhanced oil recovery (EOR) and sequestration site, Mississippi, U.S.A.. The program included extensive field geochemical monitoring, a detailed petrographic study, and an autoclave experiment under in situ reservoir conditions. Results show that mineral reactions in the Lower Tuscaloosa reservoir were minor during CO2 injection. Brine chemistry remained largely unchanged, which contrasts with significant changes observed in other field tests. Field fluid sampling and laboratory experiments show consistently slow reactions. Carbon isotopic composition and CO2 content in the gas phase reveal simple two-end-member mixing between injected and original formation gas. We conclude that the reservoir rock, which is composed mainly of minerals with low reactivity (average quartz 79.4%, chlorite 11.8%, kaolinite 3.1%, illite 1.3%, concretionary calcite and dolomite 1.5%, and feldspar 0.2%), is relatively unreactive to CO2. The significance of low reactivity is both positive, in that the reservoir is not impacted, and negative, in that mineral trapping is insignificant.

  14. The ER Stress Sensor PERK Coordinates ER-Plasma Membrane Contact Site Formation through Interaction with Filamin-A and F-Actin Remodeling.

    PubMed

    van Vliet, Alexander R; Giordano, Francesca; Gerlo, Sarah; Segura, Inmaculada; Van Eygen, Sofie; Molenberghs, Geert; Rocha, Susana; Houcine, Audrey; Derua, Rita; Verfaillie, Tom; Vangindertael, Jeroen; De Keersmaecker, Herlinde; Waelkens, Etienne; Tavernier, Jan; Hofkens, Johan; Annaert, Wim; Carmeliet, Peter; Samali, Afshin; Mizuno, Hideaki; Agostinis, Patrizia

    2017-03-02

    Loss of ER Ca(2+) homeostasis triggers endoplasmic reticulum (ER) stress and drives ER-PM contact sites formation in order to refill ER-luminal Ca(2+). Recent studies suggest that the ER stress sensor and mediator of the unfolded protein response (UPR) PERK regulates intracellular Ca(2+) fluxes, but the mechanisms remain elusive. Here, using proximity-dependent biotin identification (BioID), we identified the actin-binding protein Filamin A (FLNA) as a key PERK interactor. Cells lacking PERK accumulate F-actin at the cell edges and display reduced ER-PM contacts. Following ER-Ca(2+) store depletion, the PERK-FLNA interaction drives the expansion of ER-PM juxtapositions by regulating F-actin-assisted relocation of the ER-associated tethering proteins Stromal Interaction Molecule 1 (STIM1) and Extended Synaptotagmin-1 (E-Syt1) to the PM. Cytosolic Ca(2+) elevation elicits rapid and UPR-independent PERK dimerization, which enforces PERK-FLNA-mediated ER-PM juxtapositions. Collectively, our data unravel an unprecedented role of PERK in the regulation of ER-PM appositions through the modulation of the actin cytoskeleton.

  15. Origin(s) of the local structures at the Philae landing site and possible implications on the formation and evolution of the 67P nucleus

    NASA Astrophysics Data System (ADS)

    Poulet, F.; Lucchetti, A.; Bibring, J. P.

    2016-12-01

    The in situ images of the 67P/Churyumov-Gerasimenko nucleus acquired by the CIVA cameras on-board PHILAE revealed a rough, irregular and inhomogeneous terrains dominated by fractures and agglomerates of consolidated materials. While the composition of these materials is unknown, they provide unique structures to constrain the conditions prevailing at the surface of a comet and also possibly to the nucleus formation. A quantitative analysis of some microscopic structures (namely fractures and grains that look like pebbles) will be presented using a manual extraction from the CIVA data set with the software ArcGIS. Fractures/cracks are rather ubiquitous at various spatial scales with network and size (from sub-cm to 10 cm) well correlated to the texture of the landscape. The pebble size distribution are reasonably well fitted by power-laws having different cumulative indexes. The nature of the landscape of the landing site will be then discussed in relation to both endogenic and exogenic processes that could have sculpted it. The block seen in CIVA#1 is interpreted to be a close-up of fractured boulders/cliff belonging to the boulder field identified from the orbit near Abydos, this boulder field being itself the result of gravitational regressive erosion due to sublimation (Lucchetti et al. 2016). The observed fractures are best explained by thermal insolation leading to thermal fatigue and/or to loss of volatile materials (e.g., desiccation). This surficial fragmentation (up to >10 cm length) could generate macroscopic erosion that is also visible at larger scale from the orbit. While the pebbles are difficult to be formed by any current physical processes, there is at least an intriguing possibility that they are remnants of primordial accretion processes, as there are several lines of evidence that the nucleus could be primordial (Davidsson et al., 2016), and not a collisional rubble piles of a large body (Morbidelli and Rickman A&A, 2015). We thus speculate that

  16. Enhancing the revision of the static geological model of the Stuttgart Formation at the Ketzin pilot site by integration of reservoir simulations and 3D seismics

    NASA Astrophysics Data System (ADS)

    Kempka, Thomas; Norden, Ben; Ivanova, Alexandra; Lüth, Stefan

    2017-04-01

    Pilot-scale carbon dioxide storage has been performed at the Ketzin pilot site in Germany from June 2007 to August 2013 with about 67 kt of CO2 injected into the Upper Triassic Stuttgart Formation. In this context, the main aims focussed on verification of the technical feasibility of CO2 storage in saline aquifers and development of efficient strategies for CO2 behaviour monitoring and prediction. A static geological model has been already developed at an early stage of this undertaking, and continuously revised with the availability of additional geological and operational data as well as by means of reservoir simulations, allowing for revisions in line with the efforts to achieve a solid history match in view of well bottomhole pressures and CO2 arrival times at the observation wells. Three 3D seismic campaigns followed the 2005 3D seismic baseline in 2009, 2012 and 2015. Consequently, the interpreted seismic data on spatial CO2 thickness distributions in the storage reservoir as well as seismic CO2 detection limits from recent conformity studies enabled us to enhance the previous history-matching results by adding a spatial component to the previous observations, limited to points only. For that purpose, we employed the latest version of the history-matched static geological reservoir model and revised the gridding scheme of the reservoir simulation model by coarsening and introducing local grid refinements at the areas of interest. Further measures to ensure computational efficiency included the application of the MUFITS reservoir simulator (BLACKOIL module) with PVT data derived from the MUFITS GASSTORE module. Observations considered in the inverse model calibration for a simulation time of about 5 years included well bottomhole pressures, CO2 arrival times and seismically determined CO2 thickness maps for 2009 and 2012. Pilot points were employed by means of the PEST++ inverse simulation framework to apply permeability multipliers, interpolated by kriging

  17. A Model for the Active-Site Formation Process in DMSO Reductase Family Molybdenum Enzymes Involving Oxido-Alcoholato and Oxido-Thiolato Molybdenum(VI) Core Structures.

    PubMed

    Sugimoto, Hideki; Sato, Masanori; Asano, Kaori; Suzuki, Takeyuki; Mieda, Kaoru; Ogura, Takashi; Matsumoto, Takashi; Giles, Logan J; Pokhrel, Amrit; Kirk, Martin L; Itoh, Shinobu

    2016-02-15

    New bis(ene-1,2-dithiolato)-oxido-alcoholato molybdenum(VI) and -oxido-thiolato molybdenum(VI) anionic complexes, denoted as [Mo(VI)O(ER)L2](-) (E = O, S; L = dimethoxycarboxylate-1,2-ethylenedithiolate), were obtained from the reaction of the corresponding dioxido-molybdenum(VI) precursor complex with either an alcohol or a thiol in the presence of an organic acid (e.g., 10-camphorsulfonic acid) at low temperature. The [Mo(VI)O(ER)L2](-) complexes were isolated and characterized, and the structure of [Mo(VI)O(OEt)L2](-) was determined by X-ray crystallography. The Mo(VI) center in [Mo(VI)O(OEt)L2](-) exhibits a distorted octahedral geometry with the two ene-1,2-dithiolate ligands being symmetry inequivalent. The computed structure of [Mo(VI)O(SR)L2](-) is essentially identical to that of [Mo(VI)O(OR)L2](-). The electronic structures of the resulting molybdenum(VI) complexes were evaluated using electronic absorption spectroscopy and bonding calculations. The nature of the distorted O(h) geometry in these [Mo(VI)O(EEt)L2](-) complexes results in a lowest unoccupied molecular orbital wave function that possesses strong π* interactions between the Mo(d(xy)) orbital and the cis S(p(z)) orbital localized on one sulfur donor from a single ene-1,2-dithiolate ligand. The presence of a covalent Mo-S(dithiolene) bonding interaction in these monooxido Mo(VI) compounds contributes to their low-energy ligand-to-metal charge transfer transitions. A second important d-p π bonding interaction derives from the ∼180° O(oxo)-Mo-E-C dihedral angle involving the alcoholate and thiolate donors, and this contributes to ancillary ligand contributions to the electronic structure of these species. The formation of [Mo(VI)O(OEt)L2](-) and [Mo(VI)O(SEt)L2](-) from the dioxidomolybdenum(VI) precursor may be regarded as a model for the active-site formation process that occurs in the dimethyl sulfoxide reductase family of pyranopterin molybdenum enzymes.

  18. Substitution of glutamine for lysine at the pyridoxal phosphate binding site of bacterial D-amino acid transaminase. Effects of exogenous amines on the slow formation of intermediates.

    PubMed

    Futaki, S; Ueno, H; Martinez del Pozo, A; Pospischil, M A; Manning, J M; Ringe, D; Stoddard, B; Tanizawa, K; Yoshimura, T; Soda, K

    1990-12-25

    In bacterial D-amino acid transaminase, Lys-145, which binds the coenzyme pyridoxal 5'-phosphate in Schiff base linkage, was changed to Gln-145 by site-directed mutagenesis (K145Q). The mutant enzyme had 0.015% the activity of the wild-type enzyme and was capable of forming a Schiff base with D-alanine; this external aldimine was formed over a period of minutes depending upon the D-alanine concentration. The transformation of the pyridoxal-5'-phosphate form of the enzyme to the pyridoxamine-5'-phosphate form (i.e. the half-reaction of transamination) occurred over a period of hours with this mutant enzyme. Thus, information on these two steps in the reaction and on the factors that influence them can readily be obtained with this mutant enzyme. In contrast, these reactions with the wild-type enzyme occur at much faster rates and are not easily studied separately. The mutant enzyme shows distinct preference for D- over L-alanine as substrates but it does so about 50-fold less effectively than the wild-type enzyme. Thus, Lys-145 probably acts in concert with the coenzyme and other functional side chain(s) to lead to efficient and stereochemically precise transamination in the wild-type enzyme. The addition of exogenous amines, ethanolamine or methyl amine, increased the rate of external aldimine formation with D-alanine and the mutant enzyme but the subsequent transformation to the pyridoxamine-5'-phosphate form of the enzyme was unaffected by exogenous amines. The wild-type enzyme displayed a large negative trough in the circular dichroic spectrum at 420 nm, which was practically absent in the mutant enzyme. However, addition of D-alanine to the mutant enzyme generated this negative Cotton effect (due to formation of the external aldimine with D-alanine). This circular dichroism band gradually collapsed in parallel with the transformation to the pyridoxamine-5'-phosphate enzyme. Further studies on this mutant enzyme, which displays the characteristics of the wild

  19. Soil use and hydraulic systems in the Terramara S. Rosa (Poviglio, northern Italy). The role of micromorphology in decrypting site formation processes

    NASA Astrophysics Data System (ADS)

    Cremaschi, Mauro; Chiara, Pizzi

    2010-05-01

    The S. Rosa moated site (Terramara), which dates back to the Middle-Recent Bronze age, is under excavation since 1984, by the Soprintendenza ai Beni Archeologici dell Emilia Romagna, in cooperation with the Università degli Studi di Milano, CNR-IDPA of Milano, and the sponsorship of the Comune di Poviglio and Coopsette. The field seasons of the last ten years were concentrated in the south-western part of the fringe of the site and the adjoining ditch, and unearthed a complex hydraulic system composed of several wells, the moat, a canal converging to it, and minor ditches connecting these structure to the countryside surrounding the Terramara. During the early phase of occupation (late Middle Bronze age), a large number of wells, located at the fringe of the village, in coincidence with the fence were dug to reach the water table. They were kept in use for a long time and the water extracted from them was not directed to the interior of the village but it was carried inside the moat throughout a system of ditches. Outside the moat, a large canal has been recently discovered. Its large size and the sophisticated knowledge in hydraulic engineering that its construction required, make it the first archaeological proof of a large scale water management during the Bronze Age. During the last phase of the village (late Recent Bronze age) the wells of the fence and the canal were deactivated and the flow inside the moat interrupted. Consequently, more wells were excavated in a very short time at the bottom of the moat, as indicated by refitting of the potsherds included in the fill. These wells are surrounded by reservoirs connected by small ditches to make the extracted water available to be used at the outer fringe of the moat. An intensive program of micromorphological studies has been undertaken to reconstruct the formation processes of the excavated deposits. Thin section study led to the differentiation of long lasting phases of use, maintenance and abandonment on

  20. Hydrothermal Alteration of Glass from Underground Nuclear Tests: Formation and Transport of Pu-clay Colloids at the Nevada National Security Site

    SciTech Connect

    Zavarin, M.; Zhao, P.; Joseph, C.; Begg, J.; Boggs, M.; Dai, Z.; Kersting, A. B.

    2015-05-27

    The testing of nuclear weapons at the Nevada National Security Site (NNSS), formerly the Nevada Test Site (NTS), has led to the deposition of substantial quantities of plutonium into the environment. Approximately 2.8 metric tons (3.1×104 TBq) of Pu were deposited in the NNSS subsurface as a result of underground nuclear testing. While 3H is the most abundant anthropogenic radionuclide deposited in the NNSS subsurface (4.7×106 TBq), plutonium is the most abundant from a molar standpoint. The only radioactive elements in greater molar abundance are the naturally occurring K, Th, and U isotopes. 239Pu and 240Pu represent the majority of alpha-emitting Pu isotopes. The extreme temperatures associated with underground nuclear tests and the refractory nature of Pu results in most of the Pu (98%) being sequestered in melted rock, referred to as nuclear melt glass (Iaea, 1998). As a result, Pu release to groundwater is controlled, in large part, by the leaching (or dissolution) of nuclear melt glass over time. The factors affecting glass dissolution rates have been studied extensively. The dissolution of Pu-containing borosilicate nuclear waste glasses at 90ºC has been shown to lead to the formation of dioctahedral smectite colloids. Colloid-facilitated transport of Pu at the NNSS has been observed. Recent groundwater samples collected from a number of contaminated wells have yielded a wide range of Pu concentrations from 0.00022 to 2.0 Bq/L. While Pu concentrations tend to fall below the Maximum Contaminant Level (MCL) established by the Environmental Protection Agency (EPA) for drinking water (0.56 Bq/L), we do not yet understand what factors limit the Pu concentration or its transport behavior. To quantify the upper limit of Pu concentrations produced as a result of melt glass dissolution and determine the nature of colloids and Pu associations, we performed a 3 year nuclear melt glass dissolution experiment

  1. Particulate matter (PM) episodes at a suburban site in Hong Kong: evolution of PM characteristics and role of photochemistry in secondary aerosol formation

    NASA Astrophysics Data System (ADS)

    Qin, Yi Ming; Jie Li, Yong; Wang, Hao; Lee, Berto Paul Yok Long; Huang, Dan Dan; Keung Chan, Chak

    2016-11-01

    Episodes with high concentrations of particulate matter (PM) across the seasons were investigated during four 1-month campaigns at a suburban site in Hong Kong. High-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) measurements revealed that both regional transport and secondary formation contributed to high PM levels during the episodes at this site. Based on distinct meteorological conditions, episodes were categorized into three types: liquid water content (LWC), solar irradiance (IR), and long-range transport (LRT). Despite the difference in meteorological conditions, all episodes were characterized by a high fraction of sulfate (45-56 %) and organics (23-34 %). However, aerosols in LWC episodes were less aged, consisting of the lowest fraction of secondary organic aerosol (SOA) and the highest fraction of small particles. Large particles mixed internally while freshly formed small particles mixed externally in LWC episodes. Aerosols in LRT episodes, by contrast, were the most aged and consisted of the highest proportion of low-volatility oxygenated organic aerosol (LVOOA) and the lowest proportion of small particles. Both small and large particles mixed externally in LRT episodes. The highest proportion of semi-volatile oxygenated organic aerosol (SVOOA) and a medium proportion of small particles were observed in IR episodes. Both small and large particles were likely externally mixed during IR episodes. Furthermore, aerosols experienced the most dramatic size increase and diurnal variation, with a time lag between SVOOA and LVOOA and a gradual increase in carbon oxidation state (OSc ≈ 2 × O : C - H : C). Five out of 10 episodes were of the IR type, further reflecting the importance of this type of episode. The evolution of aerosol components in one particular episode of the IR type, which exhibited a clear land-sea breeze pattern, was examined in detail. Sulfate and SOA due to photochemical aging

  2. Analysis of Site Formation and Assemblage Integrity Does Not Support Attribution of the Uluzzian to Modern Humans at Grotta del Cavallo.

    PubMed

    Zilhão, João; Banks, William E; d'Errico, Francesco; Gioia, Patrizia

    2015-01-01

    Based on the morphology of two deciduous molars and radiocarbon ages from layers D and E of the Grotta del Cavallo (Lecce, Italy), assigned to the Uluzzian, it has been proposed that modern humans were the makers of this Early Upper Paleolithic culture and that this finding considerably weakens the case for an independent emergence of symbolism among western European Neandertals. Reappraisal of the new dating evidence, of the finds curated in the Taranto Antiquities depot, and of coeval publications detailing the site's 1963-66 excavations shows that (a) Protoaurignacian, Aurignacian and Early Epigravettian lithics exist in the assemblages from layers D and E, (b) even though it contains both inherited and intrusive items, the formation of layer D began during Protoaurignacian times, and (c) the composition of the extant Cavallo assemblages is influenced in a non-negligible manner by the post-hoc assignment of items to stratigraphic units distinct from that of original discovery. In addition, a major disturbance feature affected the 1960s excavation trench down to Mousterian layer F, this feature went unrecognized until 1964, the human remains assigned to the Uluzzian were discovered that year and/or the previous year, and there are contradictions between field reports and the primary anthropological description of the remains as to their morphology and level of provenience. Given these major contextual uncertainties, the Cavallo teeth cannot be used to establish the authorship of the Uluzzian. Since this technocomplex's start date is ca. 45,000 calendar years ago, a number of Neandertal fossils are dated to this period, and the oldest diagnostic European modern human fossil is the <41,400 year-old Oase 1 mandible, Neandertal authorship of the Uluzzian remains the parsimonious reading of the evidence.

  3. Observation of new particle formation and measurement of sulfuric acid, ammonia, amines and highly oxidized organic molecules at a rural site in central Germany

    NASA Astrophysics Data System (ADS)

    Kürten, Andreas; Bergen, Anton; Heinritzi, Martin; Leiminger, Markus; Lorenz, Verena; Piel, Felix; Simon, Mario; Sitals, Robert; Wagner, Andrea C.; Curtius, Joachim

    2016-10-01

    The exact mechanisms for new particle formation (NPF) under different boundary layer conditions are not known yet. One important question is whether amines and sulfuric acid lead to efficient NPF in the atmosphere. Furthermore, it is not clear to what extent highly oxidized organic molecules (HOMs) are involved in NPF. We conducted field measurements at a rural site in central Germany in the proximity of three larger dairy farms to investigate whether there is a connection between NPF and the presence of amines and/or ammonia due to the local emissions from the farms. Comprehensive measurements using a nitrate chemical ionization-atmospheric pressure interface time-of-flight (CI-APi-TOF) mass spectrometer, a proton-transfer-reaction mass spectrometer (PTR-MS), particle counters and differential mobility analyzers (DMAs), as well as measurements of trace gases and meteorological parameters, were performed. We demonstrate here that the nitrate CI-APi-TOF is suitable for sensitive measurements of sulfuric acid, amines, a nitrosamine, ammonia, iodic acid and HOMs. NPF was found to correlate with sulfuric acid, while an anti-correlation with RH, amines and ammonia is observed. The anti-correlation between NPF and amines could be due to the efficient uptake of these compounds by nucleating clusters and small particles. Much higher HOM dimer (C19/C20 compounds) concentrations during the night than during the day indicate that these HOMs do not efficiently self-nucleate as no nighttime NPF is observed. Observed iodic acid probably originates from an iodine-containing reservoir substance, but the iodine signals are very likely too low to have a significant effect on NPF.

  4. GOLPH3 Is Essential for Contractile Ring Formation and Rab11 Localization to the Cleavage Site during Cytokinesis in Drosophila melanogaster

    PubMed Central

    Sechi, Stefano; Frappaolo, Anna; Raffa, Grazia D.; Fuller, Margaret T.; Giansanti, Maria Grazia

    2014-01-01

    The highly conserved Golgi phosphoprotein 3 (GOLPH3) protein has been described as a Phosphatidylinositol 4-phosphate [PI(4)P] effector at the Golgi. GOLPH3 is also known as a potent oncogene, commonly amplified in several human tumors. However, the molecular pathways through which the oncoprotein GOLPH3 acts in malignant transformation are largely unknown. GOLPH3 has never been involved in cytokinesis. Here, we characterize the Drosophila melanogaster homologue of human GOLPH3 during cell division. We show that GOLPH3 accumulates at the cleavage furrow and is required for successful cytokinesis in Drosophila spermatocytes and larval neuroblasts. In premeiotic spermatocytes GOLPH3 protein is required for maintaining the organization of Golgi stacks. In dividing spermatocytes GOLPH3 is essential for both contractile ring and central spindle formation during cytokinesis. Wild type function of GOLPH3 enables maintenance of centralspindlin and Rho1 at cell equator and stabilization of Myosin II and Septin rings. We demonstrate that the molecular mechanism underlying GOLPH3 function in cytokinesis is strictly dependent on the ability of this protein to interact with PI(4)P. Mutations that abolish PI(4)P binding impair recruitment of GOLPH3 to both the Golgi and the cleavage furrow. Moreover telophase cells from mutants with defective GOLPH3-PI(4)P interaction fail to accumulate PI(4)P-and Rab11-associated secretory organelles at the cleavage site. Finally, we show that GOLPH3 protein interacts with components of both cytokinesis and membrane trafficking machineries in Drosophila cells. Based on these results we propose that GOLPH3 acts as a key molecule to coordinate phosphoinositide signaling with actomyosin dynamics and vesicle trafficking during cytokinesis. Because cytokinesis failures have been associated with premalignant disease and cancer, our studies suggest novel insight into molecular circuits involving the oncogene GOLPH3 in cytokinesis. PMID:24786584

  5. Pleistocene fossil woods from the Okote Member, site FwJj 14 in the Ileret region, Koobi Fora Formation, northern Kenya.

    PubMed

    Bamford, Marion K

    2017-09-04

    On the eastern side of Lake Turkana in northern Kenya are extensive Plio-Pleistocene deposits containing a rich diversity of fossil mammals, hominins and flora within the radiometrically dated tuffaceous, lacustrine and fluvial sequence. Reconstruction of this landscape and paleoenvironment are part of an ongoing multinational and multidisciplinary human evolution project in the eastern Turkana Basin. Today there is a huge lake in the Rift Valley but it has fluctuated since the early Pliocene. Silicified wood is fairly common in some areas of the Koobi Fora Formation. One such site is FwJj 14E, alongside one of the tributaries of the Ileret River. Hominin hand and arm bones have been excavated from here in the Okote Member and dated at 1.56-1.36 Ma. The fossils are associated with hominin and bovid footprints. Sixty of the over 100 wood specimens collected have been sectioned and studied. In general the woods have large vessels and an average vulnerability index of 40, which implies a mesic megathermal environment with no water stress. Taxonomically the woods belong to large African families: Caesalpiniaceae (Didelotia idae), Combretaceae (Anogeissus sp.), Putranjivaceae (Euphorbiaceae; Drypetes sp.), Lamiaceae (cf Premna sp.), Malvaceae (Heritiera sp.) and Sapindaceae (Sapindoxylon sp.). Most of these taxa do not occur in the area today because now it is much drier and the local vegetation is predominantly Acacia-Commiphora-Salvadora shrubland. The reconstruction of the paleovegetation supports the interpretation from the fauna, namely, a tall riverine forest with shady refuge trees, possibly some edible fruits, and wooded grassland and more open bushland in the vicinity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Seasonal variation of atmospheric particle number concentrations, new particle formation and atmospheric oxidation capacity at the high Arctic site Villum Research Station, Station Nord

    NASA Astrophysics Data System (ADS)

    Nguyen, Quynh T.; Glasius, Marianne; Sørensen, Lise L.; Jensen, Bjarne; Skov, Henrik; Birmili, Wolfram; Wiedensohler, Alfred; Kristensson, Adam; Nøjgaard, Jacob K.; Massling, Andreas

    2016-09-01

    This work presents an analysis of the physical properties of sub-micrometer aerosol particles measured at the high Arctic site Villum Research Station, Station Nord (VRS), northeast Greenland, between July 2010 and February 2013. The study focuses on particle number concentrations, particle number size distributions and the occurrence of new particle formation (NPF) events and their seasonality in the high Arctic, where observations and characterization of such aerosol particle properties and corresponding events are rare and understanding of related processes is lacking.A clear accumulation mode was observed during the darker months from October until mid-May, which became considerably more pronounced during the prominent Arctic haze months from March to mid-May. In contrast, nucleation- and Aitken-mode particles were predominantly observed during the summer months. Analysis of wind direction and wind speed indicated possible contributions of marine sources from the easterly side of the station to the observed summertime particle number concentrations, while southwesterly to westerly winds dominated during the darker months. NPF events lasting from hours to days were mostly observed from June until August, with fewer events observed during the months with less sunlight, i.e., March, April, September and October. The results tend to indicate that ozone (O3) might be weakly anti-correlated with particle number concentrations of the nucleation-mode range (10-30 nm) in almost half of the NPF events, while no positive correlation was observed. Calculations of air mass back trajectories using the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model for the NPF event days suggested that the onset or interruption of events could possibly be explained by changes in air mass origin. A map of event occurrence probability was computed, indicating that southerly air masses from over the Greenland Sea were more likely linked to those events.

  7. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    implantation can be evaluated as a function of Cs coverage. The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

  8. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    implantation can be evaluated as a function of Cs coverage.The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

  9. [Effects of blocking two sites of transforming growth factor-β/Smads signaling on the formation of scar-related proteins in human skin fibroblasts].

    PubMed

    Wang, Yang; Zhang, Liangping; Lei, Rui; Shen, Yichen; Shen, Hui; Wu, Zhinan; Xu, Jinghong

    2015-10-01

    To explore the effects of blocking two sites of TGF-β/Smads signaling on the formation of scar-related proteins in human skin fibroblasts. Two lentivirus vectors encoding soluble TGF-β receptor II (sTβRII) and mutant Smad 4-Smad 4ΔM4 were respectively transfected into human skin fibroblast cell line human foreskin fibroblast 1 (HFF-1) cells with the optimum multiplicity of infection (MOI) of 50. The protein expressions of sTβRII and Smad 4ΔM4 of the two types of transfected cells were determined by Western blotting so as to compare with those of the untransfected cells. The HFF-1 cells were divided into 6 groups as named below according to the random number table, with 6 dishes in each group, 1×10(4) cells per dish. Co-transfection group, transfected with the two previous lentivirus vectors, mixed with the ratio of 1:1 and MOI of 50, and then stimulated with 5 ng/mL TGF-β1 for 72 h; sTβRII group, transfected with lenti-sTβRII with MOI of 50, with the other treatment as above; Smad 4ΔM4 group, transfected with lenti-Smad 4ΔM4 with MOI of 50, with the other treatment as above; negative virus group, transfected with empty lentivirus vector, with the other treatment as above; positive control group, stimulated with 5 ng/mL TGF-β1 for 72 h; and blank control group, conventionally cultured without any other treatment. After stimulation, Western blotting and real-time fluorescent quantitative RT-PCR were respectively used to determine the protein and mRNA expressions of fibronectin in cells of each group. ELISA and Sircol collagen assay were respectively used to determine the protein expressions of connective tissue growth factor (CTGF) and total collagen in the cell culture supernate of each group. Data were processed with one-way analysis of variance and SNK-(q test). (1) HFF-1 cells transfected with lenti-sTβRII and HFF-1 cells transfected with lenti-Smad 4ΔM4 respectively expressed higher levels of sTβRII protein and Smad 4ΔM4 protein compared with

  10. Composition and origin of the Apennine Bench Formation. [pre-mare light plains unit along some Imbrium basin margins near Apollo 15 landing site

    NASA Technical Reports Server (NTRS)

    Spudis, P. D.

    1978-01-01

    Integration of stratigraphic relationships, geologic setting, surface morphology and remote sensing data suggest that the Apennine Bench Formation is composed of post-Imbrium basin volcanic KREEP basalt flows. This KREEP volcanism occurred shortly after the time of Imbrium basin formation and may have been triggered by the large basin impact which could have provided the structural 'plumbing' through which magma could reach the surface. There are indications that the Apennine Bench Formation may represent the largest surface exposure of highland (nonmare) volcanism preserved on the lunar surface and, as such, provides valuable insight into early lunar crustal processes.

  11. Natural heterogeneity and evolving geochemistry of Lower Tuscaloosa Formation brine in response to continuing CO2 injection at Cranfield EOR site, Mississippi, USA

    NASA Astrophysics Data System (ADS)

    Thordsen, J. J.; Kharaka, Y. K.; Thomas, B.; Abedini, A. A.; Conaway, C. H.; Manning, M. A.; Lu, J.

    2012-12-01

    Geochemical monitoring of Lower Tuscaloosa Formation (LTF) brine continues at the Cranfield CO2-enhanced oil recovery (EOR) and sequestration site to investigate the potential for the geologic storage of large volumes of CO2 in saline aquifers and depleted reservoirs. Cranfield oil field is a domal depleted oil and gas reservoir in the Mississippi Interior Salt Basin, with production in heterogeneous fluvial sandstones of the LTF (depth ~3000 m). CO2 flood began in July 2008. Brine samples were collected from selected production wells in March and December 2009, April 2010, and November 2011. Intensive sampling also was conducted for the first 18 days of a CO2 injection experiment below the oil-water contact (December 2009) at the Detailed Area of Study (DAS) 3-well array. The sampling objectives are to define the geochemical composition of the pre-injection brine, and to understand the geochemical changes resulting from interactions between the injected CO2, brine, and reservoir minerals. Results show that Tuscaloosa brine is Na-Ca-Cl type with total salinity ranging from ~140 to 160 g/L TDS (50 samples). Relatively large variations are observed in major divalent cations (Ca ~7,500-14,000 mg/L, Mg ~800-1,250 mg/L, Sr ~475-750 mg/L). Significant positive correlations are noted amongst Ca, Mg, Sr, Ba, and Br, whereas these solutes all trend negatively with Na and Cl. These results may be interpreted as possible binary mixing between two end-member waters: (1) high Na-Cl (51 and 97 g/L, respectively), low Ca, Mg, Sr, and Br (~7500, 800, 475, 280 mg/L, respectively); and (2) low Na-Cl (40 and 86 g/L), high Ca, Mg, Sr, and Br (~14,000, 1250, 750, 480 mg/L). This apparent binary mixing has no obvious correlation to CO2 injection, which suggests that observed variations are due to natural heterogeneities in LTF brine within the Cranfield dome. The variations may indicate vertical and/or lateral proximity to a halite source (i.e. salt dome), with the high Na-Cl, low Br

  12. Potential function of added minerals as nucleation sites and effect of humic substances on mineral formation by the nitrate-reducing Fe(II)-oxidizer Acidovorax sp. BoFeN1.

    PubMed

    Dippon, Urs; Pantke, Claudia; Porsch, Katharina; Larese-Casanova, Phil; Kappler, Andreas

    2012-06-19

    The mobility of toxic metals and the transformation of organic pollutants in the environment are influenced and in many cases even controlled by iron minerals. Therefore knowing the factors influencing iron mineral formation and transformation by Fe(II)-oxidizing and Fe(III)-reducing bacteria is crucial for understanding the fate of contaminants and for the development of remediation technologies. In this study we followed mineral formation by the nitrate-reducing Fe(II)-oxidizing strain Acidovorax sp. BoFeN1 in the presence of the crystalline Fe(III) (oxyhydr)oxides goethite, magnetite and hematite added as potential nucleation sites. Mössbauer spectroscopy analysis of minerals precipitated by BoFeN1 in (57)Fe(II)-spiked microbial growth medium showed that goethite was formed in the absence of mineral additions as well as in the presence of goethite or hematite. The presence of magnetite minerals during Fe(II) oxidation induced the formation of magnetite in addition to goethite, while the addition of humic substances along with magnetite also led to goethite but no magnetite. This study showed that mineral formation not only depends on the aqueous geochemical conditions but can also be affected by the presence of mineral nucleation sites that initiate precipitation of the same underlying mineral phases.

  13. Breakpoint sites disclose the role of the V(D)J recombination machinery in the formation of T-cell receptor (TCR) and non-TCR associated aberrations in T-cell acute lymphoblastic leukemia.

    PubMed

    Larmonie, Nicole S D; Dik, Willem A; Meijerink, Jules P P; Homminga, Irene; van Dongen, Jacques J M; Langerak, Anton W

    2013-08-01

    Aberrant recombination between T-cell receptor genes and oncogenes gives rise to chromosomal translocations that are genetic hallmarks in several subsets of human T-cell acute lymphoblastic leukemias. The V(D)J recombination machinery has been shown to play a role in the formation of these T-cell receptor translocations. Other, non-T-cell receptor chromosomal aberrations, such as SIL-TAL1 deletions, have likewise been recognized as V(D)J recombination associated aberrations. Despite the postulated role of V(D)J recombination, the extent of the V(D)J recombination machinery involvement in the formation of T-cell receptor and non-T-cell receptor aberrations in T-cell acute lymphoblastic leukemia is still poorly understood. We performed a comprehensive in silico and ex vivo evaluation of 117 breakpoint sites from 22 different T-cell receptor translocation partners as well as 118 breakpoint sites from non-T-cell receptor chromosomal aberrations. Based on this extensive set of breakpoint data, we provide a comprehensive overview of T-cell receptor and oncogene involvement in T-ALL. Moreover, we assessed the role of the V(D)J recombination machinery in the formation of chromosomal aberrations, and propose an up-dated mechanistic classification on how the V(D)J recombination machinery contributes to the formation of T-cell receptor and non-T-cell receptor aberrations in human T-cell acute lymphoblastic leukemia.

  14. Instrumentation used for hydraulic testing of potential water-bearing formations at the Waste Isolation Pilot Plant site in southeastern New Mexico

    USGS Publications Warehouse

    Basler, J.A.

    1983-01-01

    Requirements for testing hydrologic test wells at the proposed Waste Isolation Pilot Plant near Carlsbad, New Mexico, necessitated the use of inflatable formation packers and pressure transducers. Observations during drilling and initial development indicated small formation yields which would require considerable test times by conventional open-casing methods. A pressure-monitoring system was assembled for performance evaluation utilizing commercially available components. Formation pressures were monitored with a down-hole strain-gage transducer. An inflatable packer equipped with a 1/4-inch-diameter steel tube extending through the inflation element permitted sensing formation pressures in isolated test zones. Surface components of the monitoring system provided AC transducer excitation, signal conditioning for recording directly in engineering units, and both analog and digital recording. Continuous surface monitoring of formation pressures provided a means of determining test status and projecting completion times during any phase of testing. Maximum portability was afforded by battery operation with all surface components mounted in a small self-contained trailer. (USGS)

  15. The Drosophila GAGA factor is required for dosage compensation in males and for the formation of the male-specific-lethal complex chromatin entry site at 12DE.

    PubMed Central

    Greenberg, Anthony J; Yanowitz, Judith L; Schedl, Paul

    2004-01-01

    Drosophila melanogaster males have one X chromosome, while females have two. To compensate for the resulting disparity in X-linked gene expression between the two sexes, most genes from the male X chromosome are hyperactivated by a special dosage compensation system. Dosage compensation is achieved by a complex of at least six proteins and two noncoding RNAs that specifically associate with the male X. A central question is how the X chromosome is recognized. According to a current model, complexes initially assemble at approximately 35 chromatin entry sites on the X and then spread bidirectionally along the chromosome where they occupy hundreds of sites. Here, we report that mutations in Trithorax-like (Trl) lead to the loss of a single chromatin entry site on the X, male lethality, and mislocalization of dosage compensation complexes. PMID:15020425

  16. Carbon, oxygen and strontium isotopic constraints on fluid sources, temperatures and biogeochemical processes during the formation of seep carbonates - Secchia River site, Northern Apennines

    NASA Astrophysics Data System (ADS)

    Viola, Irene; Capozzi, Rossella; Bernasconi, Stefano M.; Rickli, Jörg

    2017-07-01

    Understanding authigenic seep carbonate formation provides clues for hydrocarbon exploration and insights into contributions to gas budgets of marine environments and the atmosphere. Seep carbonates discovered in the outcropping succession along the Secchia riverbanks (near Modena, Italy) belong to the Argille Azzurre Formation of Early Pleistocene age deposited in an upper shelf environment overlying the Miocene foredeep successions, which include hydrocarbon fields. The fluid migration from the hydrocarbon fields, up to the surface, is presently active on land and started in the marine succession during the Late Miocene. Authigenic globular carbonate concretions and carbonate chimneys are interspersed along the strata throughout the section. A comprehensive geochemical characterisation of the carbonates has been carried out to understand the processes leading to their formation. The carbonate concretions are the record of past hydrocarbon vents linked to the Miocene petroleum system of the Northern Apennines. The samples are composed of > 50% microcrystalline dolomite. The δ13C signatures identify two groups in the samples according to different type of formation processes. Globular concretions have positive values that suggest an influence of CO2 associated to secondary methanogenesis due to microbial degradation of higher hydrocarbons. The analysed chimney, with negative δ13C values, is interpreted as former conduit where carbonate precipitation is promoted by Anaerobic Oxidation of Methane coupled with Sulfate Reduction. The δ18O range, coupled with 87/86Sr signatures, indicate that the contribution of deep connate water from the Miocene reservoirs is up to 23% during the formation of the globular concretions. The connate water occurrence is also documented by higher ambient temperatures. The different isotope signatures in seep carbonates result from the relative contribution of the recognised gas and water components, linked to different plumbing systems

  17. Grain-size and grain-shape analyses using digital imaging technology: Application to the fluvial formation of the Ngandong paleoanthropological site in Central Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Sipola, Maija

    2013-04-01

    This study implements grain-size and grain-shape analyses to better understand the fluvial processes responsible for forming the Ngandong paleoanthropological site along the Solo River in Central Java. The site was first discovered and excavated by the Dutch Geological Survey in the early 1930's, during which fourteen Homo erectus fossils and thousands of other macrofaunal remains were uncovered. The Homo erectus fossils discovered at Ngandong are particularly interesting to paleoanthropologists because the morphology of the excavated crania suggests they are from a recently-living variety of the species. The primary scientific focus for many years has been to determine the absolute age of the Ngandong fossils, while the question of exactly how the Ngandong site itself formed has been frequently overlooked. In this study I use Retsch CAMSIZER digital imaging technology to conduct grain-size and grain-shape analyses of sediments from the terrace stratigraphy at the Ngandong site to understand if there are significant differences between sedimentary layers in grain-size and/or grain-shape, and what these differences mean in terms of local paleoflow dynamics over time. Preliminary analyses indicate there are four distinct sedimentary layers present at Ngandong with regard to size sorting, with the fossil-bearing layers proving to be the most poorly-sorted and most similar to debris-flow deposits. These results support hypotheses by geoarchaeologists that the fossil-bearing layers present at Ngandong were deposited during special flow events rather than under normal stream flow conditions.

  18. Structural characterization of human vimentin rod 1 and the sequencing of assembly steps in intermediate filament formation in vitro using site-directed spin labeling and electron paramagnetic resonance.

    PubMed

    Hess, John F; Budamagunta, Madhu S; Voss, John C; FitzGerald, Paul G

    2004-10-22

    We have previously established the utility of site-directed spin labeling and electron paramagnetic resonance to determine structural relationships among proteins in intact intermediate filaments. Using this same approach we have introduced spin labels at 21 residues between amino acids 169 and 193 in rod domain 1 of human vimentin. The electron paramagnetic resonance spectra provide direct evidence for the coiled coil nature of the vimentin dimer in this region. This finding is consistent with predictions but has never been demonstrated previously. In a previous study we identified residue 348 in the rod domain 2 as one point of overlap between adjacent dimers in intact filaments. In the present study we defined residue 191 in the rod domain 1 as a second point of overlap and established that the dimers are arranged in an anti-parallel and staggered orientation at this site. Finally, by isolating spin-labeled samples at successive stages during the dialysis that lead to filament assembly in vitro, we have been able to establish a sequence of interactions that occurs during in vitro assembly, starting with the alpha helix and loose coiled coil dimer formation, then the formation of tetrameric species centered on residue 191, followed by interactions centered on residue 348 suggestive of octamer or higher order multimer formation. A continuation of this strategy revealed that both 191-191 and 348-348 interactions are present in low ionic strength Tris buffers when vimentin is maintained at the "protofilament" stage of assembly.

  19. Spp1, a member of the Set1 Complex, promotes meiotic DSB formation in promoters by tethering histone H3K4 methylation sites to chromosome axes.

    PubMed

    Sommermeyer, Vérane; Béneut, Claire; Chaplais, Emmanuel; Serrentino, Maria Elisabetta; Borde, Valérie

    2013-01-10

    Meiotic chromosomes are organized into arrays of loops that are anchored to the chromosome axis structure. Programmed DNA double-strand breaks (DSBs) that initiate meiotic recombination, catalyzed by Spo11 and accessory DSB proteins, form in loop sequences in promoters, whereas the DSB proteins are located on chromosome axes. Mechanisms bridging these two chromosomal regions for DSB formation have remained elusive. Here we show that Spp1, a conserved member of the histone H3K4 methyltransferase Set1 complex, is required for normal levels of DSB formation and is associated with chromosome axes during meiosis, where it physically interacts with the Mer2 DSB protein. The PHD finger module of Spp1, which reads H3K4 methylation close to promoters, promotes DSB formation by tethering these regions to chromosome axes and activating cleavage by the DSB proteins. This paper provides the molecular mechanism linking DSB sequences to chromosome axes and explains why H3K4 methylation is important for meiotic recombination.

  20. ALMA OBSERVATIONS OF A HIGH-DENSITY CORE IN TAURUS: DYNAMICAL GAS INTERACTION AT THE POSSIBLE SITE OF A MULTIPLE STAR FORMATION

    SciTech Connect

    Tokuda, Kazuki; Onishi, Toshikazu; Saigo, Kazuya; Kawamura, Akiko; Fukui, Yasuo; Inutsuka, Shu-ichiro; Tachihara, Kengo; Matsumoto, Tomoaki; Machida, Masahiro N.; Tomida, Kengo

    2014-07-01

    Starless dense cores eventually collapse dynamically, forming protostars inside them, and the physical properties of the cores determine the nature of the forming protostars. We report ALMA observations of dust continuum emission and molecular rotational lines toward MC27 or L1521F, which is considered to be very close to the first protostellar core phase. We found a few starless high-density cores, one of which has a very high density of ∼10{sup 7} cm{sup –3}, within a region of several hundred AU around a very low-luminosity protostar detected by Spitzer. A very compact bipolar outflow with a dynamical timescale of a few hundred years was found toward the protostar. The molecular line observation shows several cores with an arc-like structure, possibly due to the dynamical gas interaction. These complex structures revealed in the present observations suggest that the initial condition of star formation is highly dynamical in nature, which is considered to be a key factor in understanding fundamental issues of star formation such as the formation of multiple stars and the origin of the initial mass function of stars.

  1. Local thrombus formation in the site of intravenous injection of chlorpromazine: possible colloid-osmotic lysis of the local endothelial cells.

    PubMed

    Yabuki, M; Tani, N; Yoshioka, T; Nishibe, H; Kanamaru, H; Kaneko, H

    2000-08-01

    Since amphiphilic drugs are known to interact with biomembranes, we investigated local vessel damage and thrombosis which might be brought about by intravenous dosing using chlorpromazine (CPZ) as a representative compound. CPZ-induced hemolysis was suppressed by an increase in sucrose concentration in the medium, characterizing this hemolysis to be colloid-osmotic lysis, which includes the enhancement of membrane phospholipid fluidity and consequent small pore formation in the membranes. This was supported by the observation that hemolysis by filipin, not featuring the stage of small pore formation, was not affected by sucrose. [14C]Glucose-entrapping liposomes were degraded by CPZ, and this degradation was enhanced by an increase in the intravesicle glucose concentration. These results indicated that the compound could induce colloid-osmotic lysis in erythrocytes and artificial membrane vesicles. CPZ also injured cultured porcine aortic endothelial cells (PAEC), as evidenced by lactate dehydrogenase (LDH) leakage. This injury was also suppressed by increase in sucrose concentration in the medium, suggesting that colloid-osmotic lysis again occurred. When rats were intravenously injected with CPZ, local endothelial cell (EC) injury and associated thrombus formation were observed, suggesting that CPZ's action was also evident in vivo. To our knowledge, this is the first finding which suggests that an intravenously dosed amphiphilic drug can injure local ECs based on a colloid-osmotic lysis mechanism leading to thrombosis.

  2. Preliminary Safety Analysis of the Gorleben Site: Thermo-mechanical Analysis of the Integrity of the Geological Barrier in the Gorleben Salt Formation - 13307

    SciTech Connect

    Eickemeier, R.; Heusermann, S.; Nipp, H.K.; Knauth, M.; Minkley, W.; Popp, T.

    2013-07-01

    Exploration work at the Gorleben salt dome has been carried out since 1977 to investigate the site regarding its suitability as a final repository for high-level radioactive wastes. In the framework of the 'Preliminary Safety Analysis of the Gorleben Site' a comprehensive assessment is being performed with focus on long-term safety. Because the integrity of the geological barrier is crucial for protection from damage caused by ionising radiation during the post-operational phase, 2D and 3D thermo-mechanical calculations for a reference section through the salt dome were carried out, all looking at two different waste emplacement concepts: emplacement in drifts and in boreholes. The calculated stresses are the basis for evaluating the barrier integrity on the basis of the dilatancy criterion and the fluid pressure criterion. (authors)

  3. Bcl-xL overexpression blocks bax-mediated mitochondrial contact site formation and apoptosis in rod photoreceptors of lead-exposed mice

    NASA Astrophysics Data System (ADS)

    He, Lihua; Perkins, Guy A.; Poblenz, Ann T.; Harris, Jeffrey B.; Hung, Michael; Ellisman, Mark H.; Fox, Donald A.

    2003-02-01

    Photoreceptor apoptosis and resultant visual deficits occur in humans and animals with inherited and disease-, injury-, and chemical-induced retinal degeneration. A clinically relevant mouse model of progressive rod photoreceptor-selective apoptosis was produced by low-level developmental lead exposure and studied in combination with transgenic mice overexpressing Bcl-xL only in the photoreceptors. A multiparametric analysis of rod apoptosis and mitochondrial structure-function was performed. Mitochondrial cristae topography and connectivity, matrix volume, and contact sites were examined by using 3D electron tomography. Lead-induced rod-selective apoptosis was accompanied by rod Ca2+ overload, rhodopsin loss, translocation of Bax from the cytosol to the mitochondria, decreased rod mitochondrial respiration and membrane potential, mitochondrial cytochrome c release, caspase-3 activation, and an increase in the number of mitochondrial contact sites. These effects occurred without mitochondrial matrix swelling, outer membrane rupture, caspase-8 activation, or Bid cleavage. Bcl-xL overexpression completely blocked all apoptotic events, except Ca2+ overload, and maintained normal rod mitochondrial function throughout adulthood. This study presents images of mitochondrial contact sites in an in vivo apoptosis model and shows that Bcl-xL overexpression blocks increased contact sites and apoptosis. These findings extend our in vitro retinal studies with Pb2+ and Ca2+ and suggest that developmental lead exposure produced rod-selective apoptosis without mitochondrial swelling by translocating cytosolic Bax to the mitochondria, which likely sensitized the Pb2+ and Ca2+ overloaded rod mitochondria to release cytochrome c. These results have relevance for therapies in a wide variety of progressive retinal and neuronal degenerations where Ca2+ overload, lead exposure, and/or mitochondrial dysfunction occur.

  4. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

    PubMed

    Walsh, M A; Otwinowski, Z; Perrakis, A; Anderson, P M; Joachimiak, A

    2000-05-15

    Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

  5. Water-Level Reconstruction and its Implications for Late Pleistocene Paleontological Site Formation in Hoyo Negro, a Submerged Subterranean Pit in Quintana Roo, Mexico

    NASA Astrophysics Data System (ADS)

    Rissolo, D.; Reinhardt, E. G.; Collins, S.; Kovacs, S. E.; Beddows, P. A.; Chatters, J. C.; Nava Blank, A.; Luna Erreguerena, P.

    2014-12-01

    A massive pit deep within the now submerged cave system of Sac Actun, located along the central east coast of the Yucatan Peninsula, contains a diverse fossil assemblage of extinct megafauna as well as a nearly complete human skeleton. The inundated site of Hoyo Negro presents a unique and promising opportunity for interdisciplinary Paleoamerican and paleoenvironmental research in the region. Investigations have thus far revealed a range of associated features and deposits which make possible a multi-proxy approach to identifying and reconstructing the natural and cultural processes that have formed and transformed the site over millennia. Understanding water-level fluctuations (both related to, and independent from, eustatic sea level changes), with respect to cave morphology is central to understanding the movement of humans and animals into and through the cave system. Recent and ongoing studies involve absolute dating of human, faunal, macrobotanical, and geological samples; taphonomic analyses; and a characterization of site hydrogeology and sedimentological facies, including microfossil assemblages and calcite raft deposits.

  6. Programming for SITE.

    ERIC Educational Resources Information Center

    Mody, Bella

    1979-01-01

    Describes the Satellite Instructional Television Experiment (SITE) project in India during 1975-76, including programing patterns, formats, and audiences. Demonstrates that countries like India have the technical and managerial capability to design, operate, and maintain advanced communication technology. (JMF)

  7. Programming for SITE.

    ERIC Educational Resources Information Center

    Mody, Bella

    1979-01-01

    Describes the Satellite Instructional Television Experiment (SITE) project in India during 1975-76, including programing patterns, formats, and audiences. Demonstrates that countries like India have the technical and managerial capability to design, operate, and maintain advanced communication technology. (JMF)

  8. Ketoconazole inhibition of the bifunctional cytochrome P450c17 does not affect androgen formation from the endogenous lyase substrate. The catalytic site remains refractory in the course of intermediary hydroxyprogesterone processing.

    PubMed

    Kühn-Velten, W N; Lessmann, M

    1992-12-15

    The inhibition of the bifunctional steroidogenic cytochrome P450c17 (CYP17: steroid-17 alpha-hydroxylase/steroid-17,20-lyase) by the imidazole-type fungicide, [(+/-)-cis-1-acetyl-4-[4-[[2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl- methyl)-1,3-dioxolan-4-yl]methoxy]phenyl]piperazine) (ketoconazole), was investigated with the aim of differentiating between effects on androgen formation from exogenously added and endogenously produced 17 alpha-hydroxyprogesterone. Using microsomal membranes from rat testis, turnover of progesterone by P450c17 was competitively inhibited by ketoconazole with KI = 0.40 microM. Ketoconazole did not affect the linear relationship between the ratio of productive events (corresponding to androgen formation rates) versus abortive events (corresponding to 17 alpha-hydroxyprogesterone formation rates) and the sum of catalytic events. This was an indication that this inhibitor did not interfere with intermediate processing by P450c17. Androgen formation from exogenous but not from endogenous 17 alpha-hydroxyprogesterone was competitively inhibited by ketoconazole. The simultaneous conversion of 1 microM each of [3H]progesterone and 17 alpha-hydroxy[14C]progesterone was also reduced by ketoconazole. Calculation of 3H/14C ratios in the 17 alpha-hydroxyprogesterone and androgen fractions revealed that the endogenous 17 alpha-hydroxyprogesterone pool was metabolized to androgens at rates 6.4, 11.6, 17.6 and 21.2-fold faster than the exogenous pool in the presence of 0.5, 1, 2 and 4 microM ketoconazole, respectively; this value was only 4.0 in controls. It is concluded that ketoconazole inhibits turnover of steroid ligands only when they approach the P450c17 active site in a substrate-state and that inhibition of androgen formation from progesterone is due to inhibition of the first catalytic step only. A model is described in which the P450c17 active site is refractory towards ketoconazole when the intermediary steroid is retained and being

  9. Identification of critical amino acid residues of Saccharomyces cerevisiae carbamoyl-phosphate synthetase: definition of the ATP site involved in carboxy-phosphate formation.

    PubMed

    Zheng, W; Lim, A L; Powers-Lee, S G

    1997-08-15

    Carbamoyl-phosphate synthetases (CPSases) utilize two molecules of ATP at two homologous domains, B and C, with ATP(B) used to form the enzyme-bound intermediate carboxy-phosphate and ATP(C) used to phosphorylate the carbamate intermediate. To further define the role of one CPSase peptide suggested by affinity labeling studies to be near the ATP(B) site, we have carried out site-directed mutagenic analysis of peptide 234-242 of the Saccharomyces cerevisiae arginine-specific CPSase. Mutants E234A, E234D, E236A, E236D and E238A were unable to complement the CPSase-deficient yeast strain LPL26 whereas mutants Y237A, E238D, R241K, R241E and R241P supported LPL26 growth as well as wild-type CPSase. Kinetic analysis of E234A and Y237A indicated impaired utilization of ATP(B) but not of ATP(C). D242A, a temperature-sensitive mutant, retained no detectable activity when assayed in vitro. These findings, together with the affinity labeling data and primary sequence analysis, strongly suggest that the yeast CPSase peptide 234-242 is located at the ATP(B) site and that some of its residues are important for functioning of the enzyme. D242 appears to occupy a critical structural position and E234, E236 and E238 appear to be critical for function, with the spatial arrangement of the carboxyl side chain also critical for E234 and E236.

  10. Stratigraphic correlation of the Awahab and Tafelberg Formations, Etendeka Group, Namibia, and location of an eruptive site for flood basalt volcanism

    NASA Astrophysics Data System (ADS)

    Marsh, J. S.; Milner, S. C.

    2007-08-01

    Detailed field and geochemical investigations in the vicinity of the type section of the Tafelberg Formation of the early Cretaceous Etendeka Group, NW Namibia, have revealed the existence of a large eruptive vent in the lower part of the regional volcanic sequence produced by Strombolian and Vulcanian eruptions. The vent is filled with the thick, differentiated, ponded Kudu-Run olivine-rich basaltic flow, which has a distinctive low Zr/Y geochemical signature as well as a Tafelberg-type tabular basalt and the Nil Desperandum latite. Field evidence indicates that the Kudu-Run basalt and the latite were erupted from fissures located within the vent. Associated with the vent is an extensive pyroclastic apron extending from the vent edge and which is interbedded with the regional stratigraphy. Blocks of Precambrain basement lithologies occur within this deposit and indicate that the vent was excavated to a depth of at least 350 m below the palaeosurface at that time. The original Tafelberg Formation type section described by Erlank et al. [Erlank, A.J., Marsh, J.S., Duncan, A.R., Miller, R.McG., Hawkesworth, C.H., Betton, P.J., Rex, D.C. 1984. Geochemistry and petrogenesis of the Etendeka volcanic rocks from SWA/Namibia, 195-247. In: Erlank, A.J. (Ed.), Petrogenesis of Volcanic Rocks of the Karoo province. Special Publication of the Geological Society of South Africa, vol. 13, 395 p.] the Tafelberg Gully section, crosses from the lower part of the regional sequence into the intra-vent sequence and returns to the regional sequence higher up. In doing so it includes some of the localized intra-vent flows and excludes a number of flows which are part of the regional sequence in its lower part, thus rendering it inappropriate as a type section. A revised type section for the Tafelberg Formation is described by combining the upper part of the Tafelberg Gully section with a new section of 14 flows at the base of the regional sequence in the Tafelberg North (TBN) section

  11. Contributions of Selected Biogenic and Aromatic Compounds to the Formation of Tropospheric Secondary Organic Aerosol over Several Sites in the United States

    NASA Astrophysics Data System (ADS)

    Jaoui, M.; Kleindienst, T. E.; Lewandowski, M.; Offenberg, J. H.; Corse, E. W.; Gerald, T.; Edney, E.

    2009-12-01

    The National Exposure Research Laboratory of the U.S. Environmental Protection Agency recently undertook an integrated laboratory and field research effort to better understand the contribution of biogenic and aromatic hydrocarbons to the formation of submicron ambient secondary organic aerosol (SOA). In the laboratory, isoprene, α-pinene, β-caryophyllene, 1,3-butadiene, 2-methyl-3-buten-2-ol, benzene, and toluene were individually irradiated under a wide range of conditions in a photochemical reaction chamber in the presence of nitrogen oxide (NOx). These hydrocarbons are thought to contribute to ambient SOA formation. In field studies conducted in Research Triangle Park, NC; Duke Forest in Chapel Hill, NC; Atlanta, GA; Pensacola, FL; Birmingham and Centerville, AL; Riverside, CA; Detroit, MI; Northbrook, East St. Louis and Bondville, IL; and Cincinnati, OH, ambient PM2.5 samples were collected for various periods between 2003 and 2006. The SOA collected from these laboratory experiments and the ambient PM2.5 samples were analyzed for organic carbon (OC) concentration and for organic tracer compounds by GC-MS using BSTFA derivatization for their identification and quantification. An organic tracer-based method was developed for estimating ambient SOA concentrations from individual SOA precursors to allow an assessment of SOA model predictions with ambient data. The results show that several major reaction products detected in SOA formed in the laboratory photooxidations were among the major compounds detected in field samples, effectively connecting laboratory and field results. Using the tracer-based method, the contributions of isoprene and monoterpenes to SOA formation show strong seasonal dependencies. However, no clear seasonal variations were observed for sesquiterpenes and aromatic hydrocarbons. The contribution of 2-methyl-3-buten-2-ol to ambient SOA was found to be not only season dependent but also higher in locations dominated by conifers, which are

  12. Mauna Loa lava accumulation rates at the Hilo drill site: Formation of lava deltas during a period of declining overall volcanic growth

    USGS Publications Warehouse

    Lipman, P.W.; Moore, J.G.

    1996-01-01

    Accumulation rates for lava flows erupted from Mauna Loa, as sampled in the uppermost 280 m of the Hilo drill hole, vary widely for short time intervals (several thousand years), but overall are broadly similar to those documented elsewhere on this volcano since 100 ka. Thickness variations and accumulation rates for Mauna Loa lavas at the Hilo drill site have been strongly affected by local paleotopography, including funneling and ponding between Mauna Kea and Kilauea. In addition, gentle submerged slopes of Mauna Kea in Hilo Bay have permitted large shoreline displacements by Mauna Loa flows. Ages of eruptive intervals have been determined from published isotopic data and from eustatic sea level curves modified to include the isostatic subsidence of the island of Hawaii at 2.2-2.6 mm/yr. Prior to 10 ka, rates of Mauna Loa lava accumulation at the drill site varied from 0.6 to 4.3 mm/yr for dateable intervals, with an overall rate of 1.8 mm/yr. Major eruptive pulses at about 1.3 and 10 ka, each probably representing a single long-lived eruption based on lack of weathering between flow units, increase the overall accumulation rate to 2.4 mm/yr. The higher rate since 10 ka reflects construction of thick near-shoreline lava deltas as postglacial sea levels rose rapidly. Large lava deltas form only along coastal segments where initially subaerial slopes have been submerged by the combined effects of eustatic sea level rise, isostatic subsidence, or spreading of volcano flanks. Overall accumulation of 239 m of lava at the drill site since 100-120 ka closely balances submergence of the Hilo area, suggesting that processes of coastal lava deposition have been modulated by rise in sea level. The Hilo accumulation rate is slightly higher than average rates of 1-2 mm/yr determined elsewhere along the Mauna Loa coast, based on rates of shoreline coverage and dated sea cliff and fault scarp exposures. Low rates of coastal lava accumulation since 100 ka, near or below the rate

  13. Phototriggered formation and repair of DNA containing a site-specific single strand break of the type produced by ionizing radiation or AP lyase activity.

    PubMed

    Zhang, K; Taylor, J S

    2001-01-09

    DNA strand breaks are produced by a variety of agents and processes such as ionizing radiation, xenobiotics, oxidative metabolism, and enzymatic processing of DNA base damage. One of the major types of strand breaks produced by these processes is a single nucleotide gap terminating in 5'- and 3'-phosphates. Previously, we had developed a method for sequence-specifically producing such phosphate-terminated strand breaks in an oligodeoxynucleotide by way of two photochemically activated (caged) building blocks placed in tandem. We now report the design and synthesis of a single caged building block consisting of 1,3-(2-nitrophenyl)-1,3-propanediol, for producing phosphate-terminated strand breaks, and its use producing such a break at a specific site in a double-stranded circular DNA vector. To produce the site-specific break in a duplex vector, a primer containing the caged single strand break was extended opposite the single strand form of a circular DNA vector followed by enzymatic ligation and purification. The single strand break could then be formed in quantitative yield by irradiation of the vector with 365 nm light. In contrast to a previous study, it was found that the strand break can be repaired by Escherichia coli DNA polymerase I and E. coli DNA ligase alone, though less efficiently than in the presence of the 3'-phosphate processing enzyme E. coli endonuclease IV. Repair in the absence of endonuclease IV could be attributed to hydrolysis of the 3'-phosphate in the presence of dNTP and to a lesser extent to exonucleolytic removal of the 3'-phosphate-bearing terminal nucleotide by way of the 3' --> 5' exonuclease activity of polymerase I. This work demonstrates that specialized 3'-end processing enzymes such as endonuclease IV or exonuclease III are not absolutely required for repair of phosphate-terminated gaps. In addition to preparing single strand breaks, the caged building block described should also be useful for preparing double strand breaks and

  14. Formation of HArF in solid Ar revisited: are mobile vacancies involved in the matrix-site conversion at 30 K?

    PubMed

    Khriachtchev, Leonid; Lignell, Antti; Rasanen, Markku

    2004-02-15

    The HArF molecule can occupy in solid Ar thermally unstable and stable configurations, and their microscopic structure is not understood at the moment. We present additional experimental results on the formation of two HArF configurations and analyze them with emphasis on possible reactions of the unstable configuration with matrix vacancies to form the stable configuration. We conclude that the existing computational scenarios do not describe fully the present experimental data. In order to explain qualitatively the experimental results, two tentative models are discussed. The first model is based on local mobility of matrix vacancies produced during photolysis and the second model considers isomerization of the HArF at Arn supermolecule. More importantly, the present results constitute the experimental basis for future theoretical studies.

  15. Independence and interdependence in the nest-site choice by honeybee swarms: Agent-based models, analytical approaches and pattern formation.

    PubMed

    Galla, Tobias

    2010-01-07

    In a recent paper List, Elsholtz and Seeley (List et al., 2009) have devised an agent-based model of the nest-choice dynamics in swarms of honeybees, and have concluded that both interdependence and independence are needed for the bees to reach a consensus on the best nest site. We here present a simplified version of the model which can be treated analytically with the tools of statistical physics and which largely has the same features as the original dynamics. Based on our analytical approaches it is possible to characterize the co-ordination outcome exactly on the deterministic level, and to a good approximation if stochastic effects are taken into account, reducing the need for computer simulations on the agent-based level. In the second part of the paper we present a spatial extension, and show that transient non-trivial patterns emerge, before consensus is reached. Approaches in terms of Langevin equations for continuous field variables are discussed.

  16. Habitat change by the formation of alien Crassostrea-reefs in the Wadden Sea and its role as feeding sites for waterbirds

    NASA Astrophysics Data System (ADS)

    Markert, Alexandra; Esser, Wiebke; Frank, Dietrich; Wehrmann, Achim; Exo, Klaus-Michael

    2013-10-01

    Non-indigenous Pacific oysters (Crassostrea gigas) have been invading the central Wadden Sea since 1998, predominantly settling on intertidal blue mussel (Mytilus edulis) beds which are increasingly transformed into Crassostrea-reefs. Pacific oysters are strong ecosystem engineers and the habitat change is considered to be a threat for waterbirds losing important feeding sites in the intertidal of the Wadden Sea. This study has increased our understanding of the use of foraging habitats by birds according to changing food resources. During the spring and autumn migration period in 2007, we recorded bird densities at two reef types varying in Pacific oyster density and at the adjacent sand flat as a reference site. We also recorded feeding behaviour, choice of prey and assessed peck and intake rate of three target species: Eurasian oystercatcher Haematopus ostralegus, Eurasian curlew Numenius arquata and European herring gull Larus argentatus. To evaluate the use of the Crassostrea-reef in the central Wadden Sea, we compared bird densities of the target species at different intertidal feeding habitats in various regions and compared the biomass intake of Eurasian oystercatcher feeding on different prey species. We show that Eurasian oystercatcher and Eurasian curlew have adapted to the new situation and learned to exploit the food supply offered by Crassostrea-reefs. While foraging mainly on Pacific oysters, Eurasian oystercatchers attained sustainable intake rates even though food resource at dense reef during autumn was very poor due to a lack in harvestable oysters. Consolidation of reefs limits the accessibility of prey for Eurasian oystercatchers whereas a successful recruitment of Pacific oysters enhances the suitability of the habitat. Eurasian curlew was promoted by the engineering effects of the Pacific oyster while feeding extensively on shore crabs at the reefs. In contrast, European herring gulls appear hampered in foraging during low tide and hereby

  17. The Structural Basis for Substrate Anchoring, Active Site Selectivity, and Product Formation by P450 PikC from Streptomyces venezuelae

    PubMed Central

    Sherman, David H.; Li, Shengying; Yermalitskaya, Liudmila V.; Kim, Youngchang; Smith, Jarrod A.; Waterman, Michael R.; Podust, Larissa M.

    2010-01-01

    The pikromycin (Pik)/methymycin biosynthetic pathway of Streptomyces venezuelae represents a valuable system for dissecting the fundamental mechanisms of modular polyketide biosynthesis, aminodeoxysugar assembly, glycosyltransfer, and hydroxylation leading to the production of a series of macrolide antibiotics, including the natural ketolides narbomycin and pikromycin. In this study, we describe four x-ray crystal structures and allied functional studies for PikC, the remarkable P450 monooxygenase responsible for production of a number of related macrolide products from the Pik pathway. The results provide important new insights into the structural basis for the C10/C12, and C12/C14 hydroxylation patterns for the 12- (YC-17) and 14-membered ring (narbomycin) macrolides, respectively. This includes two different ligand-free structures in an asymmetric unit (resolution 2.1 Å) and two co-crystal structures with bound endogenous substrates YC-17 (resolution 2.35 Å) or narbomycin (resolution 1.7 Å). A central feature of the enzyme-substrate interaction involves anchoring of the desosamine residue in two alternative binding pockets based on a series of distinct amino acid residues that form a salt bridge and a hydrogen bonding network with the deoxysugar C3′ dimethylamino group. Functional significance of the salt bridge was corroborated by site-directed mutagenesis that revealed a key role for E94 in YC-17 binding, and E85 for narbomycin binding. Taken together, the x-ray structure analysis, site-directed mutagenesis and corresponding product distribution studies reveal that PikC substrate tolerance, and product diversity result from a combination of alternative anchoring modes, rather than an induced fit mechanism. PMID:16825192

  18. The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae.

    PubMed

    Sherman, David H; Li, Shengying; Yermalitskaya, Liudmila V; Kim, Youngchang; Smith, Jarrod A; Waterman, Michael R; Podust, Larissa M

    2006-09-08

    The pikromycin (Pik)/methymycin biosynthetic pathway of Streptomyces venezuelae represents a valuable system for dissecting the fundamental mechanisms of modular polyketide biosynthesis, aminodeoxysugar assembly, glycosyltransfer, and hydroxylation leading to the production of a series of macrolide antibiotics, including the natural ketolides narbomycin and pikromycin. In this study, we describe four x-ray crystal structures and allied functional studies for PikC, the remarkable P450 monooxygenase responsible for production of a number of related macrolide products from the Pik pathway. The results provide important new insights into the structural basis for the C10/C12 and C12/C14 hydroxylation patterns for the 12-(YC-17) and 14-membered ring (narbomycin) macrolides, respectively. This includes two different ligand-free structures in an asymmetric unit (resolution 2.1 A) and two co-crystal structures with bound endogenous substrates YC-17 (resolution 2.35 A)or narbomycin (resolution 1.7 A). A central feature of the enzyme-substrate interaction involves anchoring of the desosamine residue in two alternative binding pockets based on a series of distinct amino acid residues that form a salt bridge and a hydrogen-bonding network with the deoxysugar C3' dimethylamino group. Functional significance of the salt bridge was corroborated by site-directed mutagenesis that revealed a key role for Glu-94 in YC-17 binding and Glu-85 for narbomycin binding. Taken together, the x-ray structure analysis, site-directed mutagenesis, and corresponding product distribution studies reveal that PikC substrate tolerance and product diversity result from a combination of alternative anchoring modes rather than an induced fit mechanism.

  19. Part I. Cobalt thiolate complexes modeling the active site of cobalt nitrile hydratase. Part II. Formation of inorganic nanoparticles on protein scaffolding in Escherichia coli glutamine synthetase

    NASA Astrophysics Data System (ADS)

    Kung, Irene Yuk Man

    Part I. A series of novel cobalt dithiolate complexes with mixed imine/amine ligand systems is presented here as electronic and structural models for the active site in the bacterial enzyme class, nitrile hydratase (NHase). Pentadentate cobalt(II) complexes with S2N 3 ligand environments are first studied as precursors to the more relevant cobalt(III) complexes. Adjustment of the backbone length by removal of a methylene group increases the reactivity of the system; whereas reduction of the two backbone imine bonds to allow free rotation about those bonds may decrease reactivity. Reactivity change due to the replacement of the backbone amine proton with a more sterically challenging methyl group is not yet clear. Upon oxidation, the monocationic pentadentate cobalt(III) complex, 1b, shows promising reactivity similar to that of NHase. The metal's open coordination site allows reversible binding of the endogenous, monoanionic ligands, N 3- and NCS-. Oxygenation of the thiolate sulfur atoms by exposure to O2 and H2O 2 produces sulfenate and sulfinate ligands in complex 8, which resembles the crystal structure of "deactivated" Fe NHase. However, its lack of reactivity argues against the oxygenated enzyme structure as the active form. Six-coordinate cobalt(III) complexes with S2N4 amine/amine ligand systems are also presented as analogues of previously reported iron(III) compounds, which mimic the spectroscopic properties of Fe NHase. The cobalt complexes do not seem to similarly model Co NHase. However, the S = 0 cobalt(III) center can be spectroscopically silent and difficult to detect, making comparison with synthetic models using common techniques hard. Part II. Dodecameric Escherichia coli glutamine synthetase mutant, E165C, stacks along its six-fold axis to produce tubular nanostructures in the presence of some divalent metal ions, as does the wild type enzyme. The centrally located, engineered Cys-165 residues appear to bind to various species and may serve as

  20. Chain Walking as a Strategy for Carbon-Carbon Bond Formation at Unreactive Sites in Organic Synthesis: Catalytic Cycloisomerization of Various 1,n-Dienes.

    PubMed

    Hamasaki, Taro; Aoyama, Yuka; Kawasaki, Junichi; Kakiuchi, Fumitoshi; Kochi, Takuya

    2015-12-30

    Carbon-carbon bond formation at unreactive sp(3)-carbons in small organic molecules via chain walking was achieved for the palladium-catalyzed cycloisomerization of 1,n-dienes. Various 1,n-dienes (n = 7-14) such as those containing cyclic alkenes, acyclic internal alkenes, and a trisubstituted alkene can be used for the chain-walking cycloisomerization/hydrogenation process, and five-membered ring compounds including simple cyclopentane and pyrrolidine derivatives can easily be prepared. Chain walking over a tertiary carbon was also found to be possible in the cycloisomerization. It is not necessary for the linker portion of the diene to contain a quaternary center, and diene substrates with two alkene moieties linked by a tertiary carbon or a nitrogen atom can also be used as substrates. Column chromatography using silica gel containing silver nitrate was found to be effective for isolating some of the cycloisomerization products without hydrogenation. Deuterium-labeling experiments provided direct evidence to show that the reaction proceeds via a chain-walking mechanism.

  1. Functional mapping of the lectin activity site on the β-prism domain of vibrio cholerae cytolysin: implications for the membrane pore-formation mechanism of the toxin.

    PubMed

    Rai, Anand Kumar; Paul, Karan; Chattopadhyay, Kausik

    2013-01-18

    Vibrio cholerae cytolysin (VCC) is a prominent member in the family of β-barrel pore-forming toxins. It induces lysis of target eukaryotic cells by forming transmembrane oligomeric β-barrel channels. VCC also exhibits prominent lectin-like activity in interacting with β1-galactosyl-terminated glycoconjugates. Apart from the cytolysin domain, VCC harbors two lectin-like domains: the β-Trefoil and the β-Prism domains; however, precise contribution of these domains in the lectin property of VCC is not known. Also, role(s) of these lectin-like domains in the mode of action of VCC remain obscure. In the present study, we show that the β-Prism domain of VCC acts as the structural scaffold to determine the lectin activity of the protein toward β1-galactosyl-terminated glycoconjugates. Toward exploring the physiological implication of the β-Prism domain, we demonstrate that the presence of the β-Prism domain-mediated lectin activity is crucial for an efficient interaction of the toxin toward the target cells. Our results also suggest that such lectin activity may act to regulate the oligomerization ability of the membrane-bound VCC toxin. Based on the data presented here, and also consistent with the existing structural information, we propose a novel mechanism of regulation imposed by the β-Prism domain's lectin activity, implicated in the process of membrane pore formation by VCC.

  2. Effects of CO2 on mechanical variability and constitutive behavior of the Lower Tuscaloosa formation, Cranfield Injection Site, USA

    SciTech Connect

    Rinehart, Alex J.; Dewers, Thomas A.; Broome, Scott T.; Eichhubl, Peter

    2016-08-25

    We characterize geomechanical constitutive behavior of reservoir sandstones at conditions simulating the “Cranfield” Southeast Regional Carbon Sequestration Partnership injection program. From two cores of Lower Tuscaloosa Formation, three sandstone lithofacies were identified for mechanical testing based on permeability and lithology. These include: chlorite-cemented conglomeratic sandstone (Facies A); quartz-cemented fine sandstone (Facies B); and quartz- and calcite-cemented very fine sandstone (Facies C). We performed a suite of compression tests for each lithofacies at 100 °C and pore pressure of 30 MPa, including hydrostatic compression and triaxial tests at several confining pressures. Plugs were saturated with supercritical CO2-saturated brine. Chemical environment affected the mechanical response of all three lithofacies, which experience initial plastic yielding at stresses far below estimated in situ stress. Measured elastic moduli degradation defines a secondary yield surface coinciding with in situ stress for Facies B and C. Facies A shows measurable volumetric creep strain and a failure envelope below estimates of in situ stress, linked to damage of chlorite cements by acidic pore solutions. Furthermore, the substantial weakening of a particular lithofacies by CO2 demonstrates a possible chemical-mechanical coupling during injection at Cranfield with implications for CO2 injection, reservoir permeability stimulation, and enhanced oil recovery.

  3. Essential Role of the C-Terminal Helical Domain in Active Site Formation of Selenoprotein MsrA from Clostridium oremlandii

    PubMed Central

    Lee, Eun Hye; Lee, Kitaik; Hwang, Kwang Yeon; Kim, Hwa-Young

    2015-01-01

    We previously determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii (CoMsrA). The overall structure of CoMsrA is unusual, consisting of two domains, the N-terminal catalytic domain and the C-terminal distinct helical domain which is absent from other known MsrA structures. Deletion of the helical domain almost completely abolishes the catalytic activity of CoMsrA. In this study, we determined the crystal structure of the helical domain-deleted (ΔH-domain) form of CoMsrA at a resolution of 1.76 Å. The monomer structure is composed of the central rolled mixed β-sheet surrounded by α-helices. However, there are significant conformational changes in the N- and C-termini and loop regions of the ΔH-domain protein relative to the catalytic domain structure of full-length CoMsrA. The active site structure in the ΔH-domain protein completely collapses, thereby causing loss of catalytic activity of the protein. Interestingly, dimer structures are observed in the crystal formed by N-terminus swapping between two molecules. The ΔH-domain protein primarily exists as a dimer in solution, whereas the full-length CoMsrA exists as a monomer. Collectively, this study provides insight into the structural basis of the essential role of the helical domain of CoMsrA in its catalysis. PMID:25692691

  4. Triplex formation at single-stranded nucleic acid target sites of unrestricted sequence by two added strands of oligonucleotides: A proposed model

    SciTech Connect

    Trapane, T.L.; Ts'o, P.O.P. )

    1994-11-16

    By using the standard purine nucleosides, guanosine and adenosine, and the pyrimidine C-nucleosides, pseudoisocytidine and pseudouridine, as complements on a probe strand, it is possible to construct a regular Watson-Crick helix with a single-stranded target sequence having any arrangement of the four naturally-occurring bases found in nucleic acids. The major groove of this helix will have a unique configuration of hydrogen-bonding sites on the probe strand for each of these four base pairs. By using this duplex as a framework, an ensemble of recognition patterns composed of base triads may be constructed. In these patterns, either a homopyrimidine or homopurine third strand binds in the major groove of the duplex formed by the target and probe strands. Ten distinct geometries, or motifs, are shown, each one consisting of four isomorphic base triads built upon recognition of C, G, A, or U(T) residues in the target strand. In order to maintain specific hydrogen bonding and to construct isomorphous triads, the use of several nonstandard bases is proposed. 33 refs., 9 figs., 3 tabs.

  5. Analysis of Site Formation and Assemblage Integrity Does Not Support Attribution of the Uluzzian to Modern Humans at Grotta del Cavallo

    PubMed Central

    Zilhão, João; Banks, William E.; d’Errico, Francesco; Gioia, Patrizia

    2015-01-01

    Based on the morphology of two deciduous molars and radiocarbon ages from layers D and E of the Grotta del Cavallo (Lecce, Italy), assigned to the Uluzzian, it has been proposed that modern humans were the makers of this Early Upper Paleolithic culture and that this finding considerably weakens the case for an independent emergence of symbolism among western European Neandertals. Reappraisal of the new dating evidence, of the finds curated in the Taranto Antiquities depot, and of coeval publications detailing the site’s 1963–66 excavations shows that (a) Protoaurignacian, Aurignacian and Early Epigravettian lithics exist in the assemblages from layers D and E, (b) even though it contains both inherited and intrusive items, the formation of layer D began during Protoaurignacian times, and (c) the composition of the extant Cavallo assemblages is influenced in a non-negligible manner by the post-hoc assignment of items to stratigraphic units distinct from that of original discovery. In addition, a major disturbance feature affected the 1960s excavation trench down to Mousterian layer F, this feature went unrecognized until 1964, the human remains assigned to the Uluzzian were discovered that year and/or the previous year, and there are contradictions between field reports and the primary anthropological description of the remains as to their morphology and level of provenience. Given these major contextual uncertainties, the Cavallo teeth cannot be used to establish the authorship of the Uluzzian. Since this technocomplex’s start date is ca. 45,000 calendar years ago, a number of Neandertal fossils are dated to this period, and the oldest diagnostic European modern human fossil is the <41,400 year-old Oase 1 mandible, Neandertal authorship of the Uluzzian remains the parsimonious reading of the evidence. PMID:26154139

  6. Origin of the local structures at the Philae landing site and possible implications on the formation and evolution of 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Poulet, F.; Lucchetti, A.; Bibring, J.-P.; Carter, J.; Gondet, B.; Jorda, L.; Langevin, Y.; Pilorget, C.; Capanna, C.; Cremonese, G.

    2016-11-01

    In situ images of the 67P/Churyumov-Gerasimenko nucleus acquired by the CIVA cameras on-board PHILAE revealed a rough landscape dominated by consolidated materials. These data provide a unique view to constrain the past and present conditions prevailing at the surface of the comet. A quantitative analysis of microscopic structures (fractures and pebbles) is derived using a manual extraction from the images. Fractures/cracks are rather ubiquitous at various spatial scales with network and size (from sub-cm to 10 cm) well correlated to the texture of the landscape. The pebble size distributions are derived and compared to the size distribution of other cometary materials. The nature of the landscape is then discussed in relation to endogenic and exogenic processes of surface modification. The block seen in CIVA no. 1 is interpreted to be close-ups of fractured boulder/cliff belonging to the boulder field identified from the orbit near Abydos, this boulder field being itself the result of gravitational regressive erosion due to sublimation. The observed fractures are best explained by thermal insolation leading to thermal fatigue and/or to loss of volatile materials. This surficial fragmentation (up to >10 cm length) could generate macroscopic erosion that is also visible at larger scale from the orbit. There is at least an intriguing possibility that the pebbles are remnants of primordial accretion processes. We thus speculate that the Abydos landscape could be in favour of pebble accretion model instead of runaway coagulation model with a formation location in the outer region of the Solar system.

  7. Rock magnetic and geochemical evidence for authigenic magnetite formation via iron reduction in coal-bearing sediments offshore Shimokita Peninsula, Japan (IODP Site C0020)

    NASA Astrophysics Data System (ADS)

    Phillips, Stephen C.; Johnson, Joel E.; Clyde, William C.; Setera, Jacob B.; Maxbauer, Daniel P.; Severmann, Silke; Riedinger, Natascha

    2017-06-01

    Sediments recovered at Integrated Ocean Drilling Program (IODP) Site C0020, in a fore-arc basin offshore Shimokita Peninsula, Japan, include numerous coal beds (0.3-7 m thick) that are associated with a transition from a terrestrial to marine depositional environment. Within the primary coal-bearing unit (˜2 km depth below seafloor) there are sharp increases in magnetic susceptibility in close proximity to the coal beds, superimposed on a background of consistently low magnetic susceptibility throughout the remainder of the recovered stratigraphic sequence. We investigate the source of the magnetic susceptibility variability and characterize the dominant magnetic assemblage throughout the entire cored record, using isothermal remanent magnetization (IRM), thermal demagnetization, anhysteretic remanent magnetization (ARM), iron speciation, and iron isotopes. Magnetic mineral assemblages in all samples are dominated by very low-coercivity minerals with unblocking temperatures between 350 and 580°C that are interpreted to be magnetite. Samples with lower unblocking temperatures (300-400°C), higher ARM, higher-frequency dependence, and isotopically heavy δ56Fe across a range of lithologies in the coal-bearing unit (between 1925 and 1995 mbsf) indicate the presence of fine-grained authigenic magnetite. We suggest that iron-reducing bacteria facilitated the production of fine-grained magnetite within the coal-bearing unit during burial and interaction with pore waters. The coal/peat acted as a source of electron donors during burial, mediated by humic acids, to supply iron-reducing bacteria in the surrounding siliciclastic sediments. These results indicate that coal-bearing sediments may play an important role in iron cycling in subsiding peat environments and if buried deeply through time, within the subsequent deep biosphere.

  8. S-glutathionylation of glyceraldehyde-3-phosphate dehydrogenase induces formation of C150-C154 intrasubunit disulfide bond in the active site of the enzyme.

    PubMed

    Barinova, K V; Serebryakova, M V; Muronetz, V I; Schmalhausen, E V

    2017-09-19

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic protein involved in numerous non-glycolytic functions. S-glutathionylated GAPDH was revealed in plant and animal tissues. The role of GAPDH S-glutathionylation is not fully understood. Rabbit muscle GAPDH was S-glutathionylated in the presence of H2O2 and reduced glutathione (GSH). The modified protein was assayed by MALDI-MS analysis, differential scanning calorimetry, dynamic light scattering, and ultracentrifugation. Incubation of GAPDH in the presence of H2O2 together with GSH resulted in the complete inactivation of the enzyme. In contrast to irreversible oxidation of GAPDH by H2O2, this modification could be reversed in the excess of GSH or dithiothreitol. By data of MALDI-MS analysis, the modified protein contained both mixed disulfide between Cys150 and GSH and the intrasubunit disulfide bond between Cys150 and Cys154 (different subunits of tetrameric GAPDH may contain different products). S-glutathionylation results in loosening of the tertiary structure of GAPDH, decreases its affinity to NAD(+) and thermal stability. The mixed disulfide between Cys150 and GSH is an intermediate product of S-glutathionylation: its subsequent reaction with Cys154 results in the intrasubunit disulfide bond in the active site of GAPDH. The mixed disulfide and the C150-C154 disulfide bond protect GAPDH from irreversible oxidation and can be reduced in the excess of thiols. Conformational changes that were observed in S-glutathionylated GAPDH may affect interactions between GAPDH and other proteins (ligands), suggesting the role of S-glutathionylation in the redox signaling. The manuscript considers one of the possible mechanisms of redox regulation of cell functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Evidence for habitual use of fire at the end of the Lower Paleolithic: site-formation processes at Qesem Cave, Israel.

    PubMed

    Karkanas, Panagiotis; Shahack-Gross, Ruth; Ayalon, Avner; Bar-Matthews, Mira; Barkai, Ran; Frumkin, Amos; Gopher, Avi; Stiner, Mary C

    2007-08-01

    The Amudian (late Lower Paleolithic) site of Qesem Cave in Israel represents one of the earliest examples of habitual use of fire by middle Pleistocene hominids. The Paleolithic layers in this cave were studied using a suite of mineralogical and chemical techniques and a contextual sedimentological analysis (i.e., micromorphology). We show that the lower ca. 3m of the stratigraphic sequence are dominated by clastic sediments deposited within a closed karstic environment. The deposits were formed by small-scale, concentrated mud slurries (infiltrated terra rosa soil) and debris flows. A few intervening lenses of mostly in situ burnt remains were also identified. The main part of the upper ca. 4.5 m consists of anthropogenic sediment with only moderate amounts of clastic geogenic inputs. The deposits are strongly cemented with calcite that precipitated from dripping water. The anthropogenic component is characterized by completely combusted, mostly reworked wood ash with only rare remnants of charred material. Micromorphological and isotopic evidence indicates recrystallization of the wood ash. Large quantities of burnt bone, defined by a combination of microscopic and macroscopic criteria, and moderately heated soil lumps are closely associated with the wood-ash remains. The frequent presence of microscopic calcified rootlets indicates that the upper sequence formed in the vicinity of the former cave entrance. Burnt remains in the sediments are associated with systematic blade production and faunas that are dominated by the remains of fallow deer. Use-wear damage on blades and blade tools in conjunction with numerous cut marks on bones indicate an emphasis on butchering and prey-defleshing activities in the vicinity of fireplaces.

  10. A Novel Computational Model Predicts Key Regulators of Chemokine Gradient Formation in Lymph Nodes and Site-Specific Roles for CCL19 and ACKR4

    PubMed Central

    Brook, Bindi S.

    2017-01-01

    The chemokine receptor CCR7 drives leukocyte migration into and within lymph nodes (LNs). It is activated by chemokines CCL19 and CCL21, which are scavenged by the atypical chemokine receptor ACKR4. CCR7-dependent navigation is determined by the distribution of extracellular CCL19 and CCL21, which form concentration gradients at specific microanatomical locations. The mechanisms underpinning the establishment and regulation of these gradients are poorly understood. In this article, we have incorporated multiple biochemical processes describing the CCL19–CCL21–CCR7–ACKR4 network into our model of LN fluid flow to establish a computational model to investigate intranodal chemokine gradients. Importantly, the model recapitulates CCL21 gradients observed experimentally in B cell follicles and interfollicular regions, building confidence in its ability to accurately predict intranodal chemokine distribution. Parameter variation analysis indicates that the directionality of these gradients is robust, but their magnitude is sensitive to these key parameters: chemokine production, diffusivity, matrix binding site availability, and CCR7 abundance. The model indicates that lymph flow shapes intranodal CCL21 gradients, and that CCL19 is functionally important at the boundary between B cell follicles and the T cell area. It also predicts that ACKR4 in LNs prevents CCL19/CCL21 accumulation in efferent lymph, but does not control intranodal gradients. Instead, it attributes the disrupted interfollicular CCL21 gradients observed in Ackr4-deficient LNs to ACKR4 loss upstream. Our novel approach has therefore generated new testable hypotheses and alternative interpretations of experimental data. Moreover, it acts as a framework to investigate gradients at other locations, including those that cannot be visualized experimentally or involve other chemokines. PMID:28807994

  11. Spectroscopic characterization of active-site variants of the PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri: insights into the mechanism of four-coordinate Co(II)corrinoid formation.

    PubMed

    Park, Kiyoung; Mera, Paola E; Escalante-Semerena, Jorge C; Brunold, Thomas C

    2012-04-16

    The PduO-type adenosine 5'-triphosphate (ATP):corrinoid adenosyltransferase from Lactobacillus reuteri (LrPduO) catalyzes the transfer of the adenosyl-group of ATP to Co(1+)cobalamin (Cbl) and Co(1+)cobinamide (Cbi) substrates to synthesize adenosylcobalamin (AdoCbl) and adenosylcobinamide (AdoCbi(+)), respectively. Previous studies revealed that to overcome the thermodynamically challenging Co(2+) → Co(1+) reduction, the enzyme drastically weakens the axial ligand-Co(2+) bond so as to generate effectively four-coordinate (4c) Co(2+)corrinoid species. To explore how LrPduO generates these unusual 4c species, we have used magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectroscopic techniques. The effects of active-site amino acid substitutions on the relative yield of formation of 4c Co(2+)corrinoid species were examined by performing eight single-amino acid substitutions at seven residues that are involved in ATP-binding, an intersubunit salt bridge, and the hydrophobic region surrounding the bound corrin ring. A quantitative analysis of our MCD and EPR spectra indicates that the entire hydrophobic pocket below the corrin ring, and not just residue F112, is critical for the removal of the axial ligand from the cobalt center of the Co(2+)corrinoids. Our data also show that a higher level of coordination among several LrPduO amino acid residues is required to exclude the dimethylbenzimidazole moiety of Co(II)Cbl from the active site than to remove the water molecule from Co(II)Cbi(+). Thus, the hydrophilic interactions around and above the corrin ring are more critical to form 4c Co(II)Cbl than 4c Co(II)Cbi(+). Finally, when ATP analogues were used as cosubstrate, only "unactivated" five-coordinate (5c) Co(II)Cbl was observed, disclosing an unexpectedly large role of the ATP-induced active-site conformational changes with respect to the formation of 4c Co(II)Cbl. Collectively, our results indicate that the level of control exerted by

  12. Transport, biomass burning, and in-situ formation contribute to fine particle concentrations at a remote site near Grand Teton National Park

    NASA Astrophysics Data System (ADS)

    Schurman, M. I.; Lee, T.; Desyaterik, Y.; Schichtel, B. A.; Kreidenweis, S. M.; Collett, J. L.

    2015-07-01

    Ecosystem health and visibility degradation due to fine-mode atmospheric particles have been documented in remote areas and motivate particle characterization that can inform mitigation strategies. This study explores submicron (PM1) particle size, composition, and source apportionment at Grand Teton National Park using High-Resolution Time-of-Flight Aerosol Mass Spectrometer data with Positive Matrix Factorization and MODIS fire information. Particulate mass averages 2.08 μg/m3 (max = 21.91 μg/m3) of which 75.0% is organic; PMF-derived Low-Volatility Oxygenated Organic Aerosol (LV-OOA) averages 61.1% of PM1 (or 1.05 μg/m3), with sporadic but higher-concentration biomass burning (BBOA) events contributing another 13.9%. Sulfate (12.5%), ammonium (8.7%), and nitrate (3.8%) are generally low in mass. Ammonium and sulfate have correlated time-series and association with transport from northern Utah and the Snake River Valley. A regionally disperse and/or in situ photochemical LV-OOA source is suggested by 1) afternoon concentration enhancement not correlated with upslope winds, anthropogenic NOx, or ammonium sulfate, 2) smaller particle size, higher polydispersity, and lower levels of oxidation during the day and in comparison to a biomass burning plume inferred to have traveled ∼480 km, and 3) lower degree of oxidation than is usually observed in transported urban plumes and alpine sites with transported anthropogenic OA. CHN fragment spectra suggest organic nitrogen in the form of nitriles and/or pyridines during the day, with the addition of amine fragments at night. Fires near Boise, ID may be the source of a high-concentration biomass-burning event on August 15-16, 2011 associated with SW winds (upslope from the Snake River Valley) and increased sulfate, ammonium, nitrate, and CHN and CHON fragments (nominally, amines and organonitrates). Comparison to limited historical data suggests that the amounts and sources of organics and inorganics presented here

  13. Geomechanical characterization of an Upper Triassic reservoir rock (Stuttgart Formation) in the NE German Basin (pilot site for CO2 storage at Ketzin, Germany)

    NASA Astrophysics Data System (ADS)

    Klapperer, S.; Moeck, I.; Backers, T.

    2012-04-01

    behavior of rock are the angle of internal friction ψ and cohesion c, representing aspects determining failure occurrence that can be expressed and illustrated by the Mohr Coulomb failure criterion. As for the UCS there is also a wide range of values for ψ (4.06° to 36.98°) and c (10.45 MPa to 49.41 MPa) which differ distinctly within similar lithologies. With respect to these differences further geomechanical tests in combination with petrographic investigations will be in focus to evaluate the impact of lithologal as well as lithofacial characteristics on geomechanical properties. Thus the lithological and lithofacial heterogeneous characteristics of the Stuttgart formation could influence significantly the geomechanical behavior and transmission of stresses resulting from CO2 injection. Therefrom knowledge about these rock mechanical properties helps to provide a save and long term injection and prevent leakage scenarios.

  14. Assessing the impact of anthropogenic pollution on isoprene-derived secondary organic aerosol formation in PM2.5 collected from the Birmingham, Alabama, ground site during the 2013 Southern Oxidant and Aerosol Study

    NASA Astrophysics Data System (ADS)

    Rattanavaraha, Weruka; Chu, Kevin; Hapsari Budisulistiorini, Sri; Riva, Matthieu; Lin, Ying-Hsuan; Edgerton, Eric S.; Baumann, Karsten; Shaw, Stephanie L.; Guo, Hongyu; King, Laura; Weber, Rodney J.; Neff, Miranda E.; Stone, Elizabeth A.; Offenberg, John H.; Zhang, Zhenfa; Gold, Avram; Surratt, Jason D.

    2016-04-01

    In the southeastern US, substantial emissions of isoprene from deciduous trees undergo atmospheric oxidation to form secondary organic aerosol (SOA) that contributes to fine particulate matter (PM2.5). Laboratory studies have revealed that anthropogenic pollutants, such as sulfur dioxide (SO2), oxides of nitrogen (NOx), and aerosol acidity, can enhance SOA formation from the hydroxyl radical (OH)-initiated oxidation of isoprene; however, the mechanisms by which specific pollutants enhance isoprene SOA in ambient PM2.5 remain unclear. As one aspect of an investigation to examine how anthropogenic pollutants influence isoprene-derived SOA formation, high-volume PM2.5 filter samples were collected at the Birmingham, Alabama (BHM), ground site during the 2013 Southern Oxidant and Aerosol Study (SOAS). Sample extracts were analyzed by gas chromatography-electron ionization-mass spectrometry (GC/EI-MS) with prior trimethylsilylation and ultra performance liquid chromatography coupled to electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-QTOFMS) to identify known isoprene SOA tracers. Tracers quantified using both surrogate and authentic standards were compared with collocated gas- and particle-phase data as well as meteorological data provided by the Southeastern Aerosol Research and Characterization (SEARCH) network to assess the impact of anthropogenic pollution on isoprene-derived SOA formation. Results of this study reveal that isoprene-derived SOA tracers contribute a substantial mass fraction of organic matter (OM) ( ˜ 7 to ˜ 20 %). Isoprene-derived SOA tracers correlated with sulfate (SO42-) (r2 = 0.34, n = 117) but not with NOx. Moderate correlations between methacrylic acid epoxide and hydroxymethyl-methyl-α-lactone (together abbreviated MAE/HMML)-derived SOA tracers with nitrate radical production (P[NO3]) (r2 = 0.57, n = 40) were observed during nighttime, suggesting a potential role of the NO3 radical in

  15. Low-temperature formation and stabilization of rare allotropes of cyclooctasulfur (β-S8 and γ-S8) in the presence of organic carbon at a sulfur-rich glacial site in the Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Lau, Graham E.; Cosmidis, Julie; Grasby, Stephen E.; Trivedi, Christopher B.; Spear, John R.; Templeton, Alexis S.

    2017-03-01

    Large-scale deposits of elemental sulfur form annually on a glacier's surface at Borup Fiord Pass in the Canadian High Arctic. However, the mechanisms of mineralization and stabilization of elemental sulfur at this site are currently unknown. Here we show that X-ray diffraction (XRD) data for fresh sulfur precipitates collected from the surface of a melt pool over sulfide-rich ice reveal the presence of three sulfur allotropes, α-S8, β-S8, and γ-S8 (the three solid forms of cyclooctasulfur (S8)). The detection of the β-S8 allotrope of elemental sulfur is notable, since β-S8 typically only forms in high temperature environments (>96 °C). The γ-S8 allotrope is also rare in natural settings and has previously been implicated as a signature of microbial sulfur cycling. Using combustion and infrared spectroscopy approaches, organic carbon is also detected within the sample bearing the three allotropes of elemental sulfur. Electron microscopy and scanning transmission X-ray microscopy (STXM) at the C K-edge show that the sulfur precipitates are intimately associated with the organic carbon at the submicron scale. The occurrence of β-S8 and γ-S8 in this low-temperature setting indicates that there are unknown pathways for the formation and stabilization of these rare allotropes of elemental sulfur. In particular, we infer that the occurrence of these allotropes is related to their association with organic carbon. The formation of carbon-associated sulfur globules may not be a direct by-product of microbial activity; however, a potential role of direct or indirect microbial mediation in the formation and stabilization of β-S8 and γ-S8 remains to be assessed.

  16. Subsurface dolomite formation during post-depositional flow of sulphate-bearing fluids from underlying salt giants: Early Pliocene example at DSDP Leg 42A, Site 374, Ionian Abyssal Plain

    NASA Astrophysics Data System (ADS)

    McKenzie, Judith A.; Evans, Nick; Hodell, David; Aloisi, Giovanni; Vasconcelos, Crisogono

    2017-04-01

    Deciphering exact mechanisms for the formation of massive dolomite deposits has long been an enigma in sedimentary geology. The recognition that microbes can play a role in the dolomite precipitation process has added a new dimension to the study of the origin of dolomite formations in both shallow and deep-water environments. This scientific advance has evolved, particularly, through the investigation of dolomite-containing, organic-rich hemipelagic sediments cored on various continental margins during DSDP and ODP drilling campaigns, as well as intensive evaluations of modern hypersaline dolomite-precipitating environments with complementary culture experiments conducted in the laboratory. For example, the association of an active subsurface microbial community in contact with underlying brines of unknown origin leading to in situ dolomite precipitation has been observed in a Quaternary sequence of hemi-pelagic, organic carbon-rich sediments drilled on the Peru Margin, ODP Leg 201, Site 1229 (1). Specifically, it can be concluded that the long-term activity of subsurface microbes can be maintained by post-depositional flow of sulfate-bearing fluids from underlying large-scale evaporite deposits, or salt giants, promoting in situ dolomite precipitation. Another example of dolomite precipitation directly associated with the underlying Messinian salt giant was found at DSDP Leg 42A, Site 374 in the Ionian Abyssal Plain. Deep-sea drilling recovered a lowermost Pliocene sequence of diagenetically altered sediment (Unit II) separating the overlying Pliocene open-marine deposits (Unit I) and the underlying end Messinian dolomitic mudstone with gypsum layers (Unit III). The lower portion of this altered interval contained in Core 11, Section 2 (378.0 - 381.5 mbsf) comprises a dolomicrite with an unusual crystal morphology (2). The original interstitial water geochemical profiles indicate that a saline brine is diffusing upwards from below and into the dolomicrite

  17. The influence of organic and inorganic gases during New Particle Formation (NPF) events at the Mediterranean remote site of ERSA in Cape-Corsica during the summer of 2013.

    NASA Astrophysics Data System (ADS)

    Waked, Antoine; Sauvage, Stephane; Michoud, Vincent; Sellegri, Karine; Berland, Kevin; Kukui, Alexandre; Hallemans, Elise; Zannoni, Nora; Kalogridis, Cerise; Gros, Valerie; Dusanter, Sebastien; Locoge, Nadine; Doussin, Jean-francois

    2017-04-01

    As part of the CHARMEX (Chemistry Aerosol Mediterranean Experiments) project, more than one hundred organic and inorganic gaseous compounds were measured in the summer of 2013 at the Mediterranean remote site of ERSA in Cape-Corsica. During this period, New Particle formation (NPF) events were identified from July 31th to august 2nd when air masses originated from the North-eastern sector (Southern Europe). The results were compared to a non-NPF event from July 21th to July 23rd for which the same wind sectors were identified. They showed that the particles number [10-20 nm] measured by SMPS (Scanning Mobility Particle Sizer) were more correlated with carbon monoxide (CO) during non-NPF events indicating an influence of more polluted and more aged air masses (residence time of CO of 60 days). Sulfuric acid (H2SO4) and sulfur dioxide do not show a significant influence in the formation of nucleation events. On the other hand, biogenic Volatile Organic Compounds (BVOCs) such as isoprene, and mono-terpenes as well as their oxidation products (e.g. MACR+MVK, MTOP) showed good correlation during NPF-events in the range of (r from 0.45 to 0.59) higher than the ones reported during non-NPF events (0.11-0.34) highlighting the importance of these BVOCs on NPF days. The comparison of measured vs calculated reactivity (Zannoni et al, 2016) showed that during NPF-events, the missing part of OH reactivity was higher. It indicates that unmeasured species like sesquiterpenes, organo-nitrates, or oxygenated compounds may play a significant role in such events.

  18. Filipin is a reliable in situ marker of ergosterol in the plasma membrane of germinating conidia (spores) of Penicillium discolor and stains intensively at the site of germ tube formation.

    PubMed

    Van Leeuwen, M R; Smant, W; de Boer, W; Dijksterhuis, J

    2008-08-01

    Filipin, a widely used fluorescent sterol marker is also a potent antibiotic. In this study we address the reliability of filipin as a monitor of ergosterol in fungal cells. A revised staining protocol was developed to minimize any biological effect of the compound. Germinating conidia of Penicillium discolor stained with filipin, displayed a fluorescent cap at the location of germ tube appearance and formation. During germ tube emergence, the fluorescent intensity of the cap increased. This was confirmed by HPLC as an increase of the net cellular ergosterol content. Filipin staining is absent during early germination, while FM dyes, similar molecules, stain the plasma membrane after 1 h. This indicates that the conidial cell wall is no barrier for filipin. To evaluate if filipin does bind ergosterol in situ, natamycin, more specific to ergosterol, was added before filipin staining. This resulted in a marked decrease in fluorescence indicating high ergosterol levels. This was characterized further in ergDelta-mutant cells of Saccharomyces cerevisiae containing altered sterols. Here ergosterol containing cells showed a high fluorescence decrease. Taken together, these data suggest that filipin monitors an ergosterol-enriched cap in germinating conidia at the site of germ tube formation. Furthermore, the sterol-rich cap decreases and reappears after a period of actin disruption. Myriocin that affects sphingolipid synthesis results in an increase of cellular ergosterol and overall filipin fluorescence, but not at the ergosterol cap, where fluorescence is significantly lowered. In conclusion, in this work we have demonstrated an effective revised method for ergosterol staining with filipin and demonstrated its specificity in both Penicillium and Saccharomyces.

  19. Single site mutations in the hetero-oligomeric Mrp antiporter from alkaliphilic Bacillus pseudofirmus OF4 that affect Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels, or Mrp complex formation.

    PubMed

    Morino, Masato; Natsui, Shinsuke; Ono, Tomohiro; Swartz, Talia H; Krulwich, Terry A; Ito, Masahiro

    2010-10-01

    Mrp systems are widely distributed and structurally complex cation/proton antiporters. Antiport activity requires hetero-oligomeric complexes of all six or seven hydrophobic Mrp proteins (MrpA-MrpG). Here, a panel of site-directed mutants in conserved or proposed motif residues was made in the Mrp Na(+)(Li(+))/H(+) antiporter from an alkaliphilic Bacillus. The mutant operons were expressed in antiporter-deficient Escherichia coli KNabc and assessed for antiport properties, support of sodium resistance, membrane levels of each Mrp protein, and presence of monomeric and dimeric Mrp complexes. Antiport did not depend on a VFF motif or a conserved tyrosine pair, but a role for a conserved histidine in a potential quinone binding site of MrpA was supported. The importance of several acidic residues for antiport was confirmed, and the importance of additional residues was demonstrated (e.g. three lysine residues conserved across MrpA, MrpD, and membrane-bound respiratory Complex I subunits (NuoL/M/N)). The results extended indications that MrpE is required for normal membrane levels of other Mrp proteins and for complex formation. Moreover, mutations in several other Mrp proteins lead to greatly reduced membrane levels of MrpE. Thus, changes in either of the two Mrp modules, MrpA-MrpD and MrpE-MrpG, influence the other. Two mutants, MrpB-P37G and MrpC-Q70A, showed a normal phenotype but lacked the MrpA-MrpG monomeric complex while retaining the dimeric hetero-oligomeric complex. Finally, MrpG-P81A and MrpG-P81G mutants exhibited no antiport activity but supported sodium resistance and a low [Na(+)](in). Such mutants could be used to screen hypothesized but uncharacterized sodium efflux functions of Mrp apart from Na(+) (Li(+))/H(+) antiport.

  20. On the Formation and Properties of Interstrand DNA-DNA Cross-links Forged by Reaction of an Abasic Site With the Opposing Guanine Residue of 5′-CAp Sequences in Duplex DNA

    PubMed Central

    Johnson, Kevin M.; Price, Nathan E.; Wang, Jin; Fekry, Mostafa I.; Dutta, Sanjay; Seiner, Derrick R.; Wang, Yinsheng; Gates, Kent S.

    2014-01-01

    We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5′-CAp sequence under conditions of reductive amination (NaCNBH3, pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions and, once formed, the cross-link was stable to a variety of work-up conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LCMS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N2-amino group of the opposing guanine residue in 5′-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH3/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N2-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH3. PMID:23215239

  1. Effect of alteration, formation absorption, and standoff on the response of the thermal neutron porosity log in gabbros and basalts: Examples from Deep Sea Drilling Project-Ocean Drilling Program Sites

    NASA Astrophysics Data System (ADS)

    Broglia, Cristina; Ellis, Darwin

    1990-06-01

    This study focuses on the effects of hydrous alteration minerals, formation absorption, and standoff on the response of the thermal neutron porosity log in the basaltic and gabbroic rocks logged at sites 395, 418, 504, 642, and 735 during the Ocean Drilling Program. The concentration of hydrogen present in the rocks in the form of free water (pore space) and bound water (hydrous minerals) is the primary factor controlling the neutron elastic scattering process, while the presence of other elements, such as chlorine, gadolinium, boron, lithium, and samarium in the fluids and in the rock matrix can largely affect the thermal diffusion phase. These neutron absorbers cause an increase of the capture cross section, and in turn of the apparent thermal porosity. Further perturbations occur when the recording conditions depart from those under which the tool has been calibrated; a large and irregular hole diameter and a lack of eccentralization both produce erroneous porosity readings. The effect of hydrous alteration minerals on the thermal neutron porosity log has been estimated from 922 core oxide measurements using an analysis program that calculates the slowing-down length and converts it into apparent porosity. The results show that the computed apparent porosity ranges from less than 1% in fresh basalts and gabbros to about 30% in highly altered units. Depending on the alteration mineral assemblage, natural gamma ray, capture cross section, or hydrogen logs have been used to continuously predict the effect of bound hydrogen at each site. Corrected porosities generally show excellent agreement with core data for massive units, whereas they are higher for pillow basalts and fractured zones. The discrepancy is interpreted as the result of (1) difference in the volume of rock investigated (core specimens do not sample large vugs and fractures) and (2) frequent variations in the hole size and lack of tool contact with the borehole wall (standoff), not completely

  2. Mutagenesis by peroxy radical is dominated by transversions at deoxyguanosine: evidence for the lack of involvement of 8-oxo-dG1 and/or abasic site formation.

    PubMed

    Valentine, M R; Rodriguez, H; Termini, J

    1998-05-12

    Oxidative damage of DNA by endogenously generated oxygen radicals contributes to the mutagenic process. Hydroxy, alkoxy, and peroxy radicals all have the potential to react with DNA, giving rise to strand breaks and potentially mutagenic oxidative base damage. Although reactions of the hydroxy radical with DNA have been well studied, far less is known about the reactivities of these other radicals with DNA and their mutation-inducing potential. Frequencies of DNA base modifications and strand break densities caused by peroxy radical (ROO*) oxidation were measured by glyoxal gel electrophoretic analysis. We report the spectrum of mutations induced in Escherichia coli upon transfection with peroxy radical treated DNA carrying the lacZ alpha gene as a reporter. Transfection of DNA exposed to micromolar amounts of peroxy radical resulted in a 30-fold increase in mutation frequency in non-SOS-inducible cells. Sequencing analysis of DNA isolated from mutants showed that among base substitution mutants 88% consisted of transversions at G, with a nearly equal number of G --> C and G --> T mutants. Transition mutations were rarely detected, in contrast to control experiments. Electrophoretic analysis of peroxy radical treated DNA exposed to NaOH, Nth, and Fpg proteins demonstrated that abasic sites are not formed to any detectable degree. The oxidative G lesions are sensitive to digestion by the Fpg protein. We were unable to detect the formation of 8-oxo-dG by HPLC/electrochemical analysis of peroxy radical oxidation of dG, suggesting that the G --> T transversions were not caused by this base lesion.

  3. Value siting

    SciTech Connect

    Ferrar, T.A.; Howes, J.A.

    1995-02-01

    Finding an appropriate site is becoming an increasing challenge in building new power projects. One of the first orders of business in project development is identifying a site that offers the maximum spread between the cost of fuel and net power price. The collection of sites that exhibit an adequate spread - presenting a first-order, acceptable economic expectation - must now be subjected to an ever increasing number of political, societal, technical, and economic exclusion screens. The barriers can include cooling water constraints, community resistance, visual incompatibility, archaeological concerns and endangered species preservation issues. Most power siting difficulties can be substantially mitigated by gaining access to developed, but under-used sites, whose current owners are bound by circumstances - political or financial - that prevent them from using such locations. There are two such categories of sites: Utilities that have sites on which depreciated power production assets rest; and, The federal government, with numerous sites throughout the country, particularly military bases subject to closure under the Base Realignment and Closure (BRAC) proceedings. It is in the interests of developers, as well as consumers, investors and taxpayers, ti undertake a thorough examination of these overlooked pearls of opportunities and develop their potential.

  4. Formation of a tight 1:1 complex of Clostridium pasteurianum Fe protein-Azotobacter vinelandii MoFe protein: evidence for long-range interactions between the Fe protein binding sites during catalytic hydrogen evolution.

    PubMed

    Clarke, T A; Maritano, S; Eady, R R

    2000-09-19

    It has been well documented that the combination of the MoFe protein of Azotobacter vinelandii nitrogenase (Av1) with the Fe protein (Cp2) from Clostridium pasteurianum nitrogenase produces an inactive, stable complex. However, we report that this heterologous nitrogenase has a low level of activity for H(2) evolution, with a specific activity of 12 nmol min(-)(1) mg(-)(1) of Av1. This activity does not arise from contaminating hydrogenase since it required the presence of both Cp2 and Av1 and showed saturation kinetics when increasing amounts of Cp2 were added to the assay. Incubation of the two proteins at a 4:1 Cp2:Av1 ratio in the absence of MgATP followed by analytical gel filtration showed, surprisingly, that the stoichiometry of the isolated complex was Av1.Cp2 instead of Av1.(Cp2)(2) as determined previously. The presence of MgATP in the elution buffer did not change the elution profile of the complex. The hydrodynamic radius of the isolated complex determined by dynamic light scattering was 5.93 +/- 0.14 nm, intermediate between Av1 and a stable 2:1 nitrogenase complex, consistent with a 1:1 assignment for the Av1.Cp2 complex. When assayed with Av2, the isolated Av1.Cp2 complex showed full half-site reactivity with a specific activity of 750 nmol of C(2)H(2) reduced min(-)(1) mg(-)(1) of Av1. The EPR spectrum of the isolated complex showed the Cp2 to be oxidized and the Av1 to retain the S = (3)/(2) signal characteristic of FeMoco. In the presence of MgATP, under turnover conditions at a 2:1 ratio of Cp2:Av1, the [4Fe-4S] center of Cp2 was protected from the chelator 2,2'-bipyridyl. This is consistent with the formation of a tight 2:1 complex of Av1.(Cp2)(2) which is more stable than the homologous Cp nitrogenase. Assuming that the Lowe-Thorneley model for nitrogenase applies and that a rate-limiting dissociation of the complex is required for H(2) evolution, then with a rate of 0.032 s(-)(1) the 1:1 complex is too stable to be involved in catalysis. The

  5. Site selection

    SciTech Connect

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO/sub 2/ content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate.

  6. Expression of recombinant human serum amyloid A in mammalian cells and demonstration of the region necessary for high-density lipoprotein binding and amyloid fibril formation by site-directed mutagenesis.

    PubMed Central

    Patel, H; Bramall, J; Waters, H; De Beer, M C; Woo, P

    1996-01-01

    Site-directed mutagenesis of the acute-phase human serum amyloid A (SAA1 alpha) protein was used to evaluate the importance of the N-terminal amino acid residues, namely RSFFSFLGEAF The full-length cDNA clone of SAA1 alpha (pA1.mod.) was used to create two mutations, namely Gly-8 to Asp-8 and an 11 amino acid truncation between Arg-1 and Phe-11 respectively. Wild-type and mutant cDNAs were expressed in Chinese hamster ovary (CHO) cells under the control of the human cytomegalovirus promoter, which resulted in the secretion of the processed proteins into the culture media. Wild-type recombinant human SAA (rSAA) protein was shown to have pI values of 6.0 and 6.4, similar to the human SAA isoform SAA1 alpha and SAA1 alpha desArg found in acute-phase plasma. N-terminal sequencing of 56 residues confirmed its identity with human SAA1 alpha. The total yield of wild-type rSAA measured by ELISA was between 3.5 and 30 mg/l. The two mutations resulted in reduced expression levels of the mutant SAA proteins (3-10 mg/l). Further measurements of rSAA concentration in lipid fractions of culture medium collected at a density of 1.21 g/ml (high-density liporotein; HDL) and 1.063-1.18 g/ml (very-low-density lipoprotein/low-density lipoprotein; VLDL/LDL) showed that 76% of the wild-type protein was found in the HDL fraction and the remaining 24% in the infranatant non-lipid fraction. In contrast the relative concentration of mutant rSAA in HDL and infranatant fractions was reversed. This is consistent with the previously proposed involvement of the 11 amino acid peptide in anchoring. SAA protein on to HDL3 [Turnell, Sarra, Glover, Baum, Caspi, Baltz and Pepys (1986) Mol. Biol. Med. 3, 387-407]. Wild-type rSAA protein was shown to from amyloid fibrils in vitro under acidic conditions as shown by electron microscopy, and stained positive with Congo Red and exhibited apple-green birefringence when viewed under polarized light. Under the same conditions mutSAA(G8D) and mutSAA delta 1

  7. Diepoxybutane induces the formation of DNA-DNA rather than DNA-protein cross-links, and single-strand breaks and alkali-labile sites in human hepatocyte L02 cells.

    PubMed

    Wen, Ying; Zhang, Pan-Pan; An, Jing; Yu, Ying-Xin; Wu, Ming-Hong; Sheng, Guo-Ying; Fu, Jia-Mo; Zhang, Xin-Yu

    2011-11-01

    1,3-Butadiene (BD) is an air pollutant and a known carcinogen. 1,2,3,4-Diepoxybutane (DEB), one of the major in vivo metabolites of BD, is considered the ultimate culprit of BD mutagenicity/carcinogenicity. DEB is a bifunctional alkylating agent, being capable of inducing the formation of monoalkylated DNA adducts and DNA cross-links, including DNA-DNA and DNA-protein cross-links (DPC). In the present study, we investigated DEB-caused DNA cross-links and breaks in human hepatocyte L02 cells using comet assay. With alkaline comet assay, it was observed that DNA migration increased with the increase of DEB concentration at lower concentrations (10-200μM); however, at higher concentrations (200-1000μM), DNA migration decreased with the increase of DEB concentration. This result indicated the presence of cross-links at >200μM, which was confirmed by the co-treatment experiments using the second genotoxic agents, tert-butyl hydroperoxide and methyl methanesulfonate. At 200μM, which appeared as a threshold, the DNA migration-retarding effect of cross-links was just observable by the co-treatment experiments. At <200μM, the effect of cross-links was too weak to be detected. The DEB-induced cross-links were determined to be DNA-DNA ones rather than DPC through incubating the liberated DNA with proteinase K prior to unwinding and electrophoresis. However, at the highest DEB concentration tested (1000μM), a small proportion of DPC could be formed. In addition, the experiments using neutral and weakly alkaline comet assays showed that DEB did not cause double-strand breaks, but did induce single-strand breaks (SSB) and alkali-labile sites (ALS). Since SSB and ALS are repaired more rapidly than cross-links, the results suggested that DNA-DNA cross-links, rather than DPC, were probably responsible for mutagenicity/carcinogenicity of DEB.

  8. Concept Formation.

    ERIC Educational Resources Information Center

    Vaidya, Narendera

    This document, published in India by the Regional College of Education, deals with 13 subjects: the tough context (thinking), definitions of concept, functions of concept, the process of concept formation, discriminant learning, mediation process, second signalling system, factors affecting concept formation, studies in concept formation, the…

  9. Evaluation of Cavity Collapse and Surface Crater Formation at the Norbo Underground Nuclear Test in U8c, Nevada Nuclear Security Site, and the Impact on Stability of the Ground Surface

    SciTech Connect

    Pawloski, G A

    2012-06-18

    Lawrence Livermore National Laboratory (LLNL) Containment Program performed a review of nuclear test-related data for the Norbo underground nuclear test in U8c to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. This request is similar to one made for the Salut site in U8c (Pawloski, 2012b). Review of the Norbo site is complicated because the test first exhibited subsurface collapse, which was not unusual, but it then collapsed to the surface over one year later, which was unusual. Of particular interest is the stability of the ground surface above the Norbo detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeology due to the nuclear detonation. Aviva Sussman from the Los Alamos National Laboratory (LANL) has also proposed work at this site. Both proposals require physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Security Site (NNSS), formerly the Nevada Test Site (NTS), and focus on possible activities such as visual observation, multispectral measurements, and shallow and deep geophysical surveys.

  10. Interpretation of single-well push-pull spikings conducted in deep crystalline formations (Soultz-s.-F. in the Upper Rhine Graben, and KTB-VB at the German site of ICDP)

    NASA Astrophysics Data System (ADS)

    Ghergut, J.; Sauter, M.; Behrens, H.; (Steffen) Fischer, S.; (Steffi) Fischer, S.; Licha, T.; Nottebohm, M.

    2009-04-01

    Two somewhat contrasting model approaches are presented, both aimed at interpreting long-term return signals from tracer push-pull tests conducted at single wells penetrating increased-permeability features in crystalline rock, about 4 km deep. The general idea is that single-well tracer push-pull tests, owing to the flow-field reversal, should provide privileged access to advection-independent parameters of solute transport, like the density of fluid-rock contact surface areas (Sauter et al., 2002). The latter is equivalent to the heat exchange area for a liquid-based geothermal system. At the geothermal site of Soultz-sous-Forêts in the Upper Rhine Graben, the French BRGM, in cooperation with EGI Utah and other partners, conducted a comprehensive tracer testing programme, whose results were presented in detail by Sanjuan et al. (2004, 2006), Rose et al. (2006). Of these results, we pick the tracer return signals detected during post-stimulation backflow periods at borehole GPK-2 between 2000 and 2002 (as published by Sanjuan et al., 2004) and attempt to interpret them in terms of a single-well injection-withdrawal sequence. Two chemically dissimilar organic tracers have been used by BRGM; however the difference between their return signals seems not significant enough to allow quantifying fluid-rock contact surfaces from this difference alone (additional / a priori information on coefficients of solute exchange across these surfaces would be required). Instead, the tracer return signals enable characterizing the nature of solute exchange processes within the spiked volume of the assumed fractured-porous formation (highly altered crystalline rock). At least one rapid-exchange (E-7 / d), slightly dispersive (Pe~12) component and one moderate-exchange (2E-8 / d), less dispersive (Pe~20) component appear to act within few hundred metres and, respectively, within at least 1 km radial distance from the borehole. - An alternative component of extremely fast exchange

  11. Site Construction.

    ERIC Educational Resources Information Center

    Richardson, Eric C.

    1996-01-01

    Presents a guide to planning and building a Web site, with an emphasis on setting up a Web server. Discussion includes hiring a consultant, contracts and payment, assembly of teams, training, development of a business plan, registration of domain name, purchase of hardware and software, local area networks, and types of Internet connection. (JKP)

  12. Photoluminescence and EPR studies on Fe³⁺ doped ZnAl₂O₄: an evidence for local site swapping of Fe³⁺ and formation of inverse and normal phase.

    PubMed

    Pathak, Nimai; Gupta, Santosh K; Sanyal, Kaushik; Kumar, Mithlesh; Kadam, R M; Natarajan, V

    2014-06-28

    Considering that ZnAl2O4 spinel has two different sites (octahedral and tetrahedral) and its properties change with dopant ion distribution among these two sites; ZnAl2O4 doped with varied concentrations of Fe(3+) was synthesized by a low temperature sol-gel combustion method. Phase purity and structural investigations were carried out using Rietveld refined X-ray diffraction which shows a decrease in the value of cell parameters at higher doping levels. Photoluminescence (PL) and electron paramagnetic resonance (EPR) studies have shown that on doping, Fe(3+) ions were distributed in both tetrahedral and octahedral sites. At octahedral sites, Fe(3+) exhibited a broad red emission around 745 nm while at tetrahedral sites it exhibited well-defined vibronic sidebands at 665, 674, 684 and 693 nm along with a broad blue band with a maxima at 445 nm at room temperature. EPR studies have shown a broad spectrum at g ≈ 2.2 which corresponds to the Fe(3+) in octahedral sites, while the broad signal at g ≈ 4.2 belongs to Fe(3+) in tetrahedral sites. It was also inferred from these studies that Fe(3+) prefers to occupy octahedral sites at higher concentrations and at higher annealing temperatures. The PL decay behavior of Fe(3+) in ZnAl2O4 has also shown that two different types of Fe(3+) ions were present in this matrix. The first type was a long lived species (τ ≈ 170 μs) present at octahedral sites and the other was a short lived species (τ ≈ 40 μs) present at the tetrahedral sites; the fraction of the long lived species predominate at higher concentrations. Thus the present work is mainly focused on understanding the tuning of local site occupancy of the dopant ion among those sites with varying concentration and annealing temperature, using the dopant ion itself as a spectroscopic probe, which further helps in understanding the phase (inverse and normal) of the spinel.

  13. Evaluation of Cavity Collapse and Surface Crater Formation at the Salut Underground Nuclear Test in U20ak, Nevada National Security Site, and the Impact of Stability of the Ground Surface

    SciTech Connect

    Pawloski, G A

    2012-04-25

    At the request of Jerry Sweeney, the LLNL Containment Program performed a review of nuclear test-related data for the Salut underground nuclear test in U20ak to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. Review of the Salut site is complicated because the test experienced a subsurface, rather than surface, collapse. Of particular interest is the stability of the ground surface above the Salut detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeologogy due to the nuclear detonation. Sweeney's proposal requires physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Test Site (NNSS, formerly the Nevada Test Site), and focuses on possible activities such as visual observation, multispectral measurements, and shallow, and deep geophysical surveys.

  14. Gaussian entanglement of formation

    SciTech Connect

    Wolf, M.M.; Giedke, G.; Krueger, O.; Werner, R. F.; Cirac, J.I.

    2004-05-01

    We introduce a Gaussian version of the entanglement of formation adapted to bipartite Gaussian states by considering decompositions into pure Gaussian states only. We show that this quantity is an entanglement monotone under Gaussian operations and provide a simplified computation for states of arbitrary many modes. For the case of one mode per site the remaining variational problem can be solved analytically. If the considered state is in addition symmetric with respect to interchanging the two modes, we prove additivity of the considered entanglement measure. Moreover, in this case and considering only a single copy, our entanglement measure coincides with the true entanglement of formation.

  15. MX Siting Investigation Geotechnical Siting Status Report. Volume I.

    DTIC Science & Technology

    1978-06-21

    characteristics. Suitable siting area was delineated as soil and excavatable rock. Suitable excavatable rock was assigned to sedimentary formations which could be...refraction line 0 / ~.’ ~T ca SITE LOCATION ~ NEVADA Sd SITE THE RA Gk 0 -o o ___ n~in 72 1,250,000 10=3.2 Nautical ills (APftOXINATE) ACTIVITY LOCATION M~AP...northeastern portion of the valley are dissected into a badlands -type topography and commonly have ten feet (3 m) or more of incision. 3.6.2 Subsurface

  16. 1994 Site Environmental Report

    SciTech Connect

    1995-05-01

    The 1994 Site Environmental Report summarizes environmental activities at Lawrence Berkeley Laboratory (LBL) for the calendar year (CY) 1994. The report strives to present environmental data in a manner that characterizes the performance and compliance status of the Laboratory`s environmental management programs when measured against regulatory standards and DOE requirements. The report also discusses significant highlight and planning efforts of these programs. The format and content of the report are consistent with the requirements of the US Department of Energy (DOE) Order 5400.1, General Environmental Protection Program.

  17. Division site placement in E.coli: mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains.

    PubMed

    Shih, Yu-Ling; Fu, Xiaoli; King, Glenn F; Le, Trung; Rothfield, Lawrence

    2002-07-01

    The MinE protein functions as a topological specificity factor in determining the site of septal placement in Escherichia coli. MinE assembles into a membrane-associated ring structure near midcell and directs the localization of MinD and MinC into a membrane- associated polar zone that undergoes a characteristic pole-to-pole oscillation cycle. Single (green fluorescent protein) and double label (yellow fluorescent protein/cyan fluorescent protein) fluorescence labeling experiments showed that mutational alteration of a site on the alpha-face of MinE led to a failure to assemble the MinE ring, associated with loss of the ability to support a normal pattern of division site placement. The absence of the MinE ring did not prevent the assembly and disassembly of the MinD polar zone. Mutant cells lacking the MinE ring were characterized by the growth of MinD polar zones past their normal arrest point near midcell. The results suggested that the MinE ring acts as a stop-growth mechanism to prevent the MinCD polar zone from extending beyond the midcell division site.

  18. Motion Predicts Clinical Callus Formation

    PubMed Central

    Elkins, Jacob; Marsh, J. Lawrence; Lujan, Trevor; Peindl, Richard; Kellam, James; Anderson, Donald D.; Lack, William

    2016-01-01

    Background: Mechanotransduction is theorized to influence fracture-healing, but optimal fracture-site motion is poorly defined. We hypothesized that three-dimensional (3-D) fracture-site motion as estimated by finite element (FE) analysis would influence callus formation for a clinical series of supracondylar femoral fractures treated with locking-plate fixation. Methods: Construct-specific FE modeling simulated 3-D fracture-site motion for sixty-six supracondylar femoral fractures (OTA/AO classification of 33A or 33C) treated at a single institution. Construct stiffness and directional motion through the fracture were investigated to assess the validity of construct stiffness as a surrogate measure of 3-D motion at the fracture site. Callus formation was assessed radiographically for all patients at six, twelve, and twenty-four weeks postoperatively. Univariate and multivariate linear regression analyses examined the effects of longitudinal motion, shear (transverse motion), open fracture, smoking, and diabetes on callus formation. Construct types were compared to determine whether their 3-D motion profile was associated with callus formation. Results: Shear disproportionately increased relative to longitudinal motion with increasing bridge span, which was not predicted by our assessment of construct stiffness alone. Callus formation was not associated with open fracture, smoking, or diabetes at six, twelve, or twenty-four weeks. However, callus formation was associated with 3-D fracture-site motion at twelve and twenty-four weeks. Longitudinal motion promoted callus formation at twelve and twenty-four weeks (p = 0.017 for both). Shear inhibited callus formation at twelve and twenty-four weeks (p = 0.017 and p = 0.022, respectively). Titanium constructs with a short bridge span demonstrated greater longitudinal motion with less shear than did the other constructs, and this was associated with greater callus formation (p < 0.001). Conclusions: In this study of

  19. Characterization of Archaeological Sediments Using Fourier Transform Infrared (FT-IR) and Portable X-ray Fluorescence (pXRF): An Application to Formative Period Pyro-Industrial Sites in Pacific Coastal Southern Chiapas, Mexico.

    PubMed

    Neff, Hector; Bigney, Scott J; Sakai, Sachiko; Burger, Paul R; Garfin, Timothy; George, Richard G; Culleton, Brendan J; Kennett, Douglas J

    2016-01-01

    Archaeological sediments from mounds within the mangrove zone of far-southern Pacific coastal Chiapas, Mexico, are characterized in order to test the hypothesis that specialized pyro-technological activities of the region's prehistoric inhabitants (salt and ceramic production) created the accumulations visible today. Fourier transform infrared spectroscopy (FT-IR) is used to characterize sediment mineralogy, while portable X-ray fluorescence (pXRF) is used to determine elemental concentrations. Elemental characterization of natural sediments by both instrumental neutron activation analysis (INAA) and pXRF also contribute to understanding of processes that created the archaeological deposits. Radiocarbon dates combined with typological analysis of ceramics indicate that pyro-industrial activity in the mangrove zone peaked during the Late Formative and Terminal Formative periods, when population and monumental activity on the coastal plain and piedmont were also at their peaks.

  20. Interplay between on-site electron-phonon interaction and inter-site Coulomb repulsion

    SciTech Connect

    Nath, S.; Mondal, N. S.; Roy, K.; Ghosh, N. K.

    2016-05-23

    We present a numerical study on the interplay between on-site electron-phonon (EP) interaction and inter-site Coulomb repulsion in the U/t =0.0 limit on a small cluster. Results show the formation of only S0 bipolarons. However, two polarons or bipolarons can be present at distances |i-j|=2. It is observed that inter-site Coulomb repulsion may favor formation of S0 bipolarons.

  1. Galaxy formation

    SciTech Connect

    Silk, J.

    1984-11-01

    Implications of the isotropy of the cosmic microwave background on large and small angular scales for galaxy formation are reviewed. In primeval adiabatic fluctuations, a universe dominated by cold, weakly interacting nonbaryonic matter, e.g., the massive photino is postulated. A possible signature of photino annihilation in our galactic halo involves production of cosmic ray antiprotons. If the density is near its closure value, it is necessary to invoke a biasing mechanism for suppressing galaxy formation throughout most of the universe in order to reconcile the dark matter density with the lower astronomical determinations of the mean cosmological density. A mechanism utilizing the onset of primordial massive star formation to strip gaseous protogalaxies is described. Only the densest, early collapsing systems form luminous galaxies. (ESA)

  2. Comet formation

    NASA Astrophysics Data System (ADS)

    Blum, J.

    2014-07-01

    There has been vast progress in our understanding of planetesimal formation over the past decades, owing to a number of laboratory experiments as well as to refined models of dust and ice agglomeration in protoplanetary disks. Coagulation rapidly forms cm-sized ''pebbles'' by direct sticking in collisions at low velocities (Güttler et al. 2010; Zsom et al. 2010). For the further growth, two model approaches are currently being discussed: (1) Local concentration of pebbles in nebular instabilities until gravitational instability occurs (Johansen et al. 2007). (2) A competition between fragmentation and mass transfer in collisions among the dusty bodies, in which a few ''lucky winners'' make it to planetesimal sizes (Windmark et al. 2012a,b; Garaud et al. 2013). Predictions of the physical properties of the resulting bodies in both models allow a distinction of the two formation scenarios of planetesimals. In particular, the tensile strength (i.e, the inner cohesion) of the planetesimals differ widely between the two models (Skorov & Blum 2012; Blum et al. 2014). While model (1) predicts tensile strengths on the order of ˜ 1 Pa, model (2) results in rather compactified dusty bodies with tensile strengths in the kPa regime. If comets are km-sized survivors of the planetesimal-formation era, they should in principle hold the secret of their formation process. Water ice is the prime volatile responsible for the activity of comets. Thermophysical models of the heat and mass transport close to the comet-nucleus surface predict water-ice sublimation temperatures that relate to maximum sublimation pressures well below the kPa regime predicted for formation scenario (2). Model (1), however, is in agreement with the observed dust and gas activity of comets. Thus, a formation scenario for cometesimals involving gravitational instability is favored (Blum et al. 2014).

  3. Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine.

    PubMed

    Eisenhaber, Birgit; Eisenhaber, Stephan; Kwang, Toh Yew; Grüber, Gerhard; Eisenhaber, Frank

    2014-01-01

    The transamidase subunit GAA1/GPAA1 is predicted to be the enzyme that catalyzes the attachment of the glycosylphosphatidyl (GPI) lipid anchor to the carbonyl intermediate of the substrate protein at the ω-site. Its ~300-amino acid residue lumenal domain is a M28 family metallo-peptide-synthetase with an α/β hydrolase fold, including a central 8-strand β-sheet and a single metal (most likely zinc) ion coordinated by 3 conserved polar residues. Phosphoethanolamine is used as an adaptor to make the non-peptide GPI lipid anchor look chemically similar to the N terminus of a peptide.

  4. Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein’s omega-site and the GPI lipid anchor’s phosphoethanolamine

    PubMed Central

    Eisenhaber, Birgit; Eisenhaber, Stephan; Kwang, Toh Yew; Grüber, Gerhard; Eisenhaber, Frank

    2014-01-01

    The transamidase subunit GAA1/GPAA1 is predicted to be the enzyme that catalyzes the attachment of the glycosylphosphatidyl (GPI) lipid anchor to the carbonyl intermediate of the substrate protein at the ω-site. Its ~300-amino acid residue lumenal domain is a M28 family metallo-peptide-synthetase with an α/β hydrolase fold, including a central 8-strand β-sheet and a single metal (most likely zinc) ion coordinated by 3 conserved polar residues. Phosphoethanolamine is used as an adaptor to make the non-peptide GPI lipid anchor look chemically similar to the N terminus of a peptide. PMID:24743167

  5. Detection and imaging of the free radical DNA in cells—Site-specific radical formation induced by Fenton chemistry and its repair in cellular DNA as seen by electron spin resonance, immuno-spin trapping and confocal microscopy

    PubMed Central

    Bhattacharjee, Suchandra; Chatterjee, Saurabh; Jiang, JinJie; Sinha, Birandra Kumar; Mason, Ronald P.

    2012-01-01

    Oxidative stress-related damage to the DNA macromolecule produces lesions that are implicated in various diseases. To understand damage to DNA, it is important to study the free radical reactions causing the damage. Measurement of DNA damage has been a matter of debate as most of the available methods measure the end product of a sequence of events and provide limited information on the initial free radical formation. We report a measurement of free radical damage in DNA induced by a Cu(II)-H2O2 oxidizing system using immuno-spin trapping supplemented with electron paramagnetic resonance. In this investigation, the short-lived radical generated is trapped by the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) immediately upon formation. The DMPO adduct formed is initially electron paramagnetic resonance active, but is subsequently oxidized to the stable nitrone adduct, which can be detected and visualized by immuno-spin trapping and has the potential to be further characterized by other analytical techniques. The radical was found to be located on the 2′-deoxyadenosine (dAdo) moiety of DNA. The nitrone adduct was repaired on a time scale consistent with DNA repair. In vivo experiments for the purpose of detecting DMPO–DNA nitrone adducts should be conducted over a range of time in order to avoid missing adducts due to the repair processes. PMID:22387463

  6. Combined Survey Format (CSF) Archaeogeophysical (Metal Detecting, Radiometrics and Resistivity) and Archaeochemical (XRF) Investigations of the 19th Century La Hacienda Y Presidio of Babocomari Military Site in Arizona

    NASA Astrophysics Data System (ADS)

    Lundin, R. J.; Aydin, N.; Brackett, C.

    2007-05-01

    Recent archaeological investigations of Historic Era Mexican and Anglo-American and Prehistoric and Protohistoric Hohokam and Sobaipuri culture sites on the Babacomari Land Grant near Sierra Vista Arizona by Carothers Environmental, LLC (CE), Wondjina Research Institute (WRI) and DMG Four Corners Research (FCR) led to the discovery of two major 19th Century military sites that were known from the literature but had not been scientifically investigated. It was decided by WRI and BABACOMARI RANCH that this project was ideal for an experimental cooperative training program for archaeologists and geologists from the anthropology and geology departments of UA, ASU, NAU, PC, and members of AAS, AAHS, AAC, THS and USFS personnel in the use of the new CSF archaeogeophysical, archaeochemical and airbourne remote sensing technologies and field techniques that have just been recently introduced in the US. WRI, CE and Statistical Research Inc. (SRI) conducted CSF VLF Metal Detecting, Radiometrics and Resistivity studies and portable X-Ray Fluorescence (XRF) archaeochemical studies. The results will be presented along with suggestions as to use of these technologies in CSF studies.

  7. Preshot Geophysical Properties of Palanquin Crater Site

    DTIC Science & Technology

    2007-11-02

    The rocks at the Palanquin site are of volcanic origin, and consist predominantly of trachyte porphyry of the Ribbon Cliff formation of Pliocene age...Pyroclastic volcanic tuff underlies the trachyte porphyry at a depth of 175 m and caps low hills adjacent to the site. The volcanic units have a

  8. Planet Formation

    NASA Technical Reports Server (NTRS)

    Lissauer, Jack J.; Young, Richard E. (Technical Monitor)

    1997-01-01

    Modern theories of star and planet formation, which are based upon observations of the Solar System and of young stars and their environments, predict that most single stars should have rocky planets in orbit about them; the frequency of gas giant planets is more difficult to predict theoretically. Terrestrial planets are believed to grow via pairwise accretion until the spacing of planetary orbits becomes large enough that the configuration is stable for the age of the system. Giant planets begin their growth like terrestrial planets, but they become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. Models for the formation of the giant planets found in recent radial velocity searches are discussed.

  9. Planet Formation

    NASA Technical Reports Server (NTRS)

    Lissauer, Jack J.; Young, Richard E. (Technical Monitor)

    1998-01-01

    An overview of current theories of star and planet formation is presented. These models are based upon observations of the Solar System and of young stars and their environments. They predict that rocky planets should form around most single stars, although it is possible that in some cases such planets are lost to orbital decay within the protoplanetary disk. The frequency of formation of gas giant planets is more difficult to predict theoretically. Terrestrial planets are believed to grow via pairwise accretion until the spacing of planetary orbits becomes large enough that the configuration is stable for the age of the system. Giant planets begin their growth like terrestrial planets, but they become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates.

  10. Galaxy formation

    PubMed Central

    Peebles, P. J. E.

    1998-01-01

    It is argued that within the standard Big Bang cosmological model the bulk of the mass of the luminous parts of the large galaxies likely had been assembled by redshift z ∼ 10. Galaxy assembly this early would be difficult to fit in the widely discussed adiabatic cold dark matter model for structure formation, but it could agree with an isocurvature version in which the cold dark matter is the remnant of a massive scalar field frozen (or squeezed) from quantum fluctuations during inflation. The squeezed field fluctuations would be Gaussian with zero mean, and the distribution of the field mass therefore would be the square of a random Gaussian process. This offers a possibly interesting new direction for the numerical exploration of models for cosmic structure formation. PMID:9419326

  11. Planet formation

    NASA Technical Reports Server (NTRS)

    Lissauer, Jack J.

    1993-01-01

    Models of planetary formation are developed using the present single example of a planetary system, supplemented by limited astrophysical observations of star-forming regions and circumstellar disks. The solar nebula theory and the planetesimal hypothesis are discussed. The latter is found to provide a viable theory of the growth of the terrestrial planets, the cores of the giant planets, and the smaller bodies present in the solar system. The formation of solid bodies of planetary size should be a common event, at least around young stars which do not have binary companions orbiting at planetary distances. Stochastic impacts of large bodies provide sufficient angular momentum to produce the obliquities of the planets. The masses and bulk compositions of the planets can be understood in a gross sense as resulting from planetary growth within a disk whose temperature and surface density decreased with distance from the growing sun.

  12. Examining the effects of anthropogenic emissions on isoprene-derived secondary organic aerosol formation during the 2013 Southern Oxidant and Aerosol Study (SOAS) at the Look Rock, Tennessee, ground site

    NASA Astrophysics Data System (ADS)

    Budisulistiorini, S. H.; Li, X.; Bairai, S. T.; Renfro, J.; Liu, Y.; Liu, Y. J.; McKinney, K. A.; Martin, S. T.; McNeill, V. F.; Pye, H. O. T.; Nenes, A.; Neff, M. E.; Stone, E. A.; Mueller, S.; Knote, C.; Shaw, S. L.; Zhang, Z.; Gold, A.; Surratt, J. D.

    2015-03-01

    A suite of offline and real-time gas- and particle-phase measurements was deployed at Look Rock, Tennessee (TN), during the 2013 Southern Oxidant and Aerosol Study (SOAS) to examine the effects of anthropogenic emissions on isoprene-derived secondary organic aerosol (SOA) formation. High- and low-time resolution PM2.5 samples were collected for analysis of known tracer compounds in isoprene-derived SOA by gas chromatography/electron ionization-mass spectrometry (GC/EI-MS) and ultra performance liquid chromatography/diode array detection-electrospray ionization-high-resolution quadrupole time-of-flight mass spectrometry (UPLC/DAD-ESI-HR-QTOFMS). Source apportionment of the organic aerosol (OA) was determined by positive matrix factorization (PMF) analysis of mass spectrometric data acquired on an Aerodyne Aerosol Chemical Speciation Monitor (ACSM). Campaign average mass concentrations of the sum of quantified isoprene-derived SOA tracers contributed to ~9% (up to 26%) of the total OA mass, with isoprene-epoxydiol (IEPOX) chemistry accounting for ~97% of the quantified tracers. PMF analysis resolved a factor with a profile similar to the IEPOX-OA factor resolved in an Atlanta study and was therefore designated IEPOX-OA. This factor was strongly correlated (r2>0.7) with 2-methyltetrols, C5-alkene triols, IEPOX-derived organosulfates, and dimers of organosulfates, confirming the role of IEPOX chemistry as the source. On average, IEPOX-derived SOA tracer mass was ~25% (up to 47%) of the IEPOX-OA factor mass, which accounted for 32% of the total OA. A low-volatility oxygenated organic aerosol (LV-OOA) and an oxidized factor with a profile similar to 91Fac observed in areas where emissions are biogenic-dominated were also resolved by PMF analysis, whereas no primary organic aerosol (POA) sources could be resolved. These findings were consistent with low levels of primary pollutants, such as nitric oxide (NO~0.03ppb), carbon monoxide (CO~116 ppb), and black carbon (BC~0

  13. Examining the effects of anthropogenic emissions on isoprene-derived secondary organic aerosol formation during the 2013 Southern Oxidant and Aerosol Study (SOAS) at the Look Rock, Tennessee ground site

    NASA Astrophysics Data System (ADS)

    Budisulistiorini, S. H.; Li, X.; Bairai, S. T.; Renfro, J.; Liu, Y.; Liu, Y. J.; McKinney, K. A.; Martin, S. T.; McNeill, V. F.; Pye, H. O. T.; Nenes, A.; Neff, M. E.; Stone, E. A.; Mueller, S.; Knote, C.; Shaw, S. L.; Zhang, Z.; Gold, A.; Surratt, J. D.

    2015-08-01

    A suite of offline and real-time gas- and particle-phase measurements was deployed at Look Rock, Tennessee (TN), during the 2013 Southern Oxidant and Aerosol Study (SOAS) to examine the effects of anthropogenic emissions on isoprene-derived secondary organic aerosol (SOA) formation. High- and low-time-resolution PM2.5 samples were collected for analysis of known tracer compounds in isoprene-derived SOA by gas chromatography/electron ionization-mass spectrometry (GC/EI-MS) and ultra performance liquid chromatography/diode array detection-electrospray ionization-high-resolution quadrupole time-of-flight mass spectrometry (UPLC/DAD-ESI-HR-QTOFMS). Source apportionment of the organic aerosol (OA) was determined by positive matrix factorization (PMF) analysis of mass spectrometric data acquired on an Aerodyne Aerosol Chemical Speciation Monitor (ACSM). Campaign average mass concentrations of the sum of quantified isoprene-derived SOA tracers contributed to ~ 9 % (up to 28 %) of the total OA mass, with isoprene-epoxydiol (IEPOX) chemistry accounting for ~ 97 % of the quantified tracers. PMF analysis resolved a factor with a profile similar to the IEPOX-OA factor resolved in an Atlanta study and was therefore designated IEPOX-OA. This factor was strongly correlated (r2 > 0.7) with 2-methyltetrols, C5-alkene triols, IEPOX-derived organosulfates, and dimers of organosulfates, confirming the role of IEPOX chemistry as the source. On average, IEPOX-derived SOA tracer mass was ~ 26 % (up to 49 %) of the IEPOX-OA factor mass, which accounted for 32 % of the total OA. A low-volatility oxygenated organic aerosol (LV-OOA) and an oxidized factor with a profile similar to 91Fac observed in areas where emissions are biogenic-dominated were also resolved by PMF analysis, whereas no primary organic aerosol (POA) sources could be resolved. These findings were consistent with low levels of primary pollutants, such as nitric oxide (NO ~ 0.03 ppb), carbon monoxide (CO ~ 116 ppb), and black

  14. Influence of Na+ on DNA reactions with aromatic epoxides and diol epoxides: evidence that DNA catalyzes the formation of benzo[a]pyrene and benz[a]anthracene adducts at intercalation sites.

    PubMed

    Fernando, H; Huang, C R; Milliman, A; Shu, L; LeBreton, P R

    1996-12-01

    Reactions of the benzo[a]pyrene (BP) and benz[a]anthracene (BA) metabolites, (+/-)-trans-7 8-dihydroxy-anti-9, 10-epoxy-7, 8, 9, 10-tetrahydro-BP (BPDE), (+/-)-trans-3, 4-dihydroxy-anti- 1,2-epoxy-1,2,3,4-tetrahydro-BA (BADE), (+/-)-BP-4,5-oxide (BPO), and (+/-)-BA-5, 6-oxide (BAO), were examined under pseudo-first-order conditions at varying Na+ (2.0-100 Mm) and native calf thymus DNA (ctDNA) concentrations. In 0.2 mM ctDNA and 2.0 mM Na+, at a pH of 7.3 most BPDE, BADE, BPO, and BAO (87-95%) undergo DNA catalyzed hydrolysis or rearrangement. For BPDE and BPO, overall, pseudo-first-order rate constants, k, in 2.0 mM Na+ and 0.2 mM ctDNA are 21-72 times larger than values obtained without DNA. For BADE and BAO, the rate constants are less strongly influenced by DNA; k values in 0.2 mM ctDNA are only 9-12 times larger than values obtained without DNA. Kinetic data for BPDE, BPO, BADE, and BAO and DNA intercalation association constants (KA) for BP and BA diols which are model compounds indicate that KA values for BPDE and BPO in 2.0 mM Na+ are 6.6-59 times larger than those of BADE and BAO. The greater DNA enhancement of rate constants for BPDE and BPO, versus BADE and BAO, correlates with the larger KA values of the BP metabolites. DNA adducts, which account for less than 10% of the yields, also form. For BPDE in 0.20 mM ctDNA, k decreases 5.1 times as the Na+ concentration increases from 2.0 to 100 mM. Nevertheless, the DNA adduct level remains constant over the range of Na+ concentrations examined. These results provide evidence that, for BPDE in 0.20 mM DNA and 2.0 mM Na+, ctDNA adduct formation follows a mechanism which is similar to that for DNA catalyzed hydrolysis. The pseudo-first-order rate constant for adduct formation, kAd, given approximately by kAd approximately equal to (kcat,AdKA[DNA])/(1 + KA[DNA]), where kcat,Ad is a catalytic rate constant. for BADE, BPO, and BAO, the influence of varying DNA and Na+ concentrations on k values is similar to that

  15. Cloud Formation

    NASA Astrophysics Data System (ADS)

    Graham, Mark Talmage

    2004-05-01

    Cloud formation is crucial to the heritage of modern physics, and there is a rich literature on this important topic. In 1927, Charles T.R. Wilson was awarded the Nobel Prize in physics for applications of the cloud chamber.2 Wilson was inspired to study cloud formation after working at a meteorological observatory on top of the highest mountain in Scotland, Ben Nevis, and testified near the end of his life, "The whole of my scientific work undoubtedly developed from the experiments I was led to make by what I saw during my fortnight on Ben Nevis in September 1894."3 To form clouds, Wilson used the sudden expansion of humid air.4 Any structure the cloud may have is spoiled by turbulence in the sudden expansion, but in 1912 Wilson got ion tracks to show up by using strobe photography of the chamber immediately upon expansion.5 In the interim, Millikan's study in 1909 of the formation of cloud droplets around individual ions was the first in which the electron charge was isolated. This study led to his famous oil drop experiment.6 To Millikan, as to Wilson, meteorology and physics were professionally indistinct. With his meteorological physics expertise, in WWI Millikan commanded perhaps the first meteorological observation and forecasting team essential to military operation in history.7 But even during peacetime meteorology is so much of a concern to everyone that a regular news segment is dedicated to it. Weather is the universal conversation topic, and life on land could not exist as we know it without clouds. One wonders then, why cloud formation is never covered in physics texts.

  16. 92-kD gelatinase is produced by eosinophils at the site of blister formation in bullous pemphigoid and cleaves the extracellular domain of recombinant 180-kD bullous pemphigoid autoantigen.

    PubMed Central

    Ståhle-Bäckdahl, M; Inoue, M; Guidice, G J; Parks, W C

    1994-01-01

    Eosinophils are prominent in bullous pemphigoid (BP), and proteases secreted from these and other inflammatory cells may induce disruption of the basement membrane. We used in situ hybridization and immunohistochemistry to localize the sites of 92-kD gelatinase expression in BP lesions. In all samples (20/20), a strong signal for gelatinase mRNA was detected only in eosinophils and was most pronounced where these cells accumulated at the floor of forming blisters. No other cells were positive for enzyme mRNA. Both eosinophils and neutrophils, however, contained immunoreactive 92-kD gelatinase indicating that active expression occurred only in eosinophils. Degranulated eosinophils were also seen near blisters, and as demonstrated by gelatin zymography, immunoblotting, and ELISA, 92-kD gelatinase protein was prominent in BP blister fluid. No other gelatinolytic activity was specifically detected in BP fluid, and only small amounts of 92-kD gelatinase were present in suction blister fluids. As demonstrated in vitro, 92-kD gelatinase cleaved the extracellular, collagenous domain of recombinant 180-kD BP autoantigen (BP180, BPAG2, HD4, type XVII collagen), a transmembrane molecule of the epidermal hemidesmosome. Our results suggest that production and release 92-kD gelatinase by eosinophils contributes significantly to tissue damage in BP. Images PMID:8182134

  17. An allolactose trapped at the lacZ β-galactosidase active site with its galactosyl moiety in a (4)H3 conformation provides insights into the formation, conformation, and stabilization of the transition state.

    PubMed

    Wheatley, Robert W; Huber, Reuben E

    2015-12-01

    When lactose was incubated with G794A-β-galactosidase (a variant with a "closed" active site loop that binds transition state analogs well) an allolactose was trapped with its Gal moiety in a (4)H3 conformation, similar to the oxocarbenium ion-like conformation expected of the transition state. The numerous interactions formed between the (4)H3 structure and β-galactosidase indicate that this structure is representative of the transition state. This conformation is also very similar to that of d-galactono-1,5-lactone, a good transition state analog. Evidence indicates that substrates take up the (4)H3 conformation during migration from the shallow to the deep mode. Steric forces utilizing His418 and other residues are important for positioning the O1 leaving group into a quasi-axial position. An electrostatic interaction between the O5 of the distorted Gal and Tyr503 as well as C-H-π bonds with Trp568 are also significant. Computational studies of the energy of sugar ring distortion show that the β-galactosidase reaction itinerary is driven by energetic considerations in utilization of a (4)H3 transition state with a novel (4)C1-(4)H3-(4)C1 conformation itinerary. To our knowledge, this is the first X-ray crystallographic structural demonstration that the transition state of a natural substrate of a glycosidase has a (4)H3 conformation.

  18. Site-directed mutagenesis of azurin from Pseudomonas aeruginosa enhances the formation of an electron-transfer complex with a copper-containing nitrite reductase from Alcaligenes faecalis S-6.

    PubMed

    Kukimoto, M; Nishiyama, M; Tanokura, M; Murphy, M E; Adman, E T; Horinouchi, S

    1996-09-23

    Kinetic analysis of electron transfer between azurin from Pseudomonas aeruginosa and copper-containing nitrite reductase (NIR) from Akaligenes faecalis S-6 was carried out to investigate the specificity of electron transfer between copper-containing proteins. Apparent values of kcat and Km of NIR for azurin were 300-fold smaller and 172-fold larger than those for the physiological redox partner, pseudoazurin from A. faecalis S-6, respectively, suggesting that the electron transfer between azurin and NIR was less specific than that between pseudoazurin and NIR. One of the major differences in 3-D structure between these redox proteins, azurin and pseudoazurin, is the absence and presence of lysine residues near their type 1 copper sites, respectively. Three mutated azurins, D11K, P36K, and D11K/P36K, were constructed to evaluate the importance of lysine residues in the interaction with NIR. The redox potentials of D11K, P36K, and D11K/P36K azurins were higher than that of wild-type azurin by 48, 7, and 55 mV, respectively. As suggested by the increase in the redox potential, kinetic analysis of electron transfer revealed reduced ability of electron transfer in the mutated azurins. On the other hand, although each of the single mutations caused modest effects on the decrease in the Km value, the simultaneous mutations of D11K and P36K caused significant decrease in the Km value when compared to that for wild-type azurin. These results suggest that the introduction of two lysine residues into azurin facilitated docking to NIR.

  19. Solute Probes of Conformational Changes in Open Complex Formation by E. coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo†

    PubMed Central

    Kontur, Wayne S.; Saecker, Ruth M.; Davis, Caroline A.; Capp, Michael W.; Record, M. Thomas

    2008-01-01

    Transcription initiation is a multi-step process involving a series of requisite conformational changes in RNA polymerase (R) and promoter DNA (P) that create the open complex (RPo). Here we use the small solutes urea and glycine betaine (GB) to probe the extent and type of surface area changes in the formation of RPo between Eσ70 RNA polymerase and λPR promoter DNA. Effects of urea quantitatively reflect changes in amide surface and are particularly well suited to detect coupled protein folding events. GB provides a qualitative probe for the exposure or burial of anionic surface. Kinetics of formation and dissociation of RPo reveal strikingly large effects of the solutes on the final steps of RPo formation: urea dramatically increases the dissociation rate constant kd, whereas GB decreases the rate of dissociation. Formation of the first kinetically significant intermediate I1 is disfavored in urea, and moderately favored by GB. GB slows the rate-determining step that converts I1 to the second kinetically significant intermediate I2; urea has no effect on this step. The most direct interpretation of these data is that recognition of promoter DNA in I1 involves only limited conformational changes. Notably the data support the following hypotheses: 1) the negatively charged N-terminal domain of σ70 remains bound in the “jaws” of polymerase in I1; 2) the subsequent rate-determining isomerization step involves ejecting this domain from the jaws, thereby unmasking the active site; and 3) final conversion to RPo involves coupled folding of the mobile downstream clamp of polymerase. PMID:16475805

  20. Amphiplex Formation

    NASA Astrophysics Data System (ADS)

    Petersen, Shannon; Laaser, Jennifer; Lodge, Timothy

    2015-03-01

    Polymer-micelle complexes are currently under heavy investigation due to their potential applications in targeted drug delivery and gene therapy, yet the dynamics of the complex formation is still relatively unstudied. By varying the ratios of poly(styrene sulfonate) chains and cationic poly(dimethylaminoethyl methacrylate)-b-poly(styrene) micelles and the ionic strength of the system, we created a variety of complex configurations of different sizes and charges. The complexes were characterized dynamic light scattering and zeta potential measurements which provided information regarding the hydrodynamic radius, distribution of sizes, and effective charge.

  1. Planet Formation

    NASA Technical Reports Server (NTRS)

    Lissauer, Jack J.; Fonda, Mark (Technical Monitor)

    2002-01-01

    Modern theories of star and planet formation and of the orbital stability of planetary systems are described and used to discuss possible characteristics of undiscovered planetary systems. The most detailed models of planetary growth are based upon observations of planets and smaller bodies within our own Solar System and of young stars and their environments. Terrestrial planets are believed to grow via pairwise accretion until the spacing of planetary orbits becomes large enough that the configuration is stable for the age of the system. Giant planets begin their growth as do terrestrial planets, but they become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. These models predict that rocky planets should form in orbit about most single stars. It is uncertain whether or not gas giant planet formation is common, because most protoplanetary disks may dissipate before solid planetary cores can grow large enough to gravitationally trap substantial quantities of gas. A potential hazard to planetary systems is radial decay of planetary orbits resulting from interactions with material within the disk. Planets more massive than Earth have the potential to decay the fastest, and may be able to sweep up smaller planets in their path. The implications of the giant planets found in recent radial velocity searches for the abundances of habitable planets are discussed, and the methods that are being used and planned for detecting and characterizing extrasolar planets are reviewed.

  2. Planet Formation

    NASA Technical Reports Server (NTRS)

    Lissauer, Jack J.; Fonda, Mark (Technical Monitor)

    2002-01-01

    Modern theories of star and planet formation and of the orbital stability of planetary systems are described and used to discuss possible characteristics of undiscovered planetary systems. The most detailed models of planetary growth are based upon observations of planets and smaller bodies within our own Solar System and of young stars and their environments. Terrestrial planets are believed to grow via pairwise accretion until the spacing of planetary orbits becomes large enough that the configuration is stable for the age of the system. Giant planets begin their growth as do terrestrial planets, but they become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. These models predict that rocky planets should form in orbit about most single stars. It is uncertain whether or not gas giant planet formation is common, because most protoplanetary disks may dissipate before solid planetary cores can grow large enough to gravitationally trap substantial quantities of gas. A potential hazard to planetary systems is radial decay of planetary orbits resulting from interactions with material within the disk. Planets more massive than Earth have the potential to decay the fastest, and may be able to sweep up smaller planets in their path. The implications of the giant planets found in recent radial velocity searches for the abundances of habitable planets are discussed, and the methods that are being used and planned for detecting and characterizing extrasolar planets are reviewed.

  3. Late Pleistocene ice margin fluctuations in the Nahanni National Park-UNESCO World Heritage Site and their impact on glacial lake formation and architecture of drainage systems across the Yukon-NWT continental divide

    NASA Astrophysics Data System (ADS)

    Duk-Rodkin, A.; Barendregt, R. W.

    2009-12-01

    In the late Pleistocene the southern Mackenzie region was glaciated by ice masses from a Cordilleran and continental source (Laurentide). Stratigraphic and geomorphologic evidence indicate that the two glaciers occupied this region at different times during the Late Pleistocene. The continental ice sheet advanced over the foothills and up major valleys reaching its maximum extent, ca. 30 ka. B. P. This took place when Cordilleran glaciers were in their initial stages of development. The Laurentide Ice Sheet blocked the drainage of the South Nahanni River near Virginia Falls, forming a glacial lake which inundated an area of approximately 900 km2 at its maximum stand, and had an outlet to the southwest, across the continental divide into the Yukon Territory and eventually into the Pacific Ocean. Lacustrine sediments at various sites reach thicknesses ranging from 110 to 120 metres, at an elevation of around 700 m. Cordilleran glaciers advanced eastward and approximately 5000 years later blocked this southwestward drainage, rerouting it to the east and north along the Mackenzie Mountain front. The drainage was confined between the mountains and continental ice margin where it incised major canyons into the limestone bedrock, and produced a spectacular karst landscape, which today forms part of the Nahanni National Park. During the retreat of the Laurentide and advance of Cordilleran glaciers, glacial Lake Nahanni cut an outlet to the east at First Canyon. This outlet drained into a continuous northbound network of marginal meltwater channels joining the north-flowing drainage that eventually reached the Arctic Ocean, and during further retreat of the ice sheet established the Mackenzie River in its modern location. The presence of Laurentide ice in this region is evidenced by large granite boulders carried from the Canadian Shield. Erratics are found up to 100 km west of the mountain front. Neotectonic activity in the area is interpreted from exposures such as those

  4. Habit formation

    PubMed Central

    Smith, Kyle S.; Graybiel, Ann M.

    2016-01-01

    Habits, both good ones and bad ones, are pervasive in animal behavior. Important frameworks have been developed to understand habits through psychological and neurobiological studies. This work has given us a rich understanding of brain networks that promote habits, and has also helped us to understand what constitutes a habitual behavior as opposed to a behavior that is more flexible and prospective. Mounting evidence from studies using neural recording methods suggests that habit formation is not a simple process. We review this evidence and take the position that habits could be sculpted from multiple dissociable changes in neural activity. These changes occur across multiple brain regions and even within single brain regions. This strategy of classifying components of a habit based on different brain signals provides a potentially useful new way to conceive of disorders that involve overly fixed behaviors as arising from different potential dysfunctions within the brain's habit network. PMID:27069378

  5. Habit formation.

    PubMed

    Smith, Kyle S; Graybiel, Ann M

    2016-03-01

    Habits, both good ones and bad ones, are pervasive in animal behavior. Important frameworks have been developed to understand habits through psychological and neurobiological studies. This work has given us a rich understanding of brain networks that promote habits, and has also helped us to understand what constitutes a habitual behavior as opposed to a behavior that is more flexible and prospective. Mounting evidence from studies using neural recording methods suggests that habit formation is not a simple process. We review this evidence and take the position that habits could be sculpted from multiple dissociable changes in neural activity. These changes occur across multiple brain regions and even within single brain regions. This strategy of classifying components of a habit based on different brain signals provides a potentially useful new way to conceive of disorders that involve overly fixed behaviors as arising from different potential dysfunctions within the brain's habit network.

  6. Implementation: Preparing the Site.

    ERIC Educational Resources Information Center

    Epstein, Susan Baerg

    1983-01-01

    Considers site requirements that should be specified by the library and the vendor for a library automated system located at a central site away from the library, including size of site, the environment, cleanliness, electrical power, security/safety (fire, restricted access), site certification, telecommunications, and terminal sites. (EJS)

  7. Site Evaluation for Hardwoods

    Treesearch

    John K. Francis

    1985-01-01

    Foresters evaluate sites for an indication of potential growth and yield, for an ecological descriptor, and to correctly match the hardwood species to be planted with sites suitable for them. Site indexes measured directly from trees on the site are the preferable means of quantifying site. Because this method is not always possible, other means based on soil and...

  8. Implementation: Preparing the Site.

    ERIC Educational Resources Information Center

    Epstein, Susan Baerg

    1983-01-01

    Considers site requirements that should be specified by the library and the vendor for a library automated system located at a central site away from the library, including size of site, the environment, cleanliness, electrical power, security/safety (fire, restricted access), site certification, telecommunications, and terminal sites. (EJS)

  9. Promoting Your Web Site.

    ERIC Educational Resources Information Center

    Raeder, Aggi

    1997-01-01

    Discussion of ways to promote sites on the World Wide Web focuses on how search engines work and how they retrieve and identify sites. Appropriate Web links for submitting new sites and for Internet marketing are included. (LRW)

  10. Ocean Disposal Site Monitoring

    EPA Pesticide Factsheets

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  11. Pattern Formation

    NASA Astrophysics Data System (ADS)

    Hoyle, Rebecca

    2006-03-01

    From the stripes of a zebra and the spots on a leopard's back to the ripples on a sandy beach or desert dune, regular patterns arise everywhere in nature. The appearance and evolution of these phenomena has been a focus of recent research activity across several disciplines. This book provides an introduction to the range of mathematical theory and methods used to analyse and explain these often intricate and beautiful patterns. Bringing together several different approaches, from group theoretic methods to envelope equations and theory of patterns in large-aspect ratio-systems, the book also provides insight behind the selection of one pattern over another. Suitable as an upper-undergraduate textbook for mathematics students or as a fascinating, engaging, and fully illustrated resource for readers in physics and biology, Rebecca Hoyle's book, using a non-partisan approach, unifies a range of techniques used by active researchers in this growing field. Accessible description of the mathematical theory behind fascinating pattern formation in areas such as biology, physics and materials science Collects recent research for the first time in an upper level textbook Features a number of exercises - with solutions online - and worked examples

  12. Barrier Formation

    PubMed Central

    Lyaruu, D.M.; Medina, J.F.; Sarvide, S.; Bervoets, T.J.M.; Everts, V.; DenBesten, P.; Smith, C.E.; Bronckers, A.L.J.J.

    2014-01-01

    Enamel fluorosis is an irreversible structural enamel defect following exposure to supraoptimal levels of fluoride during amelogenesis. We hypothesized that fluorosis is associated with excess release of protons during formation of hypermineralized lines in the mineralizing enamel matrix. We tested this concept by analyzing fluorotic enamel defects in wild-type mice and mice deficient in anion exchanger-2a,b (Ae2a,b), a transmembrane protein in maturation ameloblasts that exchanges extracellular Cl− for bicarbonate. Defects were more pronounced in fluorotic Ae2a,b−/− mice than in fluorotic heterozygous or wild-type mice. Phenotypes included a hypermineralized surface, extensive subsurface hypomineralization, and multiple hypermineralized lines in deeper enamel. Mineral content decreased in all fluoride-exposed and Ae2a,b−/− mice and was strongly correlated with Cl−. Exposure of enamel surfaces underlying maturation-stage ameloblasts to pH indicator dyes suggested the presence of diffusion barriers in fluorotic enamel. These results support the concept that fluoride stimulates hypermineralization at the mineralization front. This causes increased release of protons, which ameloblasts respond to by secreting more bicarbonates at the expense of Cl− levels in enamel. The fluoride-induced hypermineralized lines may form barriers that impede diffusion of proteins and mineral ions into the subsurface layers, thereby delaying biomineralization and causing retention of enamel matrix proteins. PMID:24170372

  13. Hanford Site Development Plan

    SciTech Connect

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. ); Yancey, E.F. )

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  14. School Siting Guidelines

    EPA Pesticide Factsheets

    EPA's voluntary school siting guidelines provide recommendations for local school districts and community members on how to evaluate environmental factors to make the best possible school siting decisions.

  15. 40 CFR 146.62 - Minimum criteria for siting.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... to Class I Hazardous Waste Injection Wells § 146.62 Minimum criteria for siting. (a) All Class I hazardous waste injection wells shall be sited such that they inject into a formation that is beneath the... water. (b) The siting of Class I hazardous waste injection wells shall be limited to areas that are...

  16. 40 CFR 146.62 - Minimum criteria for siting.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... to Class I Hazardous Waste Injection Wells § 146.62 Minimum criteria for siting. (a) All Class I hazardous waste injection wells shall be sited such that they inject into a formation that is beneath the... water. (b) The siting of Class I hazardous waste injection wells shall be limited to areas that are...

  17. 40 CFR 146.62 - Minimum criteria for siting.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... to Class I Hazardous Waste Injection Wells § 146.62 Minimum criteria for siting. (a) All Class I hazardous waste injection wells shall be sited such that they inject into a formation that is beneath the... water. (b) The siting of Class I hazardous waste injection wells shall be limited to areas that are...

  18. Radionuclide site survey report, Melbourne, Florida (RN-72). Final report

    SciTech Connect

    Walker, F.; Lucas, J.; Owen, M.; McKethan, E.M.; MacCartney, J.

    1998-11-16

    The format and content of this report are based on guidance provided by the Preparatory Commission for the CTBT Organization for conducting and documenting radionuclide site surveys (see GTBT/PC/IV/WGB/1) ``Requirements of Site Surveys for Radionuclide Stations``, (30 September 1997). The purpose of this report is to validate that the Melbourne site will fulfill the requirements for treaty compliance.

  19. Hanford Site Waste Management Units Report

    SciTech Connect

    Shearer, Jeffrey P.

    2014-02-19

    The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2013 version of the HSWMUR contains a comprehensive inventory of the 3438 sites and 569 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

  20. Hanford Site Waste Management Units Report

    SciTech Connect

    Shearer, Jeffrey P.

    2013-02-13

    The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2013 version of the HSWMUR contains a comprehensive inventory of the 3427 sites and 564 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

  1. Hanford Site Waste Management Units Report

    SciTech Connect

    Shearer, Jeffrey P.

    2012-02-29

    The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2012 version of the HSWMUR contains a comprehensive inventory of the 3389 sites and 540 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

  2. Children's Literature Web Sites.

    ERIC Educational Resources Information Center

    Yokota, Junko; Cai, Mingshui

    2002-01-01

    Presents annotations of approximately 80 web sites that range in coverage from idiosyncratic and focused to diverse and comprehensive metasites. Notes categories of sites include: children's literature web guides; trade book publisher web sites; author/illustrator sites (metasites and individual); book review sources and teaching ideas; web sites…

  3. Hanford Site Development Plan

    SciTech Connect

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP`s primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans.

  4. DUST FORMATION IN MACRONOVAE

    SciTech Connect

    Takami, Hajime; Ioka, Kunihito; Nozawa, Takaya E-mail: kunihito.ioka@kek.jp

    2014-07-01

    We examine dust formation in macronovae (as known as kilonovae), which are the bright ejecta of neutron star binary mergers and one of the leading sites of r-process nucleosynthesis. In light of information about the first macronova candidate associated with GRB 130603B, we find that dust grains of r-process elements have difficulty forming because of the low number density of the r-process atoms, while carbon or elements lighter than iron can condense into dust if they are abundant. Dust grains absorb emission from ejecta with an opacity even greater than that of the r-process elements, and re-emit photons at infrared wavelengths. Such dust emission can potentially account for macronovae without r-process nucleosynthesis as an alternative model. This dust scenario predicts a spectrum with fewer features than the r-process model and day-scale optical-to-ultraviolet emission.

  5. SCHOOL SITE STANDARDS AND SITE SELECTION.

    ERIC Educational Resources Information Center

    New York State Education Dept., Albany.

    THIS REPORT PRESENTS ELEMENTARY AND SECONDARY SCHOOL SITE DEVELOPMENT DATA COMPILED BY THE DIVISION OF EDUCATIONAL FACILITIES PLANNING, NEW YORK STATE EDUCATION DEPARTMENT. ENROLLMENT FIGURES USED REPRESENT THE ULTIMATE SIZE OF THE SCHOOLS. THE STANDARDS ARE MINIMUM FOR THE STATE OF NEW YORK WITH ELEMENTARY SCHOOL SITES BASED ON THREE ACRES PLUS…

  6. Lawrence Berkeley Laboratory 1993 Site Environmental Report

    SciTech Connect

    Not Available

    1994-05-01

    This annual Site Environmental Report summarizes Lawrence Berkeley Laboratory`s (LBL`s) environmental activities in calendar year (CY) 1993. The purpose of this report is to characterize site environmental management performance, confirm compliance status with environmental standards and requirements, and highlight significant programs and efforts. Its format and content are consistent with the requirements of the US Department of Energy (DOE) Order 5400.1, General Environmental Protection Program.

  7. Site amplifications for generic rock sites

    USGS Publications Warehouse

    Boore, D.M.; Joyner, W.B.

    1997-01-01

    Seismic shear-wave velocity as a function of depth for generic rock sites has been estimated from borehole data and studies of crustal velocities, and these velocities have been used to compute frequency-dependent amplifications for zero attenuation for use in simulations of strong ground motion. We define a generic rock site as one whose velocity at shallow depths equals the average of those from the rock sites sampled by the borehole data. Most of the boreholes are in populated areas; for that reason, the rock sites sampled are of particular engineering significance. We consider two generic rock sites: rock, corresponding to the bulk of the borehole data, and very hard rock, such as is found in glaciated regions in large areas of eastern North America or in portions of western North America. The amplifications on rock sites can be in excess of 3.5 at high frequencies, in contrast to the amplifications of less than 1.2 on very hard rock sites. The consideration of unattenuated amplification alone is computationally convenient, but what matters for ground-motion estimation is the combined effect of amplification and attenuation. For reasonable values of the attenuation parameter K0, the combined effect of attenuation and amplification for rock sites peaks between about 2 and 5 Hz with a maximum level of less than 1.8. The combined effect is about a factor of 1.5 at 1 Hz and is less than unity for frequencies in the range of 10 to 20 Hz (depending on K0). Using these amplifications, we find provisional values of about ???? = 70 bars and K0 = 0.035 sec for rock sites in western North America by fitting our empirically determined response spectra for an M 6.5 event to simulated values. The borehole data yield shear velocities (V??30) of 618 and 306 m/sec for "rock" and "soil" sites, respectively, when averaged over the upper 30 m. From this, we recommend that V??30 equals 620 and 310 m/sec for applications requiring the average velocity for rock and soil sites in

  8. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    EPA Pesticide Factsheets

    National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database contains a selected set of non-enforcement confidential information and is updated by the regions every 90 days. The data describes what has happened at Superfund sites prior to this quarter (updated quarterly). This database includes lists of involved parties (other Federal Agencies, states, and tribes), Human Exposure and Ground Water Migration, and Site Wide Ready for Reuse, Construction Completion, and Final Assessment Decision (GPRA-like measures) for fund lead sites. Other information that is included has been included only as a service to allow public evaluations utilizing this data. EPA does not have specific Data Quality Objectives for use of the data. Independent Quality Assessments may be made of this data by reviewing the QAPP

  9. Superfund Site Information - Site Sampling Data

    EPA Pesticide Factsheets

    This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of samples. Information is associated with a particular contaminated sate as there is no national database of this information.

  10. Remedial Action Plan and Site Design for stabilization of the inactive Uranium Mill Tailings sites at Slick Rock, Colorado: Appendix C to Attachment 3, Calculations. Final

    SciTech Connect

    1995-09-01

    This volume contains calculations for: Slick Rock processing sites background ground water quality; Slick Rock processing sites lysimeter water quality; Slick Rock processing sites on-site and downgradient ground water quality; Slick Rock disposal site background water quality; Burro Canyon disposal site, Slick Rock, Colorado, average hydraulic gradients and average liner ground water velocities in the upper, middle, and lower sandstone units of the Burro Canyon formation; Slick Rock--Burro Canyon disposal site, Burro Canyon pumping and slug tests--analyses; water balance and surface contours--Burro Canyon disposal cell; and analytical calculation of drawdown in a hypothetical well completed in the upper sandstone unit of the Burro Canyon formation.

  11. Bremerton Gasworks Superfund Site

    EPA Pesticide Factsheets

    2017-06-13

    The Bremerton Gasworks Site, a former coal gasification plant, is now used for commercial and industrial purposes. Sediments, soils, and groundwater at the site are contaminated with polyaromatic hydrocarbons from coal gas tars, along with heavy metals and benzene.

  12. Field site selection

    NASA Technical Reports Server (NTRS)

    Schwarz, D. E.; Ellefsen, R. E.

    1981-01-01

    Several general guidelines should be kept in mind when considering the selection of field sites for teaching remote sensing fundamentals. Proximity and vantage point are two very practical considerations. Only through viewing a broad enough area to place the site in context can one make efficient use of a site. The effects of inclement weather when selecting sites should be considered. If field work is to be an effective tool to illustrate remote sensing principles, the following criteria are critical: (1) the site must represent the range of class interest; (2) the site must have a theme or add something no other site offers; (3) there should be intrasite variation within the theme; (4) ground resolution and spectral signature distinction should be illustrated; and (5) the sites should not be ordered sequentially.

  13. Past Project Expo Sites

    EPA Pesticide Factsheets

    This page provides information for Project Expo sites that were featured at the LMOP Conferences in 2013 and 2014. Project Expo sites were featured as being interested in identifying project partners for the development of an LFG energy project.

  14. SMARTE'S SITE CHARACTERIZATION TOOL

    EPA Science Inventory

    Site Characterization involves collecting environmental data to evaluate the nature and extent of contamination. Environmental data could consist of chemical analyses of soil, sediment, water or air samples. Typically site characterization data are statistically evaluated for thr...

  15. Pesticide Use Site Index

    EPA Pesticide Factsheets

    The Pesticide Use Site Index will help a company (or other applicant) identify which data requirements are needed to register a pesticide product. It provides information on pesticide use sites and pesticide major use patterns.

  16. Superfund Site Assessment Process

    EPA Pesticide Factsheets

    Learn about the site assessment process used by the federal Superfund program to evaluate releases of hazardous substances that may pose a threat to human health or the environment and select an appropriate program for sites needing cleanup.

  17. Site specific synthesis and polymerase bypass of oligonucleotides containing a 6-hydroxy-3,5,6,7-tetrahydro-9H-imidazo[1,2-a]purin-9-one base, an intermediate in the formation of 1,N2-etheno-2'-deoxyguanosine.

    PubMed

    Goodenough, Angela K; Kozekov, Ivan D; Zang, Hong; Choi, Jeong-Yun; Guengerich, F Peter; Harris, Thomas M; Rizzo, Carmelo J

    2005-11-01

    The reaction of DNA with certain bis-electrophiles such as chlorooxirane and chloroacetaldehyde produces etheno adducts. These lesions are highly miscoding, and some of the chemical agents that produce them have been shown to be carcinogenic in laboratory animals and in humans. An intermediate in the formation of 1,N2-ethenoguanine is 6-hydroxy-3,5,6,7-tetrahydro-9H-imidazo[1,2-a]purin-9-one (6-hydroxyethanoguanine), which undergoes conversion to the etheno adduct. The chemical properties and miscoding potential of the hydroxyethano adduct have not been previously studied. A synthesis of the hydroxyethano-adducted nucleoside was developed, and it was site specifically incorporated into oligonucleotides. This adduct had a half-life of between 24 and 48 h at neutral pH and 25 degrees C at the nucleoside and oligonucleotide levels. The miscoding potential of the hydroxyethano adduct was examined by primer extension reactions with the DNA polymerases Dpo4 and pol T7-, and the results were compared to the corresponding etheno-adducted oligonucleotide. Dpo4 preferentially incorporated dATP opposite the hydroxyethano adduct and dGTP opposite the etheno adduct; pol T7- preferentially incorporated dATP opposite the etheno adduct while dGTP and dATP were incorporated opposite the hydroxyethano adduct with nearly equal catalytic efficiencies. Collectively, these results indicate that the hydroxyethano adduct has a sufficient lifetime and miscoding properties to contribute to the mutagenic spectrum of chlorooxirane and related genotoxic species.

  18. Educational Computing Course. [SITE 2001 Section].

    ERIC Educational Resources Information Center

    Bump, Wren, Ed.

    This document contains the following papers on the educational computing course from the SITE (Society for Information Technology & Teacher Education) 2001 conference: "Using a Flexible Format To Create a Constructivist Learning Environment in the Educational Computing Course" (Wren M. Bump); "Technological Diversity: Managing…

  19. Yes! You Can Build a Web Site.

    ERIC Educational Resources Information Center

    Holzberg, Carol

    2001-01-01

    With specially formatted templates or simple Web page editors, teachers can lay out text and graphics in a work space resembling the interface of a word processor. Several options are presented to help teachers build Web sites. ree templates include Class Homepage Builder, AppliTools: HomePage, MySchoolOnline.com, and BigChalk.com. Web design…

  20. Choosing a School Site.

    ERIC Educational Resources Information Center

    School Planning & Management, 2002

    2002-01-01

    Describes the guides to school site selection developed in Maine, British Columbia, Alaska, and California, along with information on obtaining the publication. The state and province guides address site selection issues such as historic preservation, decision- making procedures, and site evaluation criteria. (EV)

  1. Site preparation for wildlife

    Treesearch

    Ralph W. Dimmick

    1989-01-01

    Site preparation-whether for timber and/or wildlife objectives - can influence the quality of wildlife habitat on the site and surrounding forest for the entire rotation period of the regenerated stand. The site preparation you select will help determine the species and numbers of wildlife that use the stand as the stand progresses from regeneration through maturity....

  2. The ASCD Healthy School Communities Project: Formative Evaluation Results

    ERIC Educational Resources Information Center

    Valois, Robert F.; Lewallen, Theresa C.; Slade, Sean; Tasco, Adriane N.

    2015-01-01

    Purpose: The purpose of this paper is to report the formative evaluation results from the Association for Supervision and Curriculum Development Healthy School Communities (HSC) pilot project. Design/methodology/approach: This study utilized 11 HSC pilot sites in the USA (eight sites) and Canada (three sites). The evaluation question was…

  3. The ASCD Healthy School Communities Project: Formative Evaluation Results

    ERIC Educational Resources Information Center

    Valois, Robert F.; Lewallen, Theresa C.; Slade, Sean; Tasco, Adriane N.

    2015-01-01

    Purpose: The purpose of this paper is to report the formative evaluation results from the Association for Supervision and Curriculum Development Healthy School Communities (HSC) pilot project. Design/methodology/approach: This study utilized 11 HSC pilot sites in the USA (eight sites) and Canada (three sites). The evaluation question was…

  4. Site Environmental Report, 1993

    SciTech Connect

    Not Available

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ``General Environmental Protection Program.`` This 1993 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here.

  5. Hanford Site Infrastructure Plan

    SciTech Connect

    Not Available

    1990-01-01

    The Hanford Site Infrastructure Plan (HIP) has been prepared as an overview of the facilities, utilities, systems, and services that support all activities on the Hanford Site. Its purpose is three-fold: to examine in detail the existing condition of the Hanford Site's aging utility systems, transportation systems, Site services and general-purpose facilities; to evaluate the ability of these systems to meet present and forecasted Site missions; to identify maintenance and upgrade projects necessary to ensure continued safe and cost-effective support to Hanford Site programs well into the twenty-first century. The HIP is intended to be a dynamic document that will be updated accordingly as Site activities, conditions, and requirements change. 35 figs., 25 tabs.

  6. Bulk Site Reference Materials

    SciTech Connect

    Barich, J.J. III; Jones, R.R. Sr.

    1996-12-31

    The selection, manufacture and use of Bulk Site Reference Materials (BSRMs) at hazardous waste sites is discussed. BSRMs are useful in preparing stabilization/solidification (S/S) formulations for soils, ranking competing S/S processes, comparing S/S alternatives to other technologies, and in interpreting data from different test types. BSRMs are large volume samples that are representative of the physical and chemical characteristics of a site soil, and that contain contaminants at reasonably high levels. A successful BSRM is extremely homogeneous and well-characterized. While not representative of any point on the site, they contain the contaminants of the site in the matrices of the site. Design objectives for a BSRM are to produce a material that (1) maintains good fidelity to site matrices and contaminants, and (2) exhibits the lowest possible relative standard deviation.

  7. Site Development Planning Handbook

    SciTech Connect

    1981-01-01

    The Handbook provides facility managers and site planners at DOE organizations responsible for planning site developments and facilities utilization a step-by-step planning checklist to ensure that planners at each site are focusing on Department-wide goals and objectives. It begins with a brief discussion of a site development-by-objectives program design to promote, recognize, and implement opportunities for improvements in site utilization through planning. Additional information is included on: assembling existing data, plans, programs, and procedures; establishing realistic objectives; identifying site problems, opportunities; and development needs; determining priorities among development needs; developing short and long-range plans; choosing the right development solutions and meeting minimum legal site restrictions; presenting the plan; implementing elements of the plan; monitoring and reporting plan status; and modifying development program plans. (MCW)

  8. The Keystone Dame Site and other Archaic and Formative Sites in Northwest El Paso, Texas.

    DTIC Science & Technology

    1980-10-01

    the basin sediments (Strain zite, and rhyolite with granite and andesite intru- 1966). Today, runoff from the west slope of the sions (McAnulty 1967...milky white quartz Granite 1 Coarse grained, mottled or speckled buff to light gray (includes some andesite ) 16 • .. 1i8 ,a, .b .L- , -kW, . R ..Oa ’,m ’L

  9. Rulison Site corrective action report

    SciTech Connect

    1996-09-01

    Project Rulison was a joint US Atomic Energy Commission (AEC) and Austral Oil Company (Austral) experiment, conducted under the AEC`s Plowshare Program, to evaluate the feasibility of using a nuclear device to stimulate natural gas production in low-permeability gas-producing geologic formations. The experiment was conducted on September 10, 1969, and consisted of detonating a 40-kiloton nuclear device at a depth of 2,568 m below ground surface (BGS). This Corrective Action Report describes the cleanup of petroleum hydrocarbon- and heavy-metal-contaminated sediments from an old drilling effluent pond and characterization of the mud pits used during drilling of the R-EX well at the Rulison Site. The Rulison Site is located approximately 65 kilometers (40 miles) northeast of Grand Junction, Colorado. The effluent pond was used for the storage of drilling mud during drilling of the emplacement hole for the 1969 gas stimulation test conducted by the AEC. This report also describes the activities performed to determine whether contamination is present in mud pits used during the drilling of well R-EX, the gas production well drilled at the site to evaluate the effectiveness of the detonation in stimulating gas production. The investigation activities described in this report were conducted during the autumn of 1995, concurrent with the cleanup of the drilling effluent pond. This report describes the activities performed during the soil investigation and provides the analytical results for the samples collected during that investigation.

  10. 40. December 20, 1933 View of portal site, tunnel no. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    40. December 20, 1933 View of portal site, tunnel no. 1, CWA men facing the portal. "Stripping the hillside grule sic formation between tunnels 1 and 2." - Scotts Bluff Summit Road, Gering, Scotts Bluff County, NE

  11. Site Investigations with the Site Characterization and Analysis Penetrator System at Fort Dix, New Jersey

    DTIC Science & Technology

    1993-07-01

    Center (AEC), sponsored the United States Army Engineer Waterways Experiment Station (WES) to per- form site characterization and screening activities at...overlies the Vince- town Formation a yellow-to-olive quartz, carbonate and glauconite-rich sand at the top and a dark grey, poorly sorted ...poorly sorted clayey sands with some glauconite. Underlying these units are the Wenonah Formation, the Englishtown Sand, the Woodbury Clay, and the

  12. Cyclic Imide Dioxime: Formation and Hydrolytic Stability

    SciTech Connect

    Kang, S.O.; Vukovic, Sinisa; Custelcean, Radu; Hay, Benjamin

    2012-01-01

    Poly(acrylamidoximes) play an important role in the uranium extraction from seawater. The present work reports solution studies of simple analogs to address the formation and stability of two binding sites present in these polymers, open-chain amidoximes and cyclic imide dioximes, including: 1) conditions that maximize the formation of the cyclic form, 2) existence of a base-induced conversion from open-chain to cyclic form, and 3) degradation under acid and base conditions.

  13. TOPOGRAPHIC SITE RESPONSE AT HARD ROCK SITES

    NASA Astrophysics Data System (ADS)

    Yong, A. K.; Hough, S. E.

    2009-12-01

    Site (material impedance) and topographic (geometric form) effects are known to be key factors that influence seismic ground motions. To characterize site effects, Yong et al. (2009) developed a terrain-based Vs30 prediction model using an automated classification method (Iwahashi and Pike, 2007) that relied on taxonomic criteria (slope gradient, local convexity and surface texture) developed from geomorphometry to identify 16 terrain types from a 1-km spatial resolution (SRTM30 data) digital elevation model of California. On the basis that the underlying framework for this model contains parameters (esp., local convexity) which aptly describe the geometry (i.e., base to height ratio) of relief features that are known to also control the behavior of ground motions (Bouchon, 1973), we extend our investigation to study topographic effects. Focusing on sites that would generally be considered “hard rock,” the classification scheme distinguishes 7 separate terrain types ranging from “moderately eroded mountains” to “well dissected alpine summits.” Observed 1-Hz amplification factors at Southern California Seismographic Network sites reveal a weak but systematic correlation with these 7 terrain types. Significant scatter is also found within each terrain type; typical standard deviations of logarithmic amplification factors are 0.2-0.3. Considering stations that have high amplification factors, we find some that have apparently been misclassified due to data resolution limitations. Many of the remaining stations with higher than expected amplifications are located on or near topographic peaks or ridges. The unusually high amplification factors at hard-rock sites, typically factors of 1.5-2, can most plausibly be explained as a topographic effect.

  14. COCORP solicits site proposals

    NASA Astrophysics Data System (ADS)

    The Consortium for Continental Reflection Profiling (COCORP) is encouraging members of the earth science community to submit proposals for sites to be surveyed by COCORP. New proposals (as well as those previously received for sites yet to be profiled) are evaluated annually by the COCORP Site Selection Advisory Committee, and the crew schedule is updated accordingly.The committee wishes to design future sites to contribute toward building a transcontinental traverse to be presented during the 1989 International Geological Congress in Washington, D.C. Figure 1 shows the sites that have either been surveyed by COCORP or are tentatively scheduled to be surveyed in the future. The COCORP committee has recommended that COCORP continue its primary strategy of reconnaissance surveying and has emphasized the continued need for long lines guided by specific geologic problems. For information on how to submit COCORP site proposals, contact S. Kaufman, Executive Director, COCORP, Snee Hall, Cornell University, Ithaca, NY 14853; telephone 607-255-7165.

  15. Site environmental programs

    SciTech Connect

    Schmidt, J.W.; Hanf, R.W.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the site environmental programs. Effluent monitoring and environmental surveillance programs monitor for impacts from operations in several areas. The first area consists of the point of possible release into the environment. The second area consists of possible contamination adjacent to DOE facilities, and the third area is the general environment both on and off the site.

  16. Site environmental report summary

    SciTech Connect

    Not Available

    1992-12-31

    In this summary of the Fernald 1992 Site Environmental Report the authors will describe the impact of the Fernald site on man and the environment and provide results from the ongoing Environmental Monitoring Program. Also included is a summary of the data obtained from sampling conducted to determine if the site complies with DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA) requirements. These requirements are set to protect both man and the environment.

  17. Viking landing sites

    NASA Technical Reports Server (NTRS)

    Panagakos, N.

    1973-01-01

    A valley near the mouth of the 20,000-foot-deep Martian Grand Canyon has been chosen by NASA as the site of its first automated landing on the planet Mars. The landing site for the second mission of the 1975-76 Viking spacecraft will probably be an area about 1,000 miles northeast of the first site, where the likelihood of water increases the chances of finding evidence of life.

  18. Marte Valles site

    NASA Technical Reports Server (NTRS)

    Rice, Jim W.

    1994-01-01

    This site is located at 16 deg N, 177 deg W on the flood plains of Marte Valles, which is perhaps the youngest channel system on Mars. The young age of this channel warrants investigation because of climatic implications for fluvial activities in recent geologic time. The paucity of craters makes this an excellent site in terms of safety requirements. Some of the objectives stated previously for the Maja Valles region would also apply to this site (grab bag of rock types, etc.).

  19. Common File Formats.

    PubMed

    Mills, Lauren

    2014-03-21

    An overview of the many file formats commonly used in bioinformatics and genome sequence analysis is presented, including various data file formats, alignment file formats, and annotation file formats. Example workflows illustrate how some of the different file types are typically used.

  20. 1994 Site environmental report

    SciTech Connect

    1995-07-01

    The Fernald site is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1994 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  1. Otolaryngology Web site.

    PubMed

    Tan, A K

    1997-02-01

    This article describes the medical Web site developed at the Department of Otolaryngology, Queen's University, on the World Wide Web. The objectives of the Web site are: to introduce the Department of Otolaryngology at Queen's University; to provide it's users with information and new developments in various aspects of otolaryngology; to provide general public with health information on otolaryngology; and to foster academic discussion via electronic discussion forum. The development and implementation of this Web site are also presented. Physicians who have Internet access will be able to utilize the multimedia information on this site for medical education and clinical consultation.

  2. Catalysis of Dialanine Formation by Glycine in the Salt-Induced Peptide Formation Reaction.

    NASA Astrophysics Data System (ADS)

    Suwannachot, Yuttana; Rode, Bernd M.

    1998-02-01

    Mutual catalysis of amino acids in the salt-induced peptide formation (SIPF) reaction is demonstrated for the case of glycine/alanine. The presence of glycine enhances dialanine formation by a factor up to 50 and enables dialanine formation at much lower alanine concentrations. The actual amounts of glycine play an important role for this catalytic effect, the optimal glycine concentration is 1/8 of the alanine concentration. The mechanism appears to be based on the formation of the intermediate Gly-Ala-Ala tripeptide, connected to one coordination site of copper(II) ion, and subsequent hydrolysis to dialanine and glycine.

  3. Nevada Test Site Environmental Report 2003

    SciTech Connect

    Bechtel Nevada

    2004-10-01

    The Nevada Test Site Environmental Report 2003 was prepared by Bechtel Nevada to meet the requirements and guidelines of the U.S. Department of Energy and the information needs of the public. This report is meant to be useful to members of the public, public officials, regulators, and Nevada Test Site contractors. The Executive Summary strives to present in a concise format the purpose of the document, the NTS mission and major programs, a summary of radiological releases and doses to the public resulting from site operations, a summary of non-radiological releases, and an overview of the Nevada Test Site Envi