WorldWideScience

Sample records for active site constrained

  1. Management of Ground and Groundwater Contamination on a Compact Site Constrained by Ongoing Activities

    Sellafield Site is a compact and complex site which since the 1940's has been home to a range of facilities associated with the production and reprocessing of fissile material. The site contains the UK equivalent of the Chicago Pile-1 reactor, Hanford B Reactor, Rocky Flats Buildings 771 and 774, West Valley Main Process Plant Building, Savannah River Vitrification Plant, Savannah River MOX Plant, Savannah River F Canyon, Hanford 222 Analytical Laboratory, Savannah River K-, L-, and P-Basins, and the Fort St. Vrain Reactor all in an area of approximately 1000 acres. Spent fuel reprocessing is still undertaken on site; however waste management and decommissioning activities are of increasing importance. These include the emptying and removal of fragile ponds and silos containing significant radioactive inventories, the decommissioning of reactors (including the world's first commercial reactor for power generation and the Windscale Piles, the site of a reactor fire in the late 1950's) and the construction of a new generation of vitrification and encapsulation plants. Leaks, spills and on-site disposals during the site's industrial lifetime have resulted in a legacy of fission products and other radionuclides in the ground and groundwater. Volumes of contaminated ground have been estimated as being as much as 18 million m3 and an estimated below ground inventory of approximately 1.8 E16 Bq. These have all occurred within close proximity to a range of receptors including farm land and the sea. The cramped nature of the facilities on site, overlapping source terms and ongoing decommissioning, waste management and operating activities all raise significant challenges in the management and remediation of contaminated land and groundwater. The strategy to address these challenges includes: 1. Data collection, management and interpretation. The congested nature of the site and the age of some of the monitoring facilities has resulted in particular difficulties. For example

  2. Performance Characteristics of Active Constrained Layer Damping

    A. Baz; J. Ro

    1995-01-01

    Theoretical and experimental performance characteristics of the new class of actively controlled constrained layer damping (ACLD) are presented. The ACLD consists of a viscoelastic damping layer sandwiched between two layers of piezoelectric sensor and actuator. The composite ACLD when bonded to a vibrating structure acts as a “smart” treatment whose shear deformation can be controlled and tuned to the structural response in order to enhance the energy dissipation mechanism and improve the vi...

  3. Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-ht2 receptors

    Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian;

    2013-01-01

    class. Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Also the ethyl linker has been constrained providing information...... showed that the 1,2-heterocyclized compounds can be accommodated in the binding site. Conformational analysis showed that 11 can only bind in a higher-energy conformation, which would explain its absent or low affinity. The amine and 2-oxygen interactions with D3.32 and S3.36, respectively, can form but...

  4. Vibration control of cylindrical shells using active constrained layer damping

    Ray, Manas C.; Chen, Tung-Huei; Baz, Amr M.

    1997-05-01

    The fundamentals of controlling the structural vibration of cylindrical shells treated with active constrained layer damping (ACLD) treatments are presented. The effectiveness of the ACLD treatments in enhancing the damping characteristics of thin cylindrical shells is demonstrated theoretically and experimentally. A finite element model (FEM) is developed to describe the dynamic interaction between the shells and the ACLD treatments. The FEM is used to predict the natural frequencies and the modal loss factors of shells which are partially treated with patches of the ACLD treatments. The predictions of the FEM are validated experimentally using stainless steel cylinders which are 20.32 cm in diameter, 30.4 cm in length and 0.05 cm in thickness. The cylinders are treated with ACLD patches of different configurations in order to target single or multi-modes of lobar vibrations. The ACLD patches used are made of DYAD 606 visco-elastic layer which is sandwiched between two layers of PVDF piezo-electric films. Vibration attenuations of 85% are obtained with maximum control voltage of 40 volts. Such attenuations are attributed to the effectiveness of the ACLD treatment in increasing the modal damping ratios by about a factor of four over those of conventional passive constrained layer damping (PCLD) treatments. The obtained results suggest the potential of the ACLD treatments in controlling the vibration of cylindrical shells which constitute the major building block of many critical structures such as cabins of aircrafts, hulls of submarines and bodies of rockets and missiles.

  5. FXR agonist activity of conformationally constrained analogs of GW 4064

    Akwabi-Ameyaw, Adwoa; Bass, Jonathan Y.; Caldwell, Richard D.; Caravella, Justin A.; Chen, Lihong; Creech, Katrina L.; Deaton, David N.; Madauss, Kevin P.; Marr, Harry B.; McFadyen, Robert B.; Miller, Aaron B.; Navas, III, Frank; Parks, Derek J.; Spearing, Paul K.; Todd, Dan; Williams, Shawn P.; Wisely, G. Bruce; (GSKNC)

    2010-09-27

    Two series of conformationally constrained analogs of the FXR agonist GW 4064 1 were prepared. Replacement of the metabolically labile stilbene with either benzothiophene or naphthalene rings led to the identification of potent full agonists 2a and 2g.

  6. DOE site performance assessment activities

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions

  7. Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-HT2 receptors.

    Vignir Isberg

    Full Text Available Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine class. Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Also the ethyl linker has been constrained providing information about the bioactive conformation of the amine functionality. However, combined 1,2-constriction by cyclization has only been tested with one compound. Here, we present three new 1,2-cyclized phenylethylamines, 9-11, and describe their synthetic routes. Ligand docking in the 5-HT2B crystal structure showed that the 1,2-heterocyclized compounds can be accommodated in the binding site. Conformational analysis showed that 11 can only bind in a higher-energy conformation, which would explain its absent or low affinity. The amine and 2-oxygen interactions with D3.32 and S3.36, respectively, can form but shift the placement of the core scaffold. The constraints in 9-11 resulted in docking poses with the 4-bromine in closer vicinity to 5.46, which is polar only in the human 5-HT2A subtype, for which 9-11 have the lowest affinity. The new ligands, conformational analysis and docking expand the structure-activity relationships of constrained phenethylamines and contributes towards the development of 5-HT2 receptor subtype-selective ligands.

  8. Hybrid active-passive constrained layer damping treatments in beams, plates and shells

    Koh, Byungjun

    2016-01-01

    The basic concept of Hybrid Active-Passive Constrained Layer Damping (HAPCLD) treatment was proposed by introducing active control to the concept of passive constrained layer damping configuration in the 1990s to compensate for weak points in active and passive controls by using their respective merits for more robust and stable control. Since then, combinations of various configurations and applicable control strategies have been proposed and studied in many engineering areas. However, there...

  9. Constraining supernova progenitors: an integral field spectroscopic survey of the explosion sites

    Kuncarayakti, H; Anderson, J P; Arimoto, N; Doi, M; Galbany, L; Hamuy, M; Hashiba, Y; Kruehler, T; Maeda, K; Morokuma, T; Usuda, T

    2014-01-01

    We describe a survey of nearby core-collapse supernova (SN) explosion sites using integral field spectroscopy (IFS) technique, which is an extension of the work described in Kuncarayakti et al. (2013, AJ, 146, 30/31) . The project aims to constrain the SN progenitor properties based on the study of the SN immediate environment. The stellar populations present at the SN explosion sites are studied by means of integral field spectroscopy, which enables the acquisition of both spatial and spectral information of the object simultaneously. The spectrum of the SN parent stellar population gives the estimate of its age and metallicity. With this information, the initial mass and metallicity of the once coeval SN progenitor star are derived. While the survey is mostly done in optical, additionally the utilization of near-infrared integral field spectroscopy assisted with adaptive optics (AO) enables us to examine the explosion sites in high spatial details, down to a few parsecs. This work is being carried out using...

  10. Active site modeling in copper azurin molecular dynamics simulations

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  11. An Active RFID Accountability System (RAS) for Constrained Wireless Environments

    Barker, Alan M [ORNL; Hanson, Gregory R [ORNL; Sexton, Angela Kay [ORNL; Jones Jr, J P [ORNL; Freer, Eva B [ORNL; Sjoreen, Andrea L [ORNL

    2011-01-01

    A team from Oak Ridge National Laboratory (ORNL) has developed an RFID Accountability System (RAS) that allows items with active RFID tags to be tracked in environments where tags may not be able to transmit their location continuously. The system uses activators that transmit a short range signal. Active RFID tags are in a sleep state until they encounter an activator. Then they transmit a signal that is picked up by the antennas installed throughout the building. This paper presents the theory of operation, application areas, lessons learned, and key features developed over the course of seven years of development and use.

  12. Enhancer-activated plasmid transcription complexes contain constrained supercoiling.

    Bonilla, P J; Freytag, S O; Lutter, L C

    1991-01-01

    It has been proposed that transcriptionally active chromatin contains totally unconstrained supercoiling. The results of recent studies have raised the possibility that this topological state is the property of highly transcribed genes. Since the transcription rate of RNA polymerase II genes can be dramatically increased by the presence of an enhancer, we have determined if the transcription complex of an enhancer-activated plasmid contains totally unconstrained supercoils. Following transfec...

  13. DCC constrains tumour progression via its dependence receptor activity.

    Castets, Marie; Broutier, Laura; Molin, Yann; Brevet, Marie; Chazot, Guillaume; Gadot, Nicolas; Paquet, Armelle; Mazelin, Laetitia; Jarrosson-Wuilleme, Loraine; Scoazec, Jean-Yves; Bernet, Agnès; Mehlen, Patrick

    2012-02-23

    The role of deleted in colorectal carcinoma (DCC) as a tumour suppressor has been a matter of debate for the past 15 years. DCC gene expression is lost or markedly reduced in the majority of advanced colorectal cancers and, by functioning as a dependence receptor, DCC has been shown to induce apoptosis unless engaged by its ligand, netrin-1 (ref. 2). However, so far no animal model has supported the view that the DCC loss-of-function is causally implicated as predisposing to aggressive cancer development. To investigate the role of DCC-induced apoptosis in the control of tumour progression, here we created a mouse model in which the pro-apoptotic activity of DCC is genetically silenced. Although the loss of DCC-induced apoptosis in this mouse model is not associated with a major disorganization of the intestines, it leads to spontaneous intestinal neoplasia at a relatively low frequency. Loss of DCC-induced apoptosis is also associated with an increase in the number and aggressiveness of intestinal tumours in a predisposing APC mutant context, resulting in the development of highly invasive adenocarcinomas. These results demonstrate that DCC functions as a tumour suppressor via its ability to trigger tumour cell apoptosis. PMID:22158121

  14. Active Site Engineering in Electrocatalysis

    Verdaguer Casadevall, Arnau; Stephens, Ifan; Chorkendorff, Ib

    The overall goal of this thesis has been to design better catalysts for electrochemical reactions through a fundamental understanding of the materials at atomic scale. This has been achieved by combining electrochemical measurements with a variety of characterization techniques, often in ultra high...... under reaction conditions, which is ultimately controlled by the crystal structure of the underlying alloy.• Oxygen reduction to hydrogen peroxide has been investigated on single site catalysts, mainly alloys of noble metals with Hg. This resulted in a very special structure with isolated atoms of Pt or......, inexistent in other forms of Cu. The presence of strong CO binding sites correlates well with electrochemical activity, which paves the way for the rational development of even better electrocatalysts....

  15. Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs

    Wang, Xiaojun; Minasov, George; Shoichet, Brian K. (NWU)

    2010-03-08

    Pressured by antibiotic use, resistance enzymes have been evolving new activities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of the {beta}-lactamase TEM-1 were studied. When purified, mutant enzymes had increased activity against cephalosporin antibiotics but lost both thermodynamic stability and kinetic activity against their ancestral targets, penicillins. The X-ray crystallographic structures of three mutant enzymes were determined. These structures suggest that activity gain and stability loss is related to an enlarged active site cavity in the mutant enzymes. In several clinically isolated mutant enzymes, a secondary substitution is observed far from the active site (Met182 {yields} Thr). This substitution had little effect on enzyme activity but restored stability lost by substitutions near the active site. This regained stability conferred an advantage in vivo. This pattern of stability loss and restoration may be common in the evolution of new enzyme activity.

  16. Age of a prehistoric "Rodedian" cult site constrained by sediment and rock surface luminescence dating techniques

    Sohbati, Reza; Murray, Andrew; Porat, N.;

    2015-01-01

    The construction age of a pavement in a “Rodedian” prehistoric cult site in Negev desert, Israel, is established by determining the burial age of (i) a cobble used in the pavement, and (ii) the underlying sediment. The quartz OSL age and the K-feldspar corrected IR50 age from the sediment...

  17. Application of Crunch-Flow Routines to Constrain Present and Past Carbon Fluxes at Gas-Hydrate Bearing Sites

    Torres, Marta

    2014-01-31

    In November 2012, Oregon State University initiated the project entitled: Application of Crunch-Flow routines to constrain present and past carbon fluxes at gas-hydrate bearing sites. Within this project we developed Crunch-Flow based modeling modules that include important biogeochemical processes that need to be considered in gas hydrate environments. Our modules were applied to quantify carbon cycling in present and past systems, using data collected during several DOE-supported drilling expeditions, which include the Cascadia margin in US, Ulleung Basin in South Korea, and several sites drilled offshore India on the Bay of Bengal and Andaman Sea. Specifically, we completed modeling efforts that: 1) Reproduce the compositional and isotopic profiles observed at the eight drilled sites in the Ulleung Basin that constrain and contrast the carbon cycling pathways at chimney (high methane flux) and non-chimney sites (low methane, advective systems); 2) Simulate the Ba record in the sediments to quantify the past dynamics of methane flux in the southern Hydrate Ridge, Cascadia margin; and 3) Provide quantitative estimates of the thickness of individual mass transport deposits (MTDs), time elapsed after the MTD event, rate of sulfate reduction in the MTD, and time required to reach a new steady state at several sites drilled in the Krishna-Godavari (K-G) Basin off India. In addition we developed a hybrid model scheme by coupling a home-made MATLAB code with CrunchFlow to address the methane transport and chloride enrichment at the Ulleung Basins chimney sites, and contributed the modeling component to a study focusing on pore-scale controls on gas hydrate distribution in sediments from the Andaman Sea. These efforts resulted in two manuscripts currently under review, and contributed the modeling component of another pare, also under review. Lessons learned from these efforts are the basis of a mini-workshop to be held at Oregon State University (Feb 2014) to instruct

  18. Sows’ activity classification device using acceleration data – A resource constrained approach

    Marchioro, Gilberto Fernandes; Cornou, Cécile; Kristensen, Anders Ringgaard;

    2011-01-01

    This paper discusses the main architectural alternatives and design decisions in order to implement a sows’ activity classification model on electronic devices. The different possibilities are analyzed in practical and technical aspects, focusing on the implementation metrics, like cost......, performance, complexity and reliability. The target architectures are divided into: server based, where the main processing element is a central computer; and embedded based, where the processing is distributed on devices attached to the animals. The initial classification model identifies the activities...... of a heuristic classification approach, focusing on the resource constrained characteristics of embedded systems. The new approach classifies the activities performed by the sows with accuracy close to 90%. It was implemented as a hardware module that can easily be instantiated to provide preprocessed...

  19. Finite Element Modeling of a Fluid Filled Cylindrical Shell with Active Constrained Layer Damping

    ZHANG Yi; ZHANG Zhi-yi; TONG Zong-peng; HUA Hong-xing

    2005-01-01

    On the basis of the piezoelectric theory, Mindlin plate theory, viscoelastic theory and ideal fluid equa tion, the finite element modeling of a fluid-filled cylindrical shell with active constrained layer damping (ACLD) was discussed. Energy methods and Lagrange's equation were used to obtain dynamic equations of the cylindrical shell with ACLD treatments, which was modeled as well with the finite element method. The GHM (Golla-Hughes-McTavish) method was applied to model the frequency dependent damping of viscoelastic material. Ideal and incompressible fluid was considered to establish the dynamic equations of the fluid-filled cylindrical shell with ACLD treatments, Numerical results obtained from the finite element analysis were compared with those from an experiment. The comparison shows that the proposed modeling method is accurate and reliable.

  20. Foraging Habitat Quality Constrains Effectiveness of Artificial Nest-Site Provisioning in Reversing Population Declines in a Colonial Cavity Nester

    Catry, Inês; Franco, Aldina M. A.; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

    2013-01-01

    Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ±1.7 vs. 1.8 km ±0.4 and 1.9 km ±0.6) and had significant larger foraging-ranges (144 km2 vs. 18.8 and 14.8 km2) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas

  1. Characterization of Reuse Activities at Contaminated Sites

    Angela Vitulli; Charlotte Dougherty; Kimberly Bosworth

    2004-01-01

    Given the increased focus on reuse activity within EPA and state site cleanup programs, policy makers would benefit from looking across programs to better understand the extent and nature of reuse; examine site characteristics that influence reuse; leverage lessons learned; and coordinate reuse activities, data collection, and information management. This research paper begins to examine these issues. It reports the results of a preliminary review and analysis of available EPA and state progr...

  2. Fingerprinting differential active site constraints of ATPases

    Hacker, Stephan M.; Hardt, Norman; Buntru, Alexander; Pagliarini, Dana; Möckel, Martin; Mayer, Thomas U; Scheffner, Martin; Hauck, Christof R.; Marx, Andreas

    2013-01-01

    The free energy provided by adenosine triphosphate (ATP) hydrolysis is central to many cellular processes and, therefore, the number of enzymes utilizing ATP as a substrate is almost innumerable. Modified analogues of ATP are a valuable means to understand the biological function of ATPases. Although these enzymes have evolved towards binding to ATP, large differences in active site architectures were found. In order to systematically access the specific active site constraints of different A...

  3. Small constrained SP1-7 analogs bind to a unique site and promote anti-allodynic effects following systemic injection in mice.

    Jonsson, A; Fransson, R; Haramaki, Y; Skogh, A; Brolin, E; Watanabe, H; Nordvall, G; Hallberg, M; Sandström, A; Nyberg, F

    2015-07-01

    Previous results have shown that the substance P (SP) N-terminal fragment SP1-7 may attenuate hyperalgesia and produce anti-allodynia in animals using various experimental models for neuropathic pain. The heptapeptide was found to induce its effects through binding to and activating specific sites apart from any known neurokinin or opioid receptor. Furthermore, we have applied a medicinal chemistry program to develop lead compounds mimicking the effect of SP1-7. The present study was designed to evaluate the pharmacological effect of these compounds using the mouse spared nerve injury (SNI) model of chronic neuropathic pain. Also, as no comprehensive screen with the aim to identify the SP1-7 target has yet been performed we screened our lead compound H-Phe-Phe-NH2 toward a panel of drug targets. The extensive target screen, including 111 targets, did not reveal any hit for the binding site among a number of known receptors or enzymes involved in pain modulation. Our animal studies confirmed that SP1-7, but also synthetic analogs thereof, possesses anti-allodynic effects in the mouse SNI model of neuropathic pain. One of the lead compounds, a constrained H-Phe-Phe-NH2 analog, was shown to exhibit a significant anti-allodynic effect. PMID:25862586

  4. Constraining the Contribution of Galaxies and Active Galactic Nuclei to Cosmic Reionization

    Yoshiura, Shintaro; Ichiki, Kiyotomo; Tashiro, Hiroyuki; Shimabukuro, Hayato; Takahashi, Keitaro

    2016-01-01

    We constrain the contribution of high-$z$ galaxies and active galactic nuclei (AGNs) to reionization, by comparing numerically computed H/He reionization with the observed HI/HeII fractions at various redshifts and optical depth to Thomson scattering. In the model, the contribution of galaxies is controlled by a parameter $f_{\\rm esc}$ which indicates the escape fraction of ionizing photons from the galaxies, adopting an observed cosmic star formation history. On the other hand, in order to take ionizing photons from ANGs into account, observed X-ray luminosity functions and a composite spectral energy density with the energies in the range of $13.6\\rm eV$ to $100\\rm keV$ are assumed at $z\\leq3$, while the redshift evolution of AGN abundance at $z>3$ is assumed to be proportional to $(1+z)^\\beta$, where $\\beta$ is a parameter in the model. We find that there are observationally allowed sets of the parameters $f_{\\rm esc}$ and $\\beta$. According to the comparisons, $\\beta$ should satisfy $-4.20.18$ are also un...

  5. Thickness mode EMIS of constrained proof-mass piezoelectric wafer active sensors

    Kamas, Tuncay; Giurgiutiu, Victor; Lin, Bin

    2015-11-01

    This paper addresses theoretical and experimental work on thickness-mode electromechanical (E/M) impedance spectroscopy (EMIS) of proof-mass piezoelectric wafer active sensors (PMPWAS). The proof-mass (PM) concept was used to develop a new method for tuning the ultrasonic wave modes and for relatively high frequency local modal sensing by the PM affixed on PWAS. In order to develop the theoretical basis of the PMPWAS tuning concept, analytical analyses were conducted by applying the resonator theory to derive the EMIS of a PWAS constrained on one and both surfaces by isotropic elastic materials. The normalized thickness-mode shapes were obtained for the normal mode expansion (NME) method to eventually predict the thickness-mode EMIS using the correlation between PMPWAS and the structural dynamic properties of the substrate. Proof-masses of different sizes and materials were used to tune the system resonance towards an optimal frequency point. The results were verified by coupled-field finite element analyses (CF-FEA) and experimental results. An application of the tuning effect of PM on the standing wave modes was discussed as the increase in PM thickness shifts the excitation frequency of the wave mode toward the surface acoustic wave (SAW) mode.

  6. Managing Siting Activities for Nuclear Power Plants

    One of the IAEA's statutory objectives is to ''seek to accelerate and enlarge the contribution of atomic energy to peace, health and prosperity throughout the world''. One way this objective is achieved is through the publication of a range of technical series. Two of these are the IAEA Nuclear Energy Series and the IAEA Safety Standards Series. According to Article III.A.6 of the IAEA Statute, the safety standards establish 'standards of safety for protection of health and minimization of danger to life and property.' The safety standards include the Safety Fundamentals, Safety Requirements and Safety Guides. These standards are written primarily in a regulatory style, and are binding on the IAEA for its own programmes. The principal users are the regulatory bodies in Member States and other national authorities. The IAEA Nuclear Energy Series comprises reports designed to encourage and assist R and D on, and application of, nuclear energy for peaceful uses. This includes practical examples to be used by owners and operators of utilities in Member States, implementing organizations, academia, and government officials, among others. This information is presented in guides, reports on technology status and advances, and best practices for peaceful uses of nuclear energy based on inputs from international experts. The IAEA Nuclear Energy Series complements the IAEA Safety Standards Series. The introduction of nuclear power brings new challenges to States - one of them being the selection of appropriates sites. It is a project that needs to begin early, be well managed, and deploy good communications with all stakeholders; including regulators. This is important, not just for those States introducing nuclear power for the first time, but for any State looking to build a new nuclear power plant. The purpose of the siting activities goes beyond choosing a suitable site and acquiring a licence. A large part of the project is about producing and maintaining a validated

  7. Efficient oxygen electrocatalysis on special active sites

    Halck, Niels Bendtsen

    cobalt incorporated in ruthenium dioxide at high overpotentials during the oxygen reduction reaction (ORR). Density functional theory calculations were used to explain this phenomenon. The special active sites concepts are used to propose a general unified approach to increase the efficiency for oxygen...

  8. Acoustic radiation from the submerged circular cylindrical shell treated with active constrained layer damping

    Yuan, Li-Yun; Xiang, Yu; Lu, Jing; Jiang, Hong-Hua

    2015-12-01

    Based on the transfer matrix method of exploring the circular cylindrical shell treated with active constrained layer damping (i.e., ACLD), combined with the analytical solution of the Helmholtz equation for a point source, a multi-point multipole virtual source simulation method is for the first time proposed for solving the acoustic radiation problem of a submerged ACLD shell. This approach, wherein some virtual point sources are assumed to be evenly distributed on the axial line of the cylindrical shell, and the sound pressure could be written in the form of the sum of the wave functions series with the undetermined coefficients, is demonstrated to be accurate to achieve the radiation acoustic pressure of the pulsating and oscillating spheres respectively. Meanwhile, this approach is proved to be accurate to obtain the radiation acoustic pressure for a stiffened cylindrical shell. Then, the chosen number of the virtual distributed point sources and truncated number of the wave functions series are discussed to achieve the approximate radiation acoustic pressure of an ACLD cylindrical shell. Applying this method, different radiation acoustic pressures of a submerged ACLD cylindrical shell with different boundary conditions, different thickness values of viscoelastic and piezoelectric layer, different feedback gains for the piezoelectric layer and coverage of ACLD are discussed in detail. Results show that a thicker thickness and larger velocity gain for the piezoelectric layer and larger coverage of the ACLD layer can obtain a better damping effect for the whole structure in general. Whereas, laying a thicker viscoelastic layer is not always a better treatment to achieve a better acoustic characteristic. Project supported by the National Natural Science Foundation of China (Grant Nos. 11162001, 11502056, and 51105083), the Natural Science Foundation of Guangxi Zhuang Autonomous Region, China (Grant No. 2012GXNSFAA053207), the Doctor Foundation of Guangxi

  9. Multiple cooperative interactions constrain BPV-1 E2 dependent activation of transcription.

    Sowden, M; Harrison, S; Ashfield, R.; Kingsman, A J; Kingsman, S M

    1989-01-01

    Transcription directed by the BPV-1 long control region (LCR) is conditional upon activation by the virally encoded E2 protein. Within the 1.0 kb LCR there are five separate regions, A to E, that contain E2 responsive enhancers. The smallest functional region, A, is only 38 bp and contains two copies of the consensus sequence ACC(N)6GGT that is known to function as an E2 binding site in vitro. We show that a pair of these constitutes a minimal functional E2 responsive enhancer element but tha...

  10. Efficient oxygen electrocatalysis on special active sites

    Halck, Niels Bendtsen

    Oxygen electrocatalysis will be pivotal in future independent of fossil fuels. Renewable energy production will rely heavily on oxygen electrocatalysis as a method for storing energy from intermittent energy sources such as the wind and sun in the form of chemical bonds and to release the energy ...... electrocatalysis (ORR and OER) using organic functional groups on another class of catalysts. These consist of graphene sheets modified to have a local porphyrine site with different transition metals ions as model systems....... stored in these bonds in an eco-friendly fashion in fuel cells. This thesis explores catalysts for oxygen electrocatalysis and how carefully designed local structures on catalysts surfaces termed special active sites can influence the activity. Density functional theory has been used as a method...... throughout this thesis to understand these local structure effects and their influence on surface reactions. The concept of these special active sites is used to explain how oxygen evolution reaction (OER) catalysts can have activities beyond the limits of what was previously thought possible. The concept is...

  11. BET is active on Sellafield site

    Several companies, all part of BET Plant Services are carrying out work at the British Nuclear Fuels (BNFL) site at Sellafield, Cumbria, on one of the largest construction projects in Europe. The main development scheme is the THORP (Thermal Oxide Reprocessing Plant) buildings. One of the BET companies has the contract to paint the inside of the fuel storage ponds. It will also coat the surfaces of the MASWEP (Medium Active Solid Waste Encapsulation Plant) complex. Other work includes insulation and fire prevention installation. Scaffolding at the EARP (Enhanced Actinide Removal Plant) site is being provided on a common user basis so all the contractors can use the scaffolding and share the cost. Temporary office and living accommodation blocks have been provide by another BET company. (author)

  12. A primal-dual active-set method for non-negativity constrained total variation deblurring problems.

    Krishnan, D; Lin, Ping; Yip, Andy M

    2007-11-01

    This paper studies image deblurring problems using a total variation-based model, with a non-negativity constraint. The addition of the non-negativity constraint improves the quality of the solutions, but makes the solution process a difficult one. The contribution of our work is a fast and robust numerical algorithm to solve the non-negatively constrained problem. To overcome the nondifferentiability of the total variation norm, we formulate the constrained deblurring problem as a primal-dual program which is a variant of the formulation proposed by Chan, Golub, and Mulet for unconstrained problems. Here, dual refers to a combination of the Lagrangian and Fenchel duals. To solve the constrained primal-dual program, we use a semi-smooth Newton's method. We exploit the relationship between the semi-smooth Newton's method and the primal-dual active set method to achieve considerable simplification of the computations. The main advantages of our proposed scheme are: no parameters need significant adjustment, a standard inverse preconditioner works very well, quadratic rate of local convergence (theoretical and numerical), numerical evidence of global convergence, and high accuracy of solving the optimality system. The scheme shows robustness of performance over a wide range of parameters. A comprehensive set of numerical comparisons are provided against other methods to solve the same problem which show the speed and accuracy advantages of our scheme. PMID:17990753

  13. Developing a Coding Scheme to Analyse Creativity in Highly-constrained Design Activities

    Dekoninck, Elies; Yue, Huang; Howard, Thomas J.;

    2010-01-01

    This work is part of a larger project which aims to investigate the nature of creativity and the effectiveness of creativity tools in highly-constrained design tasks. This paper presents the research where a coding scheme was developed and tested with a designer-researcher who conducted two rounds...... of design and analysis on a highly constrained design task. This paper shows how design changes can be coded using a scheme based on creative ‘modes of change’. The coding scheme can show the way a designer moves around the design space, and particularly the strategies that are used by a creative...... designer to skip from one ‘train of solutions’ to new avenues. The coding scheme can be made more robust by: ensuring design change is always coded relative to a reference design; tightening up definitions of ‘system’, ‘element’ and ‘function’; and using a matrix to develop a more complete set of codes. A...

  14. Constrained wormholes

    The large wormhole problem in Coleman's theory of the cosmological constant is presented in the framework of constrained wormholes. We use semi-classical methods, similar to those used to study constrained instantons in quantum field theory. A scalar field theory serves as a toy model to analyze the problems associated with large constrained instantons. In particular, these large instantons are found to suffer from large quantum fluctuations. In gravity we find the same situation: large quantum fluctuations around large wormholes. In both cases we expect that these large fluctuations are a signal that large constrained solutions are not important in the path integral. Thus, we argue that only small wormholes are important in Coleman's theory. (orig.)

  15. Integral field spectroscopy of supernova explosion sites: constraining mass and metallicity of the progenitors - I. Type Ib and Ic supernovae

    Kuncarayakti, Hanindyo; Aldering, Greg; Arimoto, Nobuo; Maeda, Keiichi; Morokuma, Tomoki; Pereira, Rui; Usuda, Tomonori; Hashiba, Yasuhito

    2013-01-01

    Integral field spectroscopy of 11 type-Ib/c supernova explosion sites in nearby galaxies has been obtained using UH88/SNIFS and Gemini-N/GMOS. The use of integral field spectroscopy enables us to obtain both spatial and spectral information of the explosion site, allowing the identification of the parent stellar population of the supernova progenitor star. The spectrum of the parent population provides metallicity determination via strong-line method and age estimation obtained via comparison with simple stellar population (SSP) models. We adopt this information as the metallicity and age of the supernova progenitor, under the assumption that it was coeval with the parent stellar population. The age of the star corresponds to its lifetime, which in turn gives the estimate of its initial mass. With this method we were able to determine both the metallicity and initial (ZAMS) mass of the progenitor stars of the type Ib and Ic supernovae. We found that on average SN Ic explosion sites are more metal-rich and you...

  16. Promoter proximal polyadenylation sites reduce transcription activity

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  17. Activities on the site during construction phase

    A survey is given of the work done on the site from site-opening till turn over of the plant to the client. After a short introduction to time schedules, manpower on site, site facilities and civil work and constructions, the commissioning and trial operation phase is discussed in detail. This phase begins with finishing the assembly of individual systems and components and ends with the trial operation and the acceptance measurement. During this period the subsystems are started-up in a useful sequence, first from cold, then from hot conditions and are finally operated as a total with nuclear energy. The single steps are: a) commissioning of indivudal systems; b) hot functional test 1 (without fuels) c) baseline inspection at the reactor pressure vessel; d) hot functional test 2 (with fuels); e) preparation for first criticality; f) postcriticality test program; g) trial operation: h) acceptance measurement. (HP)

  18. Constraining AGN triggering mechanisms through the clustering analysis of active black holes

    Gatti, M; Bouillot, V; Menci, N; Lamastra, A; Hirschmann, M; Fiore, F

    2015-01-01

    The triggering mechanisms for Active Galactic Nuclei (AGN) are still debated. Some of the most popular ones include galaxy interactions (IT) and disk instabilities (DI). Using an advanced semi analytic model (SAM) of galaxy formation, coupled to accurate halo occupation distribution modeling, we investigate the imprint left by each separate triggering process on the clustering strength of AGN at small and large scales. Our main results are as follows: i) DIs, irrespective of their exact implementation in the SAM, tend to fall short in triggering AGN activity in galaxies at the center of halos with $M_h>10^{13.5} h^{-1}M_{\\odot}$. On the contrary, the IT scenario predicts abundance of active, central galaxies that generally agrees well with observations at every halo mass. ii) The relative number of satellite AGN in DIs at intermediate-to-low luminosities is always significantly higher than in IT models, especially in groups and clusters. The low AGN satellite fraction predicted for the IT scenario might sugge...

  19. Constraining AGN triggering mechanisms through the clustering analysis of active black holes

    Gatti, M.; Shankar, F.; Bouillot, V.; Menci, N.; Lamastra, A.; Hirschmann, M.; Fiore, F.

    2016-02-01

    The triggering mechanisms for active galactic nuclei (AGN) are still debated. Some of the most popular ones include galaxy interactions (IT) and disc instabilities (DIs). Using an advanced semi-analytic model (SAM) of galaxy formation, coupled to accurate halo occupation distribution modelling, we investigate the imprint left by each separate triggering process on the clustering strength of AGN at small and large scales. Our main results are as follows: (i) DIs, irrespective of their exact implementation in the SAM, tend to fall short in triggering AGN activity in galaxies at the centre of haloes with Mh > 1013.5 h-1 M⊙. On the contrary, the IT scenario predicts abundance of active central galaxies that generally agrees well with observations at every halo mass. (ii) The relative number of satellite AGN in DIs at intermediate-to-low luminosities is always significantly higher than in IT models, especially in groups and clusters. The low AGN satellite fraction predicted for the IT scenario might suggest that different feeding modes could simultaneously contribute to the triggering of satellite AGN. (iii) Both scenarios are quite degenerate in matching large-scale clustering measurements, suggesting that the sole average bias might not be an effective observational constraint. (iv) Our analysis suggests the presence of both a mild luminosity and a more consistent redshift dependence in the AGN clustering, with AGN inhabiting progressively less massive dark matter haloes as the redshift increases. We also discuss the impact of different observational selection cuts in measuring AGN clustering, including possible discrepancies between optical and X-ray surveys.

  20. Crystallographic B factor of critical residues at enzyme active site

    张海龙; 宋时英; 林政炯

    1999-01-01

    Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzymes were calculated respectively. The statistical results showed that the critical residues at the active site of most of the enzymes had lower B factors than did the whole molecules, indicating that in the crystalline state the critical residues at the active site of the natural enzymes possess more stable conformation than do the whole molecules. The flexibility of the active site during the unfolding by denaturing was also discussed.

  1. A NEW APPROACH TO CONSTRAIN BLACK HOLE SPINS IN ACTIVE GALAXIES USING OPTICAL REVERBERATION MAPPING

    A tight relation between the size of the broad-line region (BLR) and optical luminosity has been established in about 50 active galactic nuclei studied through reverberation mapping of the broad Hβ emission line. The R BLR-L relation arises from simple photoionization considerations. Using a general relativistic model of an optically thick, geometrically thin accretion disk, we show that the ionizing luminosity jointly depends on black hole mass, accretion rate, and spin. The non-monotonic relation between the ionizing and optical luminosity gives rise to a complicated relation between the BLR size and the optical luminosity. We show that the reverberation lag of Hβ to the varying continuum depends very sensitively on black hole spin. For retrograde spins, the disk is so cold that there is a deficit of ionizing photons in the BLR, resulting in shrinkage of the hydrogen ionization front with increasing optical luminosity, and hence shortened Hβ lags. This effect is specially striking for luminous quasars undergoing retrograde accretion, manifesting in strong deviations from the canonical R BLR-L relation. This could lead to a method to estimate black hole spins of quasars and to study their cosmic evolution. At the same time, the small scatter of the observed R BLR-L relation for the current sample of reverberation-mapped active galaxies implies that the majority of these sources have rapidly spinning black holes

  2. Seamless tube shape is constrained by endocytosis-dependent regulation of active Moesin.

    Schottenfeld-Roames, Jodi; Rosa, Jeffrey B; Ghabrial, Amin S

    2014-08-01

    Most tubes have seams (intercellular or autocellular junctions that seal membranes together into a tube), but "seamless" tubes also exist. In Drosophila, stellate-shaped tracheal terminal cells make seamless tubes, with single branches running through each of dozens of cellular extensions. We find that mutations in braided impair terminal cell branching and cause formation of seamless tube cysts. We show that braided encodes Syntaxin7 and that cysts also form in cells deficient for other genes required either for membrane scission (shibire) or for early endosome formation (Rab5, Vps45, and Rabenosyn-5). These data define a requirement for early endocytosis in shaping seamless tube lumens. Importantly, apical proteins Crumbs and phospho-Moesin accumulate to aberrantly high levels in braided terminal cells. Overexpression of either Crumbs or phosphomimetic Moesin induced lumenal cysts and decreased terminal branching. Conversely, the braided seamless tube cyst phenotype was suppressed by mutations in crumbs or Moesin. Indeed, mutations in Moesin dominantly suppressed seamless tube cyst formation and restored terminal branching. We propose that early endocytosis maintains normal steady-state levels of Crumbs, which recruits apical phosphorylated (active) Moe, which in turn regulates seamless tube shape through modulation of cortical actin filaments. PMID:25065756

  3. Flux Tensor Constrained Geodesic Active Contours with Sensor Fusion for Persistent Object Tracking

    Filiz Bunyak

    2007-08-01

    Full Text Available This paper makes new contributions in motion detection, object segmentation and trajectory estimation to create a successful object tracking system. A new efficient motion detection algorithm referred to as the flux tensor is used to detect moving objects in infrared video without requiring background modeling or contour extraction. The flux tensor-based motion detector when applied to infrared video is more accurate than thresholding ”hot-spots”, and is insensitive to shadows as well as illumination changes in the visible channel. In real world monitoring tasks fusing scene information from multiple sensors and sources is a useful core mechanism to deal with complex scenes, lighting conditions and environmental variables. The object segmentation algorithm uses level set-based geodesic active contour evolution that incorporates the fusion of visible color and infrared edge informations in a novel manner. Touching or overlapping objects are further refined during the segmentation process using an appropriate shapebased model. Multiple object tracking using correspondence graphs is extended to handle groups of objects and occlusion events by Kalman filter-based cluster trajectory analysis and watershed segmentation. The proposed object tracking algorithm was successfully tested on several difficult outdoor multispectral videos from stationary sensors and is not confounded by shadows or illumination variations.

  4. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites

  5. Savannah River Site prioritization of transition activities

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D ampersand D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities

  6. Savannah River Site prioritization of transition activities

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  7. The active site of low-temperature methane hydroxylation in iron-containing zeolites.

    Snyder, Benjamin E R; Vanelderen, Pieter; Bols, Max L; Hallaert, Simon D; Böttger, Lars H; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2016-08-18

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts. PMID:27535535

  8. Muscular activity during uphill cycling: effect of slope, posture, hand grip position and constrained bicycle lateral sways.

    Duc, S; Bertucci, W; Pernin, J N; Grappe, F

    2008-02-01

    Despite the wide use of surface electromyography (EMG) to study pedalling movement, there is a paucity of data concerning the muscular activity during uphill cycling, notably in standing posture. The aim of this study was to investigate the muscular activity of eight lower limb muscles and four upper limb muscles across various laboratory pedalling exercises which simulated uphill cycling conditions. Ten trained cyclists rode at 80% of their maximal aerobic power on an inclined motorised treadmill (4%, 7% and 10%) with using two pedalling postures (seated and standing). Two additional rides were made in standing at 4% slope to test the effect of the change of the hand grip position (from brake levers to the drops of the handlebar), and the influence of the lateral sways of the bicycle. For this last goal, the bicycle was fixed on a stationary ergometer to prevent the lean of the bicycle side-to-side. EMG was recorded from M. gluteus maximus (GM), M. vastus medialis (VM), M. rectus femoris (RF), M. biceps femoris (BF), M. semimembranosus (SM), M. gastrocnemius medialis (GAS), M. soleus (SOL), M. tibialis anterior (TA), M. biceps brachii (BB), M. triceps brachii (TB), M. rectus abdominis (RA) and M. erector spinae (ES). Unlike the slope, the change of pedalling posture in uphill cycling had a significant effect on the EMG activity, except for the three muscles crossing the ankle's joint (GAS, SOL and TA). Intensity and duration of GM, VM, RF, BF, BB, TA, RA and ES activity were greater in standing while SM activity showed a slight decrease. In standing, global activity of upper limb was higher when the hand grip position was changed from brake level to the drops, but lower when the lateral sways of the bicycle were constrained. These results seem to be related to (1) the increase of the peak pedal force, (2) the change of the hip and knee joint moments, (3) the need to stabilize pelvic in reference with removing the saddle support, and (4) the shift of the mass

  9. Interpretation of Flow Logs from Nevada Test Site Boreholes to Estimate Hydraulic conductivity Using Numerical Simulations Constrained by Single-Well Aquifer Tests

    Garcia, C. Amanda; Halford, Keith J.; Laczniak, Randell J.

    2010-02-12

    Hydraulic conductivities of volcanic and carbonate lithologic units at the Nevada Test Site were estimated from flow logs and aquifer-test data. Borehole flow and drawdown were integrated and interpreted using a radial, axisymmetric flow model, AnalyzeHOLE. This integrated approach is used because complex well completions and heterogeneous aquifers and confining units produce vertical flow in the annular space and aquifers adjacent to the wellbore. AnalyzeHOLE simulates vertical flow, in addition to horizontal flow, which accounts for converging flow toward screen ends and diverging flow toward transmissive intervals. Simulated aquifers and confining units uniformly are subdivided by depth into intervals in which the hydraulic conductivity is estimated with the Parameter ESTimation (PEST) software. Between 50 and 150 hydraulic-conductivity parameters were estimated by minimizing weighted differences between simulated and measured flow and drawdown. Transmissivity estimates from single-well or multiple-well aquifer tests were used to constrain estimates of hydraulic conductivity. The distribution of hydraulic conductivity within each lithology had a minimum variance because estimates were constrained with Tikhonov regularization. AnalyzeHOLE simulated hydraulic-conductivity estimates for lithologic units across screened and cased intervals are as much as 100 times less than those estimated using proportional flow-log analyses applied across screened intervals only. Smaller estimates of hydraulic conductivity for individual lithologic units are simulated because sections of the unit behind cased intervals of the wellbore are not assumed to be impermeable, and therefore, can contribute flow to the wellbore. Simulated hydraulic-conductivity estimates vary by more than three orders of magnitude across a lithologic unit, indicating a high degree of heterogeneity in volcanic and carbonate-rock units. The higher water transmitting potential of carbonate-rock units relative

  10. Mrk 421 active state in 2008: the MAGIC view, simultaneous multi-wavelength observations and SSC model constrained

    Aleksić, J.; Alvarez, E. A.; Antonelli, L. A.; Antoranz, P.; Asensio, M.; Backes, M.; Barrio, J. A.; Bastieri, D.; Becerra González, J.; Bednarek, W.; Berdyugin, A.; Berger, K.; Bernardini, E.; Biland, A.; Blanch, O.; Bock, R. K.; Boller, A.; Bonnoli, G.; Borla Tridon, D.; Braun, I.; Bretz, T.; Cañellas, A.; Carmona, E.; Carosi, A.; Colin, P.; Colombo, E.; Contreras, J. L.; Cortina, J.; Cossio, L.; Covino, S.; Dazzi, F.; De Angelis, A.; De Caneva, G.; De Cea del Pozo, E.; De Lotto, B.; Delgado Mendez, C.; Diago Ortega, A.; Doert, M.; Domínguez, A.; Dominis Prester, D.; Dorner, D.; Doro, M.; Elsaesser, D.; Ferenc, D.; Fonseca, M. V.; Font, L.; Fruck, C.; García López, R. J.; Garczarczyk, M.; Garrido, D.; Giavitto, G.; Godinović, N.; Hadasch, D.; Häfner, D.; Herrero, A.; Hildebrand, D.; Höhne-Mönch, D.; Hose, J.; Hrupec, D.; Huber, B.; Jogler, T.; Kellermann, H.; Klepser, S.; Krähenbühl, T.; Krause, J.; La Barbera, A.; Lelas, D.; Leonardo, E.; Lindfors, E.; Lombardi, S.; López, A.; López, M.; Lorenz, E.; Makariev, M.; Maneva, G.; Mankuzhiyil, N.; Mannheim, K.; Maraschi, L.; Mariotti, M.; Martínez, M.; Mazin, D.; Meucci, M.; Miranda, J. M.; Mirzoyan, R.; Miyamoto, H.; Moldón, J.; Moralejo, A.; Munar-Adrover, P.; Nieto, D.; Nilsson, K.; Orito, R.; Oya, I.; Paneque, D.; Paoletti, R.; Pardo, S.; Paredes, J. M.; Partini, S.; Pasanen, M.; Pauss, F.; Perez-Torres, M. A.; Persic, M.; Peruzzo, L.; Pilia, M.; Pochon, J.; Prada, F.; Prada Moroni, P. G.; Prandini, E.; Puljak, I.; Reichardt, I.; Reinthal, R.; Rhode, W.; Ribó, M.; Rico, J.; Rügamer, S.; Saggion, A.; Saito, K.; Saito, T. Y.; Salvati, M.; Satalecka, K.; Scalzotto, V.; Scapin, V.; Schultz, C.; Schweizer, T.; Shayduk, M.; Shore, S. N.; Sillanpää, A.; Sitarek, J.; Sobczynska, D.; Spanier, F.; Spiro, S.; Stamerra, A.; Steinke, B.; Storz, J.; Strah, N.; Surić, T.; Takalo, L.; Takami, H.; Tavecchio, F.; Temnikov, P.; Terzić, T.; Tescaro, D.; Teshima, M.; Tibolla, O.; Torres, D. F.; Treves, A.; Uellenbeck, M.; Vankov, H.; Vogler, P.; Wagner, R. M.; Weitzel, Q.; Zabalza, V.; Zandanel, F.; Zanin, R.

    2012-06-01

    Context. The blazar Markarian 421 is one of the brightest TeV gamma-ray sources of the northern sky. From December 2007 until June 2008 it was intensively observed in the very high energy (VHE, E > 100 GeV) band by the single-dish Major Atmospheric Gamma-ray Imaging Cherenkov telescope (MAGIC-I). Aims: We aimed to measure the physical parameters of the emitting region of the blazar jet during active states. Methods: We performed a dense monitoring of the source in VHE with MAGIC-I, and also collected complementary data in soft X-rays and optical-UV bands; then, we modeled the spectral energy distributions (SED) derived from simultaneous multi-wavelength data within the synchrotron self-Compton (SSC) framework. Results: The source showed intense and prolonged γ-ray activity during the whole period, with integral fluxes (E > 200 GeV) seldom below the level of the Crab Nebula, and up to 3.6 times this value. Eight datasets of simultaneous optical-UV (KVA, Swift/UVOT), soft X-ray (Swift/XRT) and MAGIC-I VHE data were obtained during different outburst phases. The data constrain the physical parameters of the jet, once the spectral energy distributions obtained are interpreted within the framework of a single-zone SSC leptonic model. Conclusions: The main outcome of the study is that within the homogeneous model high Doppler factors (40 ≤ δ ≤ 80) are needed to reproduce the observed SED; but this model cannot explain the observed short time-scale variability, while it can be argued that inhomogeneous models could allow for less extreme Doppler factors, more intense magnetic fields and shorter electron cooling times compatible with hour or sub-hour scale variability.

  11. The Surface Groups and Active Site of Fibrous Mineral Materials

    DONG Fa-qin; WAN Pu; FENG Qi-ming; SONG Gong-bao; PENG Tong-jiang; LI Ping; LI Guo-wu

    2004-01-01

    The exposed and transformed groups of fibrous brucite,wollastonite,chrysotile asbestos,sepiolite,palygorskite,clinoptilolite,crocidolite and diatomaceous earth mineral materials are analyzed by IR spectra after acid and alikali etching,strong mechanical and polarity molecular interaction.The results show the active sites concentrate on the ends in stick mineral materials and on the defect or hole edge in pipe mineral materials.The inside active site of mineral materials plays a main role in small molecular substance.The shape of minerals influence their distribution and density of active site.The strong mechanical impulsion and weak chemical force change the active site feature of minerals,the powder process enables minerals exposed more surface group and more combined types.The surface processing with the small polarity molecular or the brand of middle molecular may produce ionation and new coordinate bond,and change the active properties and level of original mineral materials.

  12. The active site behaviour of electrochemically synthesised gold nanomaterials.

    Plowman, Blake J; O'Mullane, Anthony P; Bhargava, Suresh K

    2011-01-01

    Even though gold is the noblest of metals, a weak chemisorber and is regarded as being quite inert, it demonstrates significant electrocatalytic activity in its nanostructured form. It is demonstrated here that nanostructured and even evaporated thin films of gold are covered with active sites which are responsible for such activity. The identification of these sites is demonstrated with conventional electrochemical techniques such as cyclic voltammetry as well as a large amplitude Fourier transformed alternating current (FT-ac) method under acidic and alkaline conditions. The latter technique is beneficial in determining if an electrode process is either Faradaic or capacitive in nature. The observed behaviour is analogous to that observed for activated gold electrodes whose surfaces have been severely disrupted by cathodic polarisation in the hydrogen evolution region. It is shown that significant electrochemical oxidation responses occur at discrete potential values well below that for the formation of the compact monolayer oxide of bulk gold and are attributed to the facile oxidation of surface active sites. Several electrocatalytic reactions are explored in which the onset potential is determined by the presence of such sites on the surface. Significantly, the facile oxidation of active sites is used to drive the electroless deposition of metals such as platinum, palladium and silver from their aqueous salts on the surface of gold nanostructures. The resultant surface decoration of gold with secondary metal nanoparticles not only indicates regions on the surface which are rich in active sites but also provides a method to form interesting bimetallic surfaces. PMID:22455038

  13. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

    Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

    2016-06-17

    Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes. PMID:26990764

  14. Fluorescence energy transfer studies on the active site of papain

    Henes, Jill B.; Briggs, Martha S.; Sligar, Stephen G.; Fruton, Joseph S.

    1980-01-01

    Measurements have been performed of the excited-state lifetimes and fluorescence yields of papain tryptophan units when acyl derivatives of Phe-glycinal are bound at the active site of the enzyme. The enhancement of tryptophan fluorescence in complexes of papain with the acetyl or benzyloxycarbonyl derivatives is not stereospecific with respect to the configuration of the phenylalanyl residue, and the L and D isomers are equally effective as active-site-directed inhibitors of papain action. E...

  15. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

    Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

    2016-06-28

    Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes. PMID:27259687

  16. Key messages from active CO2 storage sites

    Wildenborg, T.; Wollenweber, J. [TNO, Princetonlaan 6, 3584 CB Utrecht (Netherlands); Chadwick, A. [BGS, Environmental Science Centre, Keyworth, Nottingham, NG12 5GG (United Kingdom); Deflandre, J.P. [IFP Energies nouvelles, 1-4 avenue de Bois Preau, 92852 Rueil-Malmaison (France); Eiken, O. [Statoil Research Centre, Rotvoll, Arkitekt Ebbells vei 10, 7005 Trondheim (Norway); Mathieson, A. [BP, Alternative Energy, Chertsey Road, Sunbury on Thames (United Kingdom); Metcalfe, R. [QUINTESSA, The Hub, 14 Station Road, Henley-on-Thames, Oxfordshire (United Kingdom); Schmidt Hattenberger, C. [GFZ German Research Centre for Geosciences, Centre for CO2Storage, Potsdam (Germany)

    2013-07-01

    An extensive programme of modelling, monitoring and verification activities was deployed at a set of active storage sites worldwide including Sleipner, In Salah, Ketzin, Weyburn, K12-B and Snoehvit (EU CO2ReMoVe project). All investigated storage sites were well managed and did not have a negative impact on humans or the environment. Time-lapse seismic and pressure monitoring are key in verifying the deep subsurface performance of the storage sites. Evidence gathered during the site characterisation and operational phases is key to handover responsibility of the storage site to governmental authorities after injection has definitely ceased, which is the focus of the follow-up EU project CO2CARE.

  17. Klipperaas study site. Scope of activities and main results

    During the period from 1977 - 1986 SKB (Swedish Nuclear Fuel and Waste Management Co.) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection rpogramme will be to perform detailed characterisation, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if any of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favorable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concern the Klipperaas study site. The main topics are the scope of activities, geologic model, geohydrological model, groundwater chemistry, assessment of solute transport, and rock mechanics

  18. Dashboard applications to monitor experiment activities at sites

    Andreeva, Julia; Belforte, Stefano; Boehm, Max; Casajus, Adrian; Flix, Josep; Gaidioz, Benjamin; Grigoras, Costin; Kokoszkiewicz, Lukasz; Lanciotti, Elisa; Rocha, Ricardo; Saiz, Pablo; Santinelli, Roberto; Sidorova, Irina; Sciabà, Andrea; Tsaregorodtsev, Andrei

    2010-04-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  19. Dashboard applications to monitor experiment activities at sites

    Andreeva, J; Boehm, M; Casajus, A; Flix, J; Gaidioz, B; Grigoras, C; Kokoszkiewicz, L; Lanciotti, E; Rocha, R; Saiz, P; Santinelli, R; Sidorova, I; Sciabà, A; Tsaregorodtsev, A

    2010-01-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  20. Dashboard applications to monitor experiment activities at sites

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  1. Gideaa study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish Nuclear Fuel and Waste Management Co) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other site with geological and/or socio-economical characteristics judged more favourable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concerns the Gideaa study site. (au)

  2. Fjaellveden study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish Nuclear Fuel and Waste Management CO) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favourable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need for complementary investigations. This report concerns the Fjaellveden study site. (au)

  3. Kamlunge study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish nuclear Fuel and Waste Management Co.) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favourable may very well be selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concerns the Kamlunge study site. (79 refs.) (au)

  4. Constrained Appropriations

    Wildermuth, Norbert

    2008-01-01

      A discussion of the contingent character of young Brazilian's media culture is the focus of my contribution's theoretical approach. Thus, while giving recognition to young people's active agency in the creation of media-centred lifestyles and youth cultures, I will seek to demonstrate their pra...

  5. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  6. INTEGRAL FIELD SPECTROSCOPY OF SUPERNOVA EXPLOSION SITES: CONSTRAINING THE MASS AND METALLICITY OF THE PROGENITORS. I. TYPE Ib AND Ic SUPERNOVAE

    Kuncarayakti, Hanindyo; Maeda, Keiichi [Kavli Institute for the Physics and Mathematics of the Universe (WPI), Todai Institutes for Advanced Study, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8583 (Japan); Doi, Mamoru; Morokuma, Tomoki; Hashiba, Yasuhito [Institute of Astronomy, Graduate School of Science, The University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Aldering, Greg [Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Arimoto, Nobuo [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Pereira, Rui [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, 4 Rue Enrico Fermi, F-69622 Villeurbanne Cedex (France); Usuda, Tomonori, E-mail: hanindyo.kuncarayakti@ipmu.jp [Subaru Telescope, National Astronomical Observatory of Japan, 650 North A' ohoku Place, Hilo, HI 96720 (United States)

    2013-08-01

    Integral field spectroscopy of 11 Type Ib/Ic supernova (SN Ib/Ic) explosion sites in nearby galaxies has been obtained using UH88/SNIFS and Gemini-N/GMOS. The use of integral field spectroscopy enables us to obtain both spatial and spectral information about the explosion site, enabling the identification of the parent stellar population of the SN progenitor star. The spectrum of the parent population provides metallicity determination via strong-line method and age estimation obtained via comparison with simple stellar population models. We adopt this information as the metallicity and age of the SN progenitor, under the assumption that it was coeval with the parent stellar population. The age of the star corresponds to its lifetime, which in turn gives the estimate of its initial mass. With this method we were able to determine both the metallicity and initial (zero-age main sequence) mass of the progenitor stars of SNe Ib and Ic. We found that on average SN Ic explosion sites are more metal-rich and younger than SN Ib sites. The initial mass of the progenitors derived from parent stellar population age suggests that SN Ic has more massive progenitors than SN Ib. In addition, we also found indication that some of our SN progenitors are less massive than {approx}25 M{sub Sun }, indicating that they may have been stars in a close binary system that have lost their outer envelope via binary interactions to produce SNe Ib/Ic, instead of single Wolf-Rayet stars. These findings support the current suggestions that both binary and single progenitor channels are in effect in producing SNe Ib/Ic. This work also demonstrates the power of integral field spectroscopy in investigating SN environments and active star-forming regions.

  7. INTEGRAL FIELD SPECTROSCOPY OF SUPERNOVA EXPLOSION SITES: CONSTRAINING THE MASS AND METALLICITY OF THE PROGENITORS. I. TYPE Ib AND Ic SUPERNOVAE

    Integral field spectroscopy of 11 Type Ib/Ic supernova (SN Ib/Ic) explosion sites in nearby galaxies has been obtained using UH88/SNIFS and Gemini-N/GMOS. The use of integral field spectroscopy enables us to obtain both spatial and spectral information about the explosion site, enabling the identification of the parent stellar population of the SN progenitor star. The spectrum of the parent population provides metallicity determination via strong-line method and age estimation obtained via comparison with simple stellar population models. We adopt this information as the metallicity and age of the SN progenitor, under the assumption that it was coeval with the parent stellar population. The age of the star corresponds to its lifetime, which in turn gives the estimate of its initial mass. With this method we were able to determine both the metallicity and initial (zero-age main sequence) mass of the progenitor stars of SNe Ib and Ic. We found that on average SN Ic explosion sites are more metal-rich and younger than SN Ib sites. The initial mass of the progenitors derived from parent stellar population age suggests that SN Ic has more massive progenitors than SN Ib. In addition, we also found indication that some of our SN progenitors are less massive than ∼25 M☉, indicating that they may have been stars in a close binary system that have lost their outer envelope via binary interactions to produce SNe Ib/Ic, instead of single Wolf-Rayet stars. These findings support the current suggestions that both binary and single progenitor channels are in effect in producing SNe Ib/Ic. This work also demonstrates the power of integral field spectroscopy in investigating SN environments and active star-forming regions

  8. Integral Field Spectroscopy of Supernova Explosion Sites: Constraining the Mass and Metallicity of the Progenitors. I. Type Ib and Ic Supernovae

    Kuncarayakti, Hanindyo; Doi, Mamoru; Aldering, Greg; Arimoto, Nobuo; Maeda, Keiichi; Morokuma, Tomoki; Pereira, Rui; Usuda, Tomonori; Hashiba, Yasuhito

    2013-08-01

    Integral field spectroscopy of 11 Type Ib/Ic supernova (SN Ib/Ic) explosion sites in nearby galaxies has been obtained using UH88/SNIFS and Gemini-N/GMOS. The use of integral field spectroscopy enables us to obtain both spatial and spectral information about the explosion site, enabling the identification of the parent stellar population of the SN progenitor star. The spectrum of the parent population provides metallicity determination via strong-line method and age estimation obtained via comparison with simple stellar population models. We adopt this information as the metallicity and age of the SN progenitor, under the assumption that it was coeval with the parent stellar population. The age of the star corresponds to its lifetime, which in turn gives the estimate of its initial mass. With this method we were able to determine both the metallicity and initial (zero-age main sequence) mass of the progenitor stars of SNe Ib and Ic. We found that on average SN Ic explosion sites are more metal-rich and younger than SN Ib sites. The initial mass of the progenitors derived from parent stellar population age suggests that SN Ic has more massive progenitors than SN Ib. In addition, we also found indication that some of our SN progenitors are less massive than ~25 M ⊙, indicating that they may have been stars in a close binary system that have lost their outer envelope via binary interactions to produce SNe Ib/Ic, instead of single Wolf-Rayet stars. These findings support the current suggestions that both binary and single progenitor channels are in effect in producing SNe Ib/Ic. This work also demonstrates the power of integral field spectroscopy in investigating SN environments and active star-forming regions.

  9. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  10. Resonant active sites in catalytic ammonia synthesis: A structural model

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  11. Probing the active sites for CO dissociation on ruthenium nanoparticles

    Strebel, Christian Ejersbo; Murphy, Shane; Nielsen, Rasmus Munksgård;

    2012-01-01

    The active sites for CO dissociation were probed on mass-selected Ru nanoparticles on a HOPG support by temperature programmed desorption spectroscopy using isotopically labelled CO. Combined with transmission electron microscopy we gain insight on how the size and morphology of the nanoparticles...

  12. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  13. Active Sites Environmental Monitoring Program: FY 1990 annual report

    Wickliff, D.S.; Morrissey, C.M.; Ashwood, T.L.

    1991-10-01

    Chapter 3 of US Department of Energy (DOE) Order 5820.2A (DOE 1988) sets forth requirements for environmental monitoring of active low-level waste (LLW) disposal sites. Active sites are defined as those LLW facilities that were in use on or after the date of the order (September 1988). The transuranic (TRU) waste storage areas in Solid Waste Storage Area (SWSA) 5 North are covered by Chap. 2 of the order. In both chapters, monitoring is required to provide for early warning of leaks before those leaks pose a threat to human health or the environment. Chapter 3 also requires that monitoring be conducted to evaluate the short- and long-term performance of LLW disposal facilities. In accordance with this order, the Solid Waste Operations Department at Oak Ridge National Laboratory (ORNL) has established an Active Sites Environmental Monitoring Program (ASEMP) that is implemented by staff of the Environmental Sciences Division (ESD) at ORNL. This report summarizes data from ASEMP monitoring activities for the final 6 months of FY 1990. A brief summary of the monitoring methodology for each site is presented also.

  14. The nature of the active site in heterogeneous metal catalysis

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk;

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced, and...

  15. Active Sites Environmental Monitoring Program: FY 1990 annual report

    Chapter 3 of US Department of Energy (DOE) Order 5820.2A (DOE 1988) sets forth requirements for environmental monitoring of active low-level waste (LLW) disposal sites. Active sites are defined as those LLW facilities that were in use on or after the date of the order (September 1988). The transuranic (TRU) waste storage areas in Solid Waste Storage Area (SWSA) 5 North are covered by Chap. 2 of the order. In both chapters, monitoring is required to provide for early warning of leaks before those leaks pose a threat to human health or the environment. Chapter 3 also requires that monitoring be conducted to evaluate the short- and long-term performance of LLW disposal facilities. In accordance with this order, the Solid Waste Operations Department at Oak Ridge National Laboratory (ORNL) has established an Active Sites Environmental Monitoring Program (ASEMP) that is implemented by staff of the Environmental Sciences Division (ESD) at ORNL. This report summarizes data from ASEMP monitoring activities for the final 6 months of FY 1990. A brief summary of the monitoring methodology for each site is presented also

  16. Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.

    Fransson, Rebecca; Sköld, Christian; Kratz, Jadel M; Svensson, Richard; Artursson, Per; Nyberg, Fred; Hallberg, Mathias; Sandström, Anja

    2013-06-27

    We recently reported the discovery of H-Phe-Phe-NH2 as a small and high affinity ligand for the substance P 1-7 (SP(1-7), H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH) specific binding site and its intriguing ability to reduce neuropathic pain. With the overall aim to develop stable and orally bioavailable SP(1-7) mimetics, the dipeptide was chosen as a lead compound. Herein the structure-activity relationship (SAR) of a set of modified H-Phe-Phe-NH2 analogues is presented together with their potential active uptake by PEPT1 transporter, intestinal permeability, and metabolic stability. Local constraints via peptide backbone methylation or preparation of cyclized analogues based on pyrrolidine were evaluated and were shown to significantly improve the in vitro pharmacokinetic properties. The SAR was rationalized by deriving a plausible binding pose for the high affinity ligands. Rigidification using a 3-phenylpyrrolidine moiety in the C-terminal of H-Phe-Phe-NH2 resulted in high affinity and improved intrinsic clearance and intestinal epithelial permeability. PMID:23735006

  17. Mapping the active site of vaccinia virus RNA triphosphatase

    The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery

  18. Decommissioning and decontamination activity, Gnome Site, Eddy County, New Mexico

    The purpose of this assessment is to present a brief description of the proposed activity and its potential impacts on the environment. This assessment will constitute an evaluation as to whether or not a formal Environmental Statement need be prepared. As background to the proposed activity, Project Gnome was an underground nuclear test conducted in December 1961 as part of the PLOWSHARE Program. The project site is located about 25 miles southeast of Carlsbad, New Mexico. By means of an excavated shaft and tunnel, a 3-kiloton nuclear explosive was emplaced and detonated in a salt bed about 1200 feet below the surface. The uncontaminated rock and salt muck from the original excavation and subsequent contaminated muck and minor construction debris from reentry activities into the nuclear cavity is commingled and stored in a pile near the Gnome/Coach Shaft. Other areas on the site are known to have been contaminated. In 1969, a program was conducted to cleanup and dispose of all surface contamination to whatever depth it occurred in excess of 0.1 mR/hr. Contaminated materials and soil were collected and disposed into the Gnome shaft, which was filled and sealed. Since then, NV has proposed to DOE/HQ much lower criteria for residual radioactive contamination for the Gnome Site. These proposed criteria were to collect and dispose of surficial materials which contain more than 2 x 10-5 microcuries per gram of soil for beta/gamma emitters and 3 x 10-2 microcuries per milliliter of tritium in soil moisture. According to the latest reconnaissance in 1972, low concentrations of Cs-137, Sr-90 and tritium were present at various locations on the site in excess of these proposed guidelines. Other operational areas within the site are suspected of containing radioactive contamination in much lesser volume, which are to be determined by careful probing and monitoring, as described in the next section

  19. Methodology for contaminated sites of military activity territories restoration

    Major part of Eastern Europe countries meet environmental problems related to sites of military activity. Major part of these sites is characterised with degradation of natural landscapes and contamination of geological environment with toxic and hazardous waste representing actual and potential danger for population and environment. Actual danger is caused with localisation of toxic waste, hazardous materials and waste which are preventing normal land use. Potential danger is related to successive dispersion of contamination in biosphere as well as origin of new derivatives and products having toxic and hazardous properties. The list of such sites and objects comprises bases of land, air and naval forces. These objects include a network of infrastructures: storages of fuels and lubricants (surface, underground), filling stations, pipe lines, reparation stations, garages, decontamination stations, underground storages of different purposes, depots (for ammunition, chemical products), hospitals, constructions, firing grounds (tank, artillery, aircraft bombing etc.) and waste disposal sites. Special programs aimed at military industries and bases contaminated sites remediation have been carrying out in developed countries (USA, United Kingdom, Germany etc.). This experience was used in the frames of joint programs having been founded in several countries of Central and Eastern Europe (Chesh Republic, Slovakia, Lithuania etc.). (author)

  20. Exploiting Innocuous Activity for Correlating Users Across Sites

    Goga, Oana; Lei, Howard; Parthasarathi, Sree Hari Krishnan; Friedland, Gerald; Sommer, Robin; Teixeira, Renata

    2013-01-01

    International audience We study how potential attackers can identify accounts on different social network sites that all belong to the same user, exploiting only innocuous activity that inherently comes with posted content. We examine three specific features on Yelp, Flickr, and Twitter: the geo-location attached to a user's posts, the timestamp of posts, and the user's writing style as captured by language models. We show that among these three features the location of posts is the most po...

  1. Active sites in char gasification: Final technical report

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  2. Resolving the Structure of Active Sites on Platinum Catalytic Nanoparticles

    Chang, Lan Yun; Barnard, Amanda S.; Gontard, Lionel Cervera; Dunin-Borkowski, Rafal E.

    2010-01-01

    Accurate understanding of the structure of active sites is fundamentally important in predicting catalytic properties of heterogeneous nanocatalysts. We present an accurate determination of both experimental and theoretical atomic structures of surface monatomic steps on industrial platinum...... nanoparticles. This comparison reveals that the edges of nanoparticles can significantly alter the atomic positions of monatomic steps in their proximity, which can lead to substantial deviations in the catalytic properties compared with the extended surfaces....

  3. The purification of affinity-labelled active-site peptides

    The isolation of the labelled peptide from the protein digest, following the affinity labelling of the active sites of enzymes or antibodies, is described. Single-step affinity chromatography utilises the affinity of the native enzymes or antibody for the ligand used to label the same protein. The labelled peptide is the only one in the digest that displays affinity for the immobilised protein and can be released with eluants that dissociate the protein-ligand complex. (Auth.)

  4. Brownian aggregation rate of colloid particles with several active sites

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure

  5. Site characterization techniques used in environmental remediation activities

    As a result of decades of nuclear energy research, weapons production, as well as ongoing operations, a significant amount of radioactive contamination has occurred throughout the United States Department of Energy (DOE) complex. DOE facility are in the process of assessing and potentially remediating various sites according to the regulations imposed by a Federal Facility Agreement and Consent order (FFA/CO) between DOE, the state in which the facility is located, and the U.S. Environmental Protection Agency (EPA). In support of these active site remediation efforts, the DOE has devoted considerable resources towards the development of innovative site characterization techniques that support environmental restoration activities. These resources and efforts have focused on various aspects of this complex problem. Research and technology development conducted at the Idaho National Engineering and Environmental Laboratory (INEEL) has resulted in the ability and state-of-the-art equipment required to obtain real-time, densely spaced, in situ characterization data (i.e. detection, speciation, and location) of various radionuclides and contaminants. The Remedial Action Monitoring System (RAMS), developed by the INEEL, consists of enhanced sensor technology, measurement modeling and interpretation techniques, and a suite of deployment platforms which can be interchanged to directly support remedial cleanup and site verification operations. In situ characterization techniques have advanced to the point where they are being actively deployed in support of remedial operations. The INEEL has deployed its system at various DOE and international sites. The deployment of in situ characterization systems during environmental restoration operations has shown that this approach results in several significant benefits versus conventional sampling techniques. A flexible characterization system permits rapid modification to satisfy physical site conditions, available site resources

  6. Seismic activity parameters of the Finnish potential repository sites

    Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

  7. Seismic activity parameters of the Finnish potential repository sites

    Saari, J. [Fortum Engineering Oy, Vantaa (Finland)

    2000-10-01

    Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

  8. Oxygen reduction and evolution at single-metal active sites

    Calle-Vallejo, F.; Martínez, J.I.; García Lastra, Juan Maria;

    2013-01-01

    A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large overpotent......A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large...... overpotentials and is made of precious materials. A possible solution is the use of non-noble electrocatalysts with single-metal active sites. Here, on the basis of DFT calculations of adsorbed intermediates and a thermodynamic analysis, we compare the oxygen reduction (ORR) and evolution (OER) activities of...... functionalized graphitic materials and gas-phase porphyrins with late transition metals. We find that both kinds of materials follow approximately the same activity trends, and active sites with transition metals from groups 7 to 9 may be good ORR and OER electrocatalysts. However, spin analyses show more...

  9. HDAC Inhibitors without an Active Site Zn2+-Binding Group

    Vickers, Chris J.; Olsen, Christian Adam; Leman, Luke J.;

    2012-01-01

    Natural and synthetic histone deacetylase (HDAC) inhibitors generally derive their strong binding affinity and high potency from a key functional group that binds to the Zn2+ ion within the enzyme active site. However, this feature is also thought to carry the potential liability of undesirable off......-target interactions with other metalloenzymes. As a step toward mitigating this issue, here, we describe the design, synthesis, and structure−activity characterizations of cyclic α3β-tetrapeptide HDAC inhibitors that lack the presumed indispensable Zn2+-binding group. The lead compounds (e.g., 15 and 26) display good...... potency against class 1 HDACs and are active in tissue culture against various human cancer cell lines. Importantly, enzymological analysis of 26 indicates that the cyclic α3β-tetrapeptide is a fast-on/ off competitive inhibitor of HDACs 1−3 with Ki values of 49, 33, and 37 nM, respectively. Our proof...

  10. Current activities handbook: formerly utilized sites remedial action program

    None

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  11. Overview of the activities carried out at the FEBEX site

    Missana, T.; Buil, B.; Garralon, A.; Gomez, P. [CIEMAT, Dept. de Medioambien te, 28040 Madrid (Spain); Perez-Estaun, A.; Carbonell, R. [Inst. Jaume Almera, CSIC (Spain); Suso, J.; Carretero, G.; Bueno, J.; Martinez, L. [AITEMIN (Spain) ; Hernan, P. [ENRESA (Spain)

    2007-06-15

    One of the main aim of WP 4.1 and 4.2 is to study solute migration mechanisms in crystalline host-rock in realistic conditions. Many organisations are participating in a joint study that is being performed in the FEBEX gallery (NAGRA's Grimsel Test Site, GTS, Switzerland). The FEBEX experiment reproduces at a real scale a high-level waste repository in granite and was installed more than 9 years ago. At moment, it represents the most realistic environment where the processes affecting radionuclide migration from the bentonite to granite can be studied. This paper summarises the main activities carried out at the FEBEX site during the second year of the project.

  12. Current activities handbook: formerly utilized sites remedial action program

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified

  13. 10 CFR 63.16 - Review of site characterization activities. 2

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 63.16... site characterization activities. 2 2 In addition to the review of site characterization activities... investigation and site characterization, to allow early identification of potential licensing issues for...

  14. Identification of covalent active site inhibitors of dengue virus protease

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  15. Identification of covalent active site inhibitors of dengue virus protease.

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  16. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  17. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  18. Study the active site of flavonoid applying radiation chemistry

    Flavonoid are a large and important class of naturally occurring, low molecular weight benzo-γ-pyrone derivatives which are reported to have a myriad of biological activities, but the study on the active sites of flavonoids is still ambiguous. In this paper, rutin, quercetin and baicalin have been selected as model compounds. It is well known that rutin is used in inhibiting arteriosclerosis and baicalin is antibacterial and antiviral. They have similar basic structure, but their medicinal properties are so different, why? As most flavonoids contain carbonyl group, which can capture electron effectively, we predict that flavonoids can capture electron to form radical anion. The formation of anion radical may have influence on the mitochondrial electron transport chain. The difference in the ability of forming anion radical may cause the difference in their medicinal effects. (author)

  19. SITE-DIRECTED MUTAGENESIS OF PROPOSED ACTIVE-SITE RESIDUES OF PENICILLIN-BINDING PROTEIN-5 FROM ESCHERICHIA-COLI

    VANDERLINDEN, MPG; DEHAAN, L; DIDEBERG, O; KECK, W

    1994-01-01

    Alignment of the amino acid sequence of penicillin-binding protein 5 (PBP5) with the sequences of other members of the family of active-site-serine penicillin-interacting enzymes predicted the residues playing a role in the catalytic mechanism of PBP5. Apart from the active-site (Ser(44)), Lys(47),

  20. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L. (Michigan)

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  1. Identification of covalent active site inhibitors of dengue virus protease

    Koh-Stenta X

    2015-12-01

    Full Text Available Xiaoying Koh-Stenta,1 Joma Joy,1 Si Fang Wang,1 Perlyn Zekui Kwek,1 John Liang Kuan Wee,1 Kah Fei Wan,2 Shovanlal Gayen,1 Angela Shuyi Chen,1 CongBao Kang,1 May Ann Lee,1 Anders Poulsen,1 Subhash G Vasudevan,3 Jeffrey Hill,1 Kassoum Nacro11Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR, Singapore; 2Novartis Institute for Tropical Diseases, Singapore; 3Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, SingaporeAbstract: Dengue virus (DENV protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.Keywords: flavivirus protease, small molecule optimization, covalent inhibitor, active site binding, pyrazole ester derivatives

  2. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  3. Maxey Flats low-level waste disposal site closure activities

    The Maxey Flats Radioactive Waste Disposal Facility in Fleming County, Kentucky is in the process of being closed. The facility opened for commercial business in the spring of 1963 and received approximately 4.75 million cubic feet of radioactive waste by the time it was closed in December of 1977. During fourteen years of operation approximately 2.5 million curies of by-product material, 240,000 kilograms of source material, and 430 kilograms of special nuclear material were disposed. The Commonwealth purchased the lease hold estate and rights in May 1978 from the operating company. This action was taken to stabilize the facility and prepare it for closure consisting of passive care and monitoring. To prepare the site for closure, a number of remedial activities had to be performed. The remediation activities implemented have included erosion control, surface drainage modifications, installation of a temporary plastic surface cover, leachate removal, analysis, treatment and evaporation, US DOE funded evaporator concentrates solidification project and their on-site disposal in an improved disposal trench with enhanced cover for use in a humid environment situated in a fractured geology, performance evaluation of a grout injection demonstration, USGS subsurface geologic investigation, development of conceptual closure designs, and finally being added to the US EPA National Priority List for remediation and closure under Superfund. 13 references, 3 figures

  4. Constraining the factor analytical solutions obtained from multiple-year receptor modeling of ambient PM2.5 data from five speciation sites in Ontario, Canada

    Sofowote, Uwayemi M.; Su, Yushan; Dabek-Zlotorzynska, Ewa; Rastogi, Ankit K.; Brook, Jeff; Hopke, Philip K.

    2015-05-01

    Rotational ambiguity in factor analyses leads to solutions that are not always consistent with reality. The inherent non-negativity constraints in positive matrix factorization (PMF) help to prevent factor solutions from becoming overly unrealistic, but they are not sufficient to prevent unwanted rotations that could manifest in factors that should have similar compositions varying across multiple sites. The Canadian National Air Pollution Surveillance (NAPS) network operates five fine particulate matter (PM2.5) speciation sites in Ontario. Data from these sites from 2005 to 2010 were subjected to PMF to obtain factors representing sources of particulate matter. Eight factors were found to be common across these sites. These factors had profiles that varied greatly from one site to the other, suggesting that the PMF solutions were impacted by some rotational ambiguity. New features in the EPA PMF V5 program allow the use of a priori information to impose mathematical constraints that guide the evolution of the factor solutions. These constraints reduce the rotational space. In situations where major emissions sources are known and located in the neighborhood of receptors, or emissions inventories and literature source profiles exist, it is easy to use these profiles to force the factor solutions to conform to the expected signatures. In our case, reported source profiles were neither available nor applicable due to the large spatial span of potential sources and receptor sites. This work describes how such constraints can be generated and used in these complex situations. The fundamental principle explored in this work is the concept of 'stiffness' of PMF solutions to identify the desirable non-rotating factors.

  5. Ontogeny constrains phenology: opportunities for activity and reproduction interact to dictate potential phenologies in a changing climate.

    Levy, Ofir; Buckley, Lauren B; Keitt, Timothy H; Angilletta, Michael J

    2016-06-01

    As global warming has lengthened the active seasons of many species, we need a framework for predicting how advances in phenology shape the life history and the resulting fitness of organisms. Using an individual-based model, we show how warming differently affects annual cycles of development, growth, reproduction and activity in a group of North American lizards. Populations in cold regions can grow and reproduce more when warming lengthens their active season. However, future warming of currently warm regions advances the reproductive season but reduces the survival of embryos and juveniles. Hence, stressful temperatures during summer can offset predicted gains from extended growth seasons and select for lizards that reproduce after the warm summer months. Understanding these cascading effects of climate change may be crucial to predict shifts in the life history and demography of species. PMID:26970104

  6. Active site and laminarin binding in glycoside hydrolase family 55.

    Bianchetti, Christopher M; Takasuka, Taichi E; Deutsch, Sam; Udell, Hannah S; Yik, Eric J; Bergeman, Lai F; Fox, Brian G

    2015-05-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  7. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    Yu Zhang

    Full Text Available Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL from Geobacillus kaustophilus HTA426 (GkaP exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  8. A new multi-gas constrained model of trace gas non-homogeneous transport in firn: evaluation and behaviour at eleven polar sites

    Witrant, E.; Martinerie, P.; Hogan, C.; Laube, J. C.; Kawamura, K.; Capron, E.; Montzka, S. A.; Dlugokencky, E. J.; Etheridge, D.; Blunier, T.; Sturges, W. T.

    2012-12-01

    Insoluble trace gases are trapped in polar ice at the firn-ice transition, at approximately 50 to 100 m below the surface, depending primarily on the site temperature and snow accumulation. Models of trace gas transport in polar firn are used to relate firn air and ice core records of trace gases to their atmospheric history. We propose a new model based on the following contributions. First, the firn air transport model is revised in a poromechanics framework with emphasis on the non-homogeneous properties and the treatment of gravitational settling. We then derive a nonlinear least square multi-gas optimisation scheme to calculate the effective firn diffusivity (automatic diffusivity tuning). The improvements gained by the multi-gas approach are investigated (up to ten gases for a single site are included in the optimisation process). We apply the model to four Arctic (Devon Island, NEEM, North GRIP, Summit) and seven Antarctic (DE08, Berkner Island, Siple Dome, Dronning Maud Land, South Pole, Dome C, Vostok) sites and calculate their respective depth-dependent diffusivity profiles. Among these different sites, a relationship is inferred between the snow accumulation rate and an increasing thickness of the lock-in zone defined from the isotopic composition of molecular nitrogen in firn air (denoted δ15N). It is associated with a reduced diffusivity value and an increased ratio of advective to diffusive flux in deep firn, which is particularly important at high accumulation rate sites. This has implications for the understanding of δ15N of N2 records in ice cores, in relation with past variations of the snow accumulation rate. As the snow accumulation rate is clearly a primary control on the thickness of the lock-in zone, our new approach that allows for the estimation of the lock-in zone width as a function of accumulation may lead to a better constraint on the age difference between the ice and entrapped gases.

  9. Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase

    Peters, Günther H.j.; Svendsen, A.; Langberg, H.; Vind, J.; Patkar, S.A.; Toxvaerd, S.; Kinnunen, P.K.J.

    1998-01-01

    reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S 146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to...

  10. Integral field spectroscopy of supernova explosion sites: constraining mass and metallicity of the progenitors -- II. Type II-P and II-L supernovae

    Kuncarayakti, Hanindyo; Aldering, Greg; Arimoto, Nobuo; Maeda, Keiichi; Morokuma, Tomoki; Pereira, Rui; Usuda, Tomonori; Hashiba, Yasuhito

    2013-01-01

    Thirteen explosion sites of type II-P and II-L supernovae in nearby galaxies have been observed using integral field spectroscopy, enabling both spatial and spectral study of the explosion sites. We used the properties of the parent stellar population of the coeval supernova progenitor star to derive its metallicity and initial mass (c.f. Paper I). The spectrum of the parent stellar population yields the estimates of metallicity via strong-line method, and age via comparison with simple stellar population (SSP) models. These metallicity and age parameters are adopted for the progenitor star. Age, or lifetime of the star, was used to derive initial (ZAMS) mass of the star by comparing with stellar evolution models. With this technique, we were able to determine metallicity and initial mass of the SN progenitors in our sample. Our result indicates that some type-II supernova progenitors may have been stars with mass comparable to SN Ib/c progenitors.

  11. Constraining magnetic-activity modulations in three solar-like stars observed by CoRoT and NARVAL

    Mathur, S; García, R. A.; Morgenthaler, A.; Salabert, D.; Petit, P.; Ballot, J.; Régulo, C.; Catala, C.

    2013-01-01

    International audience Context. Stellar activity cycles are the manifestation of dynamo process running in the stellar interiors. They have been observed from years to decades thanks to the measurement of stellar magnetic proxies on the surface of the stars, such as the chromospheric and X-ray emissions, and to the measurement of the magnetic field with spectropolarimetry. However, all of these measurements rely on external features that cannot be visible during, for example, a Maunder-typ...

  12. Constrained Random Walk of a Carrier in Two-Dimensional Site-Percolation Lattice, Exemplified by Virtual and Real World Scenarios

    A Random Walk (RW) realization in the square lattice, upon which a percolation cluster of sites, visited one by one by random walkers is built up (by direct Monte Carlo method), has been carried out towards its basic tendencies. It turns out that if the RW is realized near the site-percolation threshold, the process, as expected, decelerates. If, in turn, one systematically goes above the percolation threshold, being roughly about 0.6, towards the isotropic site-cluster regime, the process accelerates. Some drift superimposed on the RW realization as well as boundary conditions of certain types change the system behavior in a quite predictive way. Both new and interesting examples, emphasizing a possible applications of the phenomenon under study, are carefully mentioned. A finite-size effect always incorporated in the realized MC-algorithm is going to make the process apparently closer to reality. The notion of continuous phase (sub)transition has been discussed in the presented context. (author)

  13. Constraining magnetic-activity modulations in three solar-like stars observed by CoRoT and NARVAL

    Mathur, S.; García, R. A.; Morgenthaler, A.; Salabert, D.; Petit, P.; Ballot, J.; Régulo, C.; Catala, C.

    2013-02-01

    Context. Stellar activity cycles are the manifestation of dynamo process running in the stellar interiors. They have been observed from years to decades thanks to the measurement of stellar magnetic proxies on the surface of the stars, such as the chromospheric and X-ray emissions, and to the measurement of the magnetic field with spectropolarimetry. However, all of these measurements rely on external features that cannot be visible during, for example, a Maunder-type minimum. With the advent of long observations provided by space asteroseismic missions, it has been possible to penetrate the stars and study their properties. Moreover, the acoustic-mode properties are also perturbed by the presence of these dynamos. Aims: We track the temporal variations of the amplitudes and frequencies of acoustic modes allowing us to search for signature of magnetic activity cycles, as has already been done in the Sun and in the CoRoT target HD 49933. Methods: We used asteroseimic tools and more classical spectroscopic measurements performed with the NARVAL spectropolarimeter to check that there are hints of any activity cycle in three solar-like stars observed continuously for more than 117 days by the CoRoT satellite: HD 49385, HD 181420, and HD 52265. To consider that we have found a hint of magnetic activity in a star we require finding a change in the amplitude of the p modes that should be anti-correlated with a change in their frequency shifts, as well as a change in the spectroscopic observations in the same direction as the asteroseismic data. Results: Our analysis gives very small variation in the seismic parameters preventing us from detecting any magnetic modulation. However, we are able to provide a lower limit of any magnetic-activity change in the three stars that should be longer than 120 days, which is the length of the time series. Moreover we computed the upper limit for the line-of-sight magnetic field component being 1, 3, and 0.6 G for HD 49385, HD 181420

  14. A new multi-gas constrained model of trace gas non-homogeneous transport in firn: evaluation and behaviour at eleven polar sites

    E. Witrant

    2012-12-01

    Full Text Available Insoluble trace gases are trapped in polar ice at the firn-ice transition, at approximately 50 to 100 m below the surface, depending primarily on the site temperature and snow accumulation. Models of trace gas transport in polar firn are used to relate firn air and ice core records of trace gases to their atmospheric history. We propose a new model based on the following contributions. First, the firn air transport model is revised in a poromechanics framework with emphasis on the non-homogeneous properties and the treatment of gravitational settling. We then derive a nonlinear least square multi-gas optimisation scheme to calculate the effective firn diffusivity (automatic diffusivity tuning. The improvements gained by the multi-gas approach are investigated (up to ten gases for a single site are included in the optimisation process. We apply the model to four Arctic (Devon Island, NEEM, North GRIP, Summit and seven Antarctic (DE08, Berkner Island, Siple Dome, Dronning Maud Land, South Pole, Dome C, Vostok sites and calculate their respective depth-dependent diffusivity profiles. Among these different sites, a relationship is inferred between the snow accumulation rate and an increasing thickness of the lock-in zone defined from the isotopic composition of molecular nitrogen in firn air (denoted δ15N. It is associated with a reduced diffusivity value and an increased ratio of advective to diffusive flux in deep firn, which is particularly important at high accumulation rate sites. This has implications for the understanding of δ15N of N2 records in ice cores, in relation with past variations of the snow accumulation rate. As the snow accumulation rate is clearly a primary control on the thickness of the lock-in zone, our new approach that allows for the estimation of the lock-in zone width as a function of accumulation may lead to a better constraint on the age difference between the ice and entrapped gases.

  15. A new multi-gas constrained model of trace gas non-homogeneous transport in firn: evaluation and behavior at eleven polar sites

    Witrant, E.; Martinerie, P.; Hogan, C.; Laube, J. C.; Kawamura, K.; Capron, E.; Montzka, S. A.; Dlugokencky, E. J.; Etheridge, D.; Blunier, T.; Sturges, W. T.

    2011-08-01

    Insoluble trace gases are trapped in polar ice at the firn-ice transition, at approximately 50 to 100 m below the surface, depending primarily on the site temperature and snow accumulation. Due to the different time scales for snow accumulation versus diffusion of gases through the snowpack, age differences between gases and the ice in which they are "trapped" can be large; e.g. several thousand years in central Antarctica (a low snow accumulation area). Models of trace gas diffusion in polar firn are used to relate firn air and ice core records of trace gases to their atmospheric history. We propose a new diffusion model based on the following contributions. First, the airflow transport model is revised in a poromechanics framework with specific emphasis on the non-homogeneous properties (convective layer, depth-dependent diffusivity and lock-in zone) and an almost-stagnant behavior described by Darcy's law (gravity effect). We then derive a non-linear least square multi-gas optimization scheme to calculate the effective firn diffusivity (automatic diffusivity tuning). The improvements associated with the additional constraints gained by the multi-gas approach are investigated (up to eleven gases for a single site are included in the optimization process). The model is applied to measured data from four Arctic (Devon Island, NEEM, North GRIP, Summit) and seven Antarctic (DE08, Berkner Island, Siple Dome, Dronning Maud Land, South Pole, Dome C, Vostok) sites and the depth-dependent diffusivity profiles are calculated. Among these different sites, a relationship between an increasing thickness of the lock-in zone defined from the isotopic composition of molecular nitrogen in firn air (denoted δ15N) and the snow accumulation rate is obtained, in accordance with observations. It is associated with reduced diffusivity depth-gradients in deep firn, which decreases gas density depth-gradients, at high accumulation rate sites. This has implications for the understanding

  16. A new multi-gas constrained model of trace gas non-homogeneous transport in firn: evaluation and behavior at eleven polar sites

    E. Witrant

    2011-08-01

    Full Text Available Insoluble trace gases are trapped in polar ice at the firn-ice transition, at approximately 50 to 100 m below the surface, depending primarily on the site temperature and snow accumulation. Due to the different time scales for snow accumulation versus diffusion of gases through the snowpack, age differences between gases and the ice in which they are "trapped" can be large; e.g. several thousand years in central Antarctica (a low snow accumulation area. Models of trace gas diffusion in polar firn are used to relate firn air and ice core records of trace gases to their atmospheric history. We propose a new diffusion model based on the following contributions. First, the airflow transport model is revised in a poromechanics framework with specific emphasis on the non-homogeneous properties (convective layer, depth-dependent diffusivity and lock-in zone and an almost-stagnant behavior described by Darcy's law (gravity effect. We then derive a non-linear least square multi-gas optimization scheme to calculate the effective firn diffusivity (automatic diffusivity tuning. The improvements associated with the additional constraints gained by the multi-gas approach are investigated (up to eleven gases for a single site are included in the optimization process. The model is applied to measured data from four Arctic (Devon Island, NEEM, North GRIP, Summit and seven Antarctic (DE08, Berkner Island, Siple Dome, Dronning Maud Land, South Pole, Dome C, Vostok sites and the depth-dependent diffusivity profiles are calculated. Among these different sites, a relationship between an increasing thickness of the lock-in zone defined from the isotopic composition of molecular nitrogen in firn air (denoted δ15N and the snow accumulation rate is obtained, in accordance with observations. It is associated with reduced diffusivity depth-gradients in deep firn, which decreases gas density depth-gradients, at high accumulation rate sites. This has implications

  17. Metavanadate at the active site of the phosphatase VHZ.

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  18. Constraining magnetic-activity modulations in 3~solar-like stars observed by CoRoT and NARVAL

    Mathur, S; Morgenthaler, A; Salabert, D; Petit, P; Ballot, J; Regulo, C; Catala, C

    2012-01-01

    Stellar activity cycles are the manifestation of dynamo process running in the stellar interiors. They have been observed during years to decades thanks to the measurement of stellar magnetic proxies at the surface of the stars such as the chromospheric and X-ray emissions, and the measurement of the magnetic field with spectropolarimetry. However, all of these measurements rely on external features that cannot be visible during for example, a Maunder-type minimum. With the advent of long observations provided by space asteroseismic missions, it has been possible to pierce inside the stars and study their properties. Moreover, the acoustic-mode properties are also perturbed by the presence of these dynamos. We track the temporal variations of the amplitudes and frequencies of acoustic modes allowing us to search for signature of magnetic activity cycles, as has already been done in the Sun and in the CoRoT target HD49933. We use asteroseimic tools and more classical spectroscopic measurements performed with t...

  19. Constraining Hot Plasma in a Non-flaring Solar Active Region with FOXSI Hard X-ray Observations

    Ishikawa, Shin-nosuke; Christe, Steven; Ishibashi, Kazunori; Brooks, David H; Williams, David R; Shimojo, Masumi; Sako, Nobuharu; Krucker, Sam

    2015-01-01

    We present new constraints on the high-temperature emission measure of a non-flaring solar active region using observations from the recently flown Focusing Optics X-ray Solar Imager sounding rocket payload. FOXSI has performed the first focused hard X-ray (HXR) observation of the Sun in its first successful flight on 2012 November 2. Focusing optics, combined with small strip detectors, enable high-sensitivity observations with respect to previous indirect imagers. This capability, along with the sensitivity of the HXR regime to high-temperature emission, offers the potential to better characterize high-temperature plasma in the corona as predicted by nanoflare heating models. We present a joint analysis of the differential emission measure (DEM) of active region 11602 using coordinated observations by FOXSI, Hinode/XRT and Hinode/EIS. The Hinode-derived DEM predicts significant emission measure between 1 MK and 3 MK, with a peak in the DEM predicted at 2.0-2.5 MK. The combined XRT and EIS DEM also shows emi...

  20. 10 CFR 60.18 - Review of site characterization activities. 2

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 60.18... IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.18 Review of site characterization activities. 2 2 In addition to the review of site characterization activities specified in this section,...

  1. Hazardous Material Storage Facilities and Sites - WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN: Active Permitted Solid Waste Sites in Indiana (Indiana Department of Environmental Management, Point Shapefile)

    NSGIC GIS Inventory (aka Ramona) — WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN is a point shapefile that contains active permitted solid waste site locations in Indiana, provided by personnel of Indiana...

  2. Constraining UV Continuum Slopes of Active Galactic Nuclei With CLOUDY Models of Broad Line Region EUV Emission Lines

    Moloney, Joshua

    2014-01-01

    Understanding the composition and structure of the broad-line region (BLR) of active galactic nuclei (AGN) is important for answering many outstanding questions in supermassive black hole evolution, galaxy evolution, and ionization of the intergalactic medium. We used single-epoch UV spectra from the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope to measure EUV emission-line fluxes from four individual AGN with $0.49 \\le z \\le 0.64$, two AGN with $0.32 \\le z \\le 0.40$, and a composite of 159 AGN. With the Cloudy photoionization code, we calculated emission-line fluxes from BLR clouds with a range of density, hydrogen ionizing flux and incident continuum spectral indices. The photoionization grids were fit to the observations using single-component and locally optimally emitting cloud (LOC) models. The LOC models provide good fits to the measured fluxes, while the single-component models do not. The UV spectral indices preferred by our LOC models are consistent with those measured from COS spe...

  3. Activity of Changbaishan Tianchi Volcano Since Late Pleistocene--The Constrain From Geochronology of High Precision U- Series Tims Method

    Wang Fei; Chen Wenji; Zhang Zhonglu; Hu Yutai; Peng Zicheng

    2000-01-01

    11 samples of lava and pumice from the cone of Changbaishan Tianchi Volcano, Jiling, China, were dated by using high precision U - series TIMS method. We conclude that the bottom of the cone formed before 350 ka, the middle part in 70~80 ka, the upper during 20~ 1ka, and the top less than 1ka, and the age based periods of the volcano eruption since Late Pleistocene is given as follows: > 350ka, 70ka, 18 ~ 25ka, 10ka, 4C5ka, 1~0.75ka, which may offer the basis for the study of volcanic disaster in future. In addition, the principle of dating young volcanic rocks by using U - series TIMS method is introduced briefly. Differentiation characteristics of U and Th in different minerals of the volcanic rocks are discussed, and the ability producing isochrons, based on U and Th differentiation, are discussed. In the last part of the paper,the closure of samples to the elements U and Th, which is important for age results, is discussed by using (234U/238U)radioactivity ratio which can be used to monitor if the samples have been weathered or eroded or leached since the time they formed. In this study, all samples have (234U/238U) activity ratios within 1% of secular equilibrium ((234U/238U) radioactivity ratios are unity), indicating no disturbance of the 234U- 238U system. All of these discussions show that the TIMS method is good to date Tianchi volcanics and the results are reliable.

  4. New Data on mid-Miocene Rhyolite Volcanism in Eastern Oregon Extend Early, co-CRBG Rhyolite Flare up and Constrain Storage Sites of Grande Ronde Flood Basalts

    Streck, M. J.; Ferns, M. L.; McIntosh, W. C.

    2015-12-01

    The classical view of relating mid-Miocene rhyolites of the tri-state area of Oregon, Nevada, and Idaho to the flood basalts of the Columbia River Basalt was that a mantle plume impinging along the Oregon-Idaho border first causes eruption of the flood basalts but shortly thereafter causes generation of rhyolites at the McDermitt volcanic field from which then hot-spot track rhyolites developed progressively younging towards Yellowstone. More recent work reveals rhyolites as old as found at McDermitt (~16.5 Ma) to occur along a wide E-W tangent along the Oregon-Nevada-Idaho border. And now, our data extend such early rhyolites (>16 Ma) to several locations further north within and in the periphery of the Lake Owyhee Volcanic Field (LOVF) adding to the geographically orphaned old age of 16.7 Ma of the Silver City Rhyolite, Idaho. Hence, the rhyolite flare-up associated with flood basalt magmatism occurred within a circular area of ~400 km centered 100 km NNE of McDermitt. Consequently, no south-to-north progression exists in the onset of rhyolite volcanism; instead, rhyolites started up at the same time over this large area. Province-wide rhyolite volcanism was strongest between ~16.4 and 15.4 Ma coincident with eruptions of the most voluminous member of the CRBG - the Grande Ronde Basalt (GRB). Field evidence for such bimodal volcanism consists of intercalated local GRB units with the Dinner Creek Tuff and Littlefield Rhyolite in the Malheur River Gorge corridor. GRB eruption sites exist and were likely fed from reservoirs residing below or near rhyolitic chambers. Presently, we have petrological evidence for pinning down GRB storages sites to areas from where rhyolites of the Dinner Creek Tuff and lava flows of the Littlefield Rhyolite erupted. In summary, input of GRG and other CRBG magmas were driving co-CRBG rhyolite volcanism which in turn may have influenced whether flood basalt magmas erupted locally or travelled in dikes to more distally located areas.

  5. Detection limit for activation measurements in ultralow background sites

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  6. Finnsjoen study site. Scope of activities and main results

    The Finnsjoen study site was selected in 1977 to provide input to the KBS-1 and KBS-2 performance assessments. The site was later used as a test site for testing new instruments and new site characterization methods, as well as a research site for studying mainly groundwater flow and groundwater transport. All together, the Finnsjoen studies have involved 11 cored boreholes, down to max 700 m depth, and extensive borehole geophysical, geochemical and geohydraulic measurements, as well as rock stress measurements and tracer tests. This report presents the scope of the Finnsjoen studies together with main results. Conceptual uncertainties in assumptions and models are discussed with emphasis on the models used for the performance assessment SKB91. Of special interest for the Finnsjoen study site is the strong influence caused by a subhorizontal fracture zone on groundwater flow, transport and chemistry

  7. Evolutionary constrained optimization

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  8. Constraining Galileon inflation

    Regan, Donough; Anderson, Gemma J.; Hull, Matthew; Seery, David, E-mail: D.Regan@sussex.ac.uk, E-mail: G.Anderson@sussex.ac.uk, E-mail: Matthew.Hull@port.ac.uk, E-mail: D.Seery@sussex.ac.uk [Astronomy Centre, University of Sussex, Falmer, Brighton BN1 9QH (United Kingdom)

    2015-02-01

    In this short paper, we present constraints on the Galileon inflationary model from the CMB bispectrum. We employ a principal-component analysis of the independent degrees of freedom constrained by data and apply this to the WMAP 9-year data to constrain the free parameters of the model. A simple Bayesian comparison establishes that support for the Galileon model from bispectrum data is at best weak.

  9. Accelerator production of tritium activities at the Savannah River Site

    The Savannah River site (SRS) has been chosen as the site to host the accelerator production of tritium (APT). This facility, which will produce tritium for national defense purposes, is a natural extension of the site's original mission. All of the tritium for U.S. weapons needs has been produced at SRS in the heavy water reactors (now shut down) that operated until 1988. Much of the tritium-handling infrastructure still exists at SRS, and the tritium recycling and purification facilities are new and fully operational. This paper summarizes the reasons for the choice of the site and describes some of the early SRS efforts to learn the new technology, to weave into it a strong operations/production ethic, and to prepare the site to host the APT

  10. Health physics and public health activities at hazardous wastes sites

    The Agency for Toxic Substances and Disease Registry (ATSDR) has worked with the U.S. Environmental Protection Agency (EPA) at several sites contaminated with radioactive materials. The Navajo Brown Vandever (B-V) uranium mine site near Bluewater, New Mexico, and the Austin Avenue Radiation Site (AAR) in Lansdowne, Pennsylvania were the subject of ATSDR health advisories. The sites were contamined with uranium or uranium byproducts but the identification of potential health effects and actions taken to prevent or reduce exposures were approached from different perspectives. At B-V contaminants included uranium and mine tailings, radium, and radon. Contaminants at the site and physical hazards were removed. At AAR, radium and radon were located in residential settings. Residents who might have had annual exposures greater than accepted standards or recommendations were relocated and contaminated building demolished

  11. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers

  12. The active sites of supported silver particle catalysts in formaldehyde oxidation.

    Chen, Yaxin; Huang, Zhiwei; Zhou, Meijuan; Hu, Pingping; Du, Chengtian; Kong, Lingdong; Chen, Jianmin; Tang, Xingfu

    2016-08-01

    Surface silver atoms with upshifted d-orbitals are identified as the catalytically active sites in formaldehyde oxidation by correlating their activity with the number of surface silver atoms, and the degree of the d-orbital upshift governs the catalytic performance of the active sites. PMID:27406403

  13. On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases

    Reggy Ekkebus; van Kasteren, Sander I.; Yogesh Kulathu; Arjen Scholten; Ilana Berlin; Geurink, Paul P; Annemieke de Jong; Soenita Goerdayal; Jacques Neefjes; Heck, Albert J.R.; David Komander; Huib Ovaa

    2013-01-01

    Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins boun...

  14. Exhumation history of an active fault to constrain a fault-based seismic hazard scenario: the Pizzalto fault (central Apennines, Italy) example.

    Tesson, Jim; Pace, Bruno; Benedetti, Lucilla; Visini, Francesco; Delli Rocioli, Mattia; Didier, Bourles; Karim, keddadouche; Gorges, Aumaitre

    2016-04-01

    A prerequisite to constrain fault-based and time-dependent earthquake rupture forecast models is to acquire data on the past large earthquake frequency on an individual seismogenic source and to compare all the recorded occurrences in the active fault-system. We investigated the Holocene seismic history of the Pizzalto normal fault, a 13 km long fault segment belonging to the Pizzalto-Rotella-Aremogna fault system in the Apennines (Italy). We collected 44 samples on the Holocene exhumed Pizzalto fault plane and analyzed their 36Cl and rare earth elements content. Conjointly used, the 36Cl and REE concentrations show that at least 6 events have exhumed 4.4 m of the fault scarp between 3 and 1 ka BP, the slip per event ranging from 0.3 to 1.2 m. No major events have been detected over the last 1 ka. The Rotella-Aremogna-Pizzalto fault system has a clustered earthquake behaviour with a mean recurrence time of 1.2 ka and a low to moderate probability (ranging from 4% to 26%) of earthquake occurrence over the next 50 years. We observed similarities between seismic histories of several faults belonging to two adjacent fault systems. This could again attest that non-random processes occurring in the release of the strain accumulated on faults, commonly referred to as fault interactions and leading to apparent synchronization. If these processes were determined as being the main parameter controlling the occurrence of earthquakes, it would be crucial to take them into account in seismic hazard models.

  15. Human population and activities in Forsmark. Site description

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km2 near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the parish has been

  16. Human population and activities in Forsmark. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km{sup 2} near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the

  17. 76 FR 7226 - Commercial Wind Lease Issuance and Site Characterization Activities; Atlantic Outer Continental...

    2011-02-09

    ... site characterization and assessment data the lessee may submit a construction and operations plan (COP... 30 CFR 285.620-.629. Although BOEMRE does not authorize site characterization activities (i.e... on the environmental effects of reasonably foreseeable site characterization surveys that may...

  18. The status of Yucca Mountain site characterization activities

    The U.S. Department of Energy (DOE) Office of Civilian Radioactive Waste Management is continuing its studies to determine if Yucca Mountain in Nevada can safely isolate high-level nuclear waste for the next ten thousand years. As mandated by Congress in 1987, DOE is studying the rocks, the climate, and the water table at Yucca Mountain to ensure that the site is suitable before building a repository about 305 meters (1,000 feet) below the surface. Yucca Mountain, located 161 kilometers (100 miles) northwest of Las Vegas, lies on the western edge of the Nevada Test Site. Nevada and DOE have been in litigation for almost two years over three environmental permits needed to conduct studies, but recent court decisions have allowed limited work to take place. This paper will examine progress made on the Yucca Mountain Site Characterization Project (YMP) during the past year and continuing into 1992, discuss the complex legal issues that are delaying progress, and describe new site drilling work. Title I and II design work on the underground exploratory studies facility (ESF) also will be discussed

  19. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  20. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria

  1. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  2. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    Miao, Yinglong [ORNL; Baudry, Jerome Y [ORNL

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  3. Human population and activities at Simpevarp. Site description

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km2 near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km2, three times lower than in Kalmar laen. The demography statistics show no

  4. Human population and activities at Simpevarp. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  5. Human population and activities at Simpevarp. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  6. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S; Drakou, Evangelia G.; Pantis, John D.

    2013-01-01

    The Natura 2000 network was established across the European Union’s (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries...

  7. Constrained Jastrow calculations

    An alternative to Pandharipande's lowest order constrained variational prescription for dense Fermi fluids is presented which is justified on both physical and strict variational grounds. Excellent results are obtained when applied to the 'homework problem' of Bethe, in sharp contrast to those obtained from the Pandharipande prescription. (Auth.)

  8. Constrained Canonical Correlation.

    DeSarbo, Wayne S.; And Others

    1982-01-01

    A variety of problems associated with the interpretation of traditional canonical correlation are discussed. A response surface approach is developed which allows for investigation of changes in the coefficients while maintaining an optimum canonical correlation value. Also, a discrete or constrained canonical correlation method is presented. (JKS)

  9. Constrained superfields in Supergravity

    Dall'Agata, Gianguido

    2015-01-01

    We analyze constrained superfields in supergravity. We investigate the consistency and solve all known constraints, presenting a new class that may have interesting applications in the construction of inflationary models. We provide the superspace Lagrangians for minimal supergravity models based on them and write the corresponding theories in component form using a simplifying gauge for the goldstino couplings.

  10. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2011-05-03

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... from eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of 1992. DATES: In our Federal Register Notice of November 24, 2010, (75...

  11. Constrained Deformable-Layer Tomography

    Zhou, H.

    2006-12-01

    The improvement on traveltime tomography depends on improving data coverage and tomographic methodology. The data coverage depends on the spatial distribution of sources and stations, as well as the extent of lateral velocity variation that may alter the raypaths locally. A reliable tomographic image requires large enough ray hit count and wide enough angular range between traversing rays over the targeted anomalies. Recent years have witnessed the advancement of traveltime tomography in two aspects. One is the use of finite frequency kernels, and the other is the improvement on model parameterization, particularly that allows the use of a priori constraints. A new way of model parameterization is the deformable-layer tomography (DLT), which directly inverts for the geometry of velocity interfaces by varying the depths of grid points to achieve a best traveltime fit. In contrast, conventional grid or cell tomography seeks to determine velocity values of a mesh of fixed-in-space grids or cells. In this study, the DLT is used to map crustal P-wave velocities with first arrival data from local earthquakes and two LARSE active surveys in southern California. The DLT solutions along three profiles are constrained using known depth ranges of the Moho discontinuity at 21 sites from a previous receiver function study. The DLT solutions are generally well resolved according to restoration resolution tests. The patterns of 2D DLT models of different profiles match well at their intersection locations. In comparison with existing 3D cell tomography models in southern California, the new DLT models significantly improve the data fitness. In comparison with the multi-scale cell tomography conducted for the same data, while the data fitting levels of the DLT and the multi-scale cell tomography models are compatible, the DLT provides much higher vertical resolution and more realistic description of the undulation of velocity discontinuities. The constraints on the Moho depth

  12. Multilayer Dye Adsorption in Activated Carbons-Facile Approach to Exploit Vacant Sites and Interlayer Charge Interaction.

    Hadi, Pejman; Guo, Jiaxin; Barford, John; McKay, Gordon

    2016-05-17

    Altering the textural properties of activated carbons (ACs) via physicochemical techniques to increase their specific surface area and/or to manipulate their pore size is a common practice to enhance their adsorption capacity. Instead, this study proposes the utilization of the vacant sites remaining unoccupied after dye uptake saturation by removing the steric hindrance and same-charge repulsion phenomena via multilayer adsorption. Herein, it has been shown that the adsorption capacity of the fresh AC is a direct function of the dye molecular size. As the cross-sectional area of the dye molecule increases, the steric hindrance effect exerted on the neighboring adsorbed molecules increases, and the geometrical packing efficiency is constrained. Thus, ACs saturated with larger dye molecules render higher concentrations of vacant adsorption sites which can accommodate an additional layer of dye molecules on the exhausted adsorbent through interlayer attractive forces. The second layer adsorption capacity (60-200 mg·g(-1)) has been demonstrated to have a linear relationship with the uncovered surface area of the exhausted AC, which is, in turn, inversely proportional to the adsorbate molecular size. Unlike the second layer adsorption, the third layer adsorption is a direct function of the charge density of the second layer. PMID:27088796

  13. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  14. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation's energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization's ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization's commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans

  15. A Significant but Constrained Geometry Pt→Al Interaction: Fixation of CO2 and CS2, Activation of H2 and PhCONH2.

    Devillard, Marc; Declercq, Richard; Nicolas, Emmanuel; Ehlers, Andreas W; Backs, Jana; Saffon-Merceron, Nathalie; Bouhadir, Ghenwa; Slootweg, J Chris; Uhl, Werner; Bourissou, Didier

    2016-04-13

    Reaction of the geminal PAl ligand [Mes2PC(═CHPh)AltBu2] (1) with [Pt(PPh3)2(ethylene)] affords the T-shape Pt complex [(1)Pt(PPh3)] (2). X-ray diffraction analysis and DFT calculations reveal the presence of a significant Pt→Al interaction in 2, despite the strain associated with the four-membered cyclic structure. The Pt···Al distance is short [2.561(1) Å], the Al center is in a pyramidal environment [Σ(C-Al-C) = 346.6°], and the PCAl framework is strongly bent (98.3°). Release of the ring strain and formation of X→Al interactions (X = O, S, H) impart rich reactivity. Complex 2 reacts with CO2 to give the T-shape adduct 3 stabilized by an O→Al interaction, which is a rare example of a CO2 adduct of a group 10 metal and actually the first with η(1)-CO2 coordination. Reaction of 2 with CS2 affords the crystalline complex 4, in which the PPtP framework is bent, the CS2 molecule is η(2)-coordinated to Pt, and one S atom interacts with Al. The Pt complex 2 also smoothly reacts with H2 and benzamide PhCONH2 via oxidative addition of H-H and H-N bonds, respectively. The ensuing complexes 5 and 7 are stabilized by Pt-H→Al and Pt-NH-C(Ph) = O→Al bridging interactions, resulting in 5- and 7-membered metallacycles, respectively. DFT calculations have been performed in parallel with the experimental work. In particular, the mechanism of reaction of 2 with H2 has been thoroughly analyzed, and the role of the Lewis acid moiety has been delineated. These results generalize the concept of constrained geometry TM→LA interactions and demonstrate the ability of Al-based ambiphilic ligands to participate in TM/LA cooperative reactivity. They extend the scope of small molecule substrates prone to such cooperative activation and contribute to improve our knowledge of the underlying factors. PMID:26977772

  16. Isolation of active site and antibody-binding fragments of human erythrocyte transglutaminase

    Catalytically active human erythrocyte transglutaminase (TGase) was purified using an immunoaffinity column prepared from a monoclonal antibody to guinea pig liver TGase. The enzyme activity was completely inhibited by incorporation of iodo[14C]acetamide to the level of 1 mole per 1 mole of TGase. The 14C-labeled TGase was digested with cyanogen bromide, subjected to HPLC, and four pure peptides were isolated with molecular weights ranging from 3-22 KDa. Only one of the peptides was radiolabeled and characterized as an active site peptide of 10 KDa. Another peptide of 18 KDa was identified as a monoclonal antibody-binding domain of TGase. Although the active site and the antibody-binding domain were present on different cyanogen bromide fragments, the mouse anti-TGase inhibited 100% of TGase activity. The results suggest that the antibody-binding site is not located on the enzyme active site sequence, but that the three dimensional space configuration of the antigen-antibody complex hinders substrate binding to the active site. The radiolabeled active site cysteine residue was not found in the N-terminal 21 amino acids of the 10 KDa peptide. Additional fragments of the active site peptide are currently being analyzed

  17. Assessment of former uranium sites and their ongoing remediation activities

    Carried out analysis on tailing's buildings operation shows that period for engineer barrier service, taking into account any catastrophic natural impacts, is too little in comparison with life-time of long-live radionuclides. Priorities should be defined by danger degree and isolation costs (protection optimization), therefore uncommon, non-traditional methods, developed taking into account natural factors for long-live waste (radionuclides) isolation are necessary. That's why, it is necessary to carry out specialized research and development, design and exploratory and other works on monitoring of social-ecological condition of these sites, as well as on demographic public diseases, living in these regions.

  18. Synthesis and characterization of 18F-labeled active site inhibited factor VII (ASIS)

    Erlandsson, Maria; Nielsen, Carsten Haagen; Jeppesen, Troels Elmer;

    2015-01-01

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example......, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an 18F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[18F]fluorobenzoate, and the [18F]ASIS was purified on a PD-10 desalting...

  19. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  20. Assessment of activation products in the Savannah River Site environment

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: 32P, 51Cr, 60C, and 65Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated

  1. Assessment of activation products in the Savannah River Site environment

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  2. Sharp spatially constrained inversion

    Vignoli, Giulio G.; Fiandaca, Gianluca G.; Christiansen, Anders Vest C A.V.C.; Kirkegaard, Casper C.; Auken, Esben

    We present sharp reconstruction of multi-layer models using a spatially constrained inversion with minimum gradient support regularization. In particular, its application to airborne electromagnetic data is discussed. Airborne surveys produce extremely large datasets, traditionally inverted by...... using smoothly varying 1D models. Smoothness is a result of the regularization constraints applied to address the inversion ill-posedness. The standard Occam-type regularized multi-layer inversion produces results where boundaries between layers are smeared. The sharp regularization overcomes this by......, the results are compatible with the data and, at the same time, favor sharp transitions. The focusing strategy can also be used to constrain the 1D solutions laterally, guaranteeing that lateral sharp transitions are retrieved without losing resolution. By means of real and synthetic datasets, sharp...

  3. The landscape degradation in the mining sites with suspended activity

    Anca IONCE

    2009-01-01

    The extracting industry, through its extraction activities, of shipping the ores, of breaking the ores, of preparing the practical substances, of stowing the useless rock, of transporting the practical substances, etc. might modify the area’s relief and the quality of ground, of thesurface waters and of the air. Suceava County has an old tradition of mining, where the results of this activity are visible, especially the visual point of view, and where not taking certain measures of ecological...

  4. Constrained noninformative priors

    The Jeffreys noninformative prior distribution for a single unknown parameter is the distribution corresponding to a uniform distribution in the transformed model where the unknown parameter is approximately a location parameter. To obtain a prior distribution with a specified mean but with diffusion reflecting great uncertainty, a natural generalization of the noninformative prior is the distribution corresponding to the constrained maximum entropy distribution in the transformed model. Examples are given

  5. Probing the putative active site of YjdL

    Jensen, Johanne Mørch; Ismat, Fouzia; Szakonyi, Gerda;

    2012-01-01

    with Glu388, a preliminary orientation model of a dipeptide in the YjdL cavity is presented. Single site mutations of particularly Ala281 and Trp278 support the presented orientation. A dipeptide bound in the cavity of YjdL appears to be oriented such that the N-terminal side chain protrudes into a sub...... pocket that opens towards the extracellular space. The C-terminal side chain faces in the opposite direction into a sub pocket that faces the cytoplasm. These data indicated a stabilizing effect on a bulky N-terminal residue by an Ala281Phe variant and on the dipeptide backbone by Trp278. In the...... presented orientation model, Tyr25 and Tyr58 both appear to be in proximity of the dipeptide backbone while Lys117 appears to be in proximity of the peptide C-terminus. Mutational studies of these conserved residues highlight their functional importance....

  6. Active site proton delivery and the lyase activity of human CYP17A1

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G., E-mail: s-sligar@illinois.edu

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  7. Active site proton delivery and the lyase activity of human CYP17A1

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis

  8. Off-site medical activities, Nevada Test Site and the medical liaison officer network: a historical review

    The ''off-site'' was originally defined as ''that area surrounding the Nevada Test Site (NTS) for a radius of about 300 miles.'' Prior to 1954, the off-site radiological safety activities were conducted by the Atomic Energy Commission. In 1954, the Public Health Service was given the responsibility for off-site monitoring, and, in addition, a physician was also on temporary assignment. This physician, in addition to functioning as a monitor, also functioned part time as a physical liaison in regard to possible or alleged radiation injury. Medical concern was based upon two crude guidelines: possible radiation ''overexposure'' based upon extrapolation from surface and air radiological monitoring; and determination of actual radiation injury based upon signs and symptoms among people alleging radiation injury. The area of concern expanded to 13 areas surrounding the Nevada Test Site, and in 1956, the first Medical Liaison Officer Network (MLON) was initiated. Over the years, MLON increased to a point where there was a representative from every state in the Union; the area of concern expanded to include the entire United States, parts of the South Pacific, Hawaii, and Alaska; and sophisticated methods of evaluation were added--urine sampling, thyroid scanning, blood counts, and whole-body counting. Epidemiological studies were initiated on body burdens of radionuclides and certain disease clusters

  9. The landscape degradation in the mining sites with suspended activity

    Anca IONCE

    2009-08-01

    Full Text Available The extracting industry, through its extraction activities, of shipping the ores, of breaking the ores, of preparing the practical substances, of stowing the useless rock, of transporting the practical substances, etc. might modify the area’s relief and the quality of ground, of thesurface waters and of the air. Suceava County has an old tradition of mining, where the results of this activity are visible, especially the visual point of view, and where not taking certain measures of ecological remediation will emphasize the disappointing image of the landscape within the areas of mining activity performing.The predominant mountainous landscape, in which mining activities have been held, is being affected also by the abandoned industrial and administrative buildings, in an advanced degradation state.The hydrographic system, very rich in mining areas, has its water quality affected by the acid rock drainage- phenomenon which appeared in many mining waste deposits.

  10. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

    Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

    2016-01-01

    Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with

  11. Reduction of urease activity by interaction with the flap covering the active site.

    Macomber, Lee; Minkara, Mona S; Hausinger, Robert P; Merz, Kenneth M

    2015-02-23

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes, and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  12. Activation of brown adipose tissue mitochondrial GDP binding sites

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of [3H]-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time

  13. Activation of brown adipose tissue mitochondrial GDP binding sites

    Swick, A.G.

    1987-01-01

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of (/sup 3/H)-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time.

  14. Activation of Mitogen-Activated Protein Kinase Is Required for Migration and Invasion of Placental Site Trophoblastic Tumor

    Köbel, Martin; Pohl, Gudrun; Schmitt, Wolfgang D.; Hauptmann, Steffen; Wang, Tian-Li; Shih, Ie-Ming

    2005-01-01

    Placental site trophoblastic tumor (PSTT) is a gestational neoplasm derived from the extravillous (intermediate) trophoblast of the implantation site. PSTT is characterized by a highly invasive phenotype, but the molecular mechanisms are poorly understood. In this report, we demonstrate that PSTTs expressed the activated (phosphorylated) form of mitogen-activated protein kinase (MAPK) in 84% of cases, whereas the normal extravillous trophoblastic cells did not. To characterize the role of MAP...

  15. Experience in decommissioning activities at the BR3 site

    Klein, Michel E-mail: mklein@sckcen.be; Dadoumont, Jerome; Demeulemeester, Yves; Massaut, Vincent

    2001-04-01

    We give an overview of the experience, SCK-CEN acquired during 11 years of decommissioning activities of a PWR fission reactor. Experience has been gained in decontamination and dismantling technologies and in waste management. Dismantling an old PWR is quite different from the dismantling of the future fusion reactor. However, we can try to find out some common generic features and draw some lessons. Our experience shows that it is important to take the decommissioning aspects into account as soon as possible.

  16. Lipolytic activity from bacteria prospected in polluted portuary sites

    Kaori Levy Fonseca

    2014-06-01

    This study demonstrates that these TBT resistant isolates have, at the same time, the capacity to produce enzymes with a large biotechnological potential but, nevertheless, their relationship is not well understood, representing a novel approach. It is expected for these organisms to produce highly biotechnological relevant biocatalysts, due to their severe adaptations (Suehiro et al., 2007. The fully characterization of these lipases, mostly for F3 with elevated lipolytic activity exhibited, presents also a future challenge.

  17. Current disposal planning for dry active wastes at Rokkasho Site

    Takeuchi, Mitsuo [Japan Nuclear Fuel Ltd., Aomori (Japan)

    1997-02-01

    In nuclear power stations, two kinds of low level radioactive wastes are generated: `uniform solidified waste` in which waste liquid, spent resin and so on are uniformly solidified and `solid waste` in which metals, lagging materials, plastics and others are solidified. In Rokkasho Low Level Radioactive Waste Burying Center, the burying facility for the first period for the uniform solidified waste started the operation in December, 1992, and this time as the second period plan, it has been planned to increase No. 2 waste burying facility for the solid waste. The kinds of the radioactive waste solidified in containers to be buried are the solid state radioactive waste generated by the operation of nuclear power stations and that generated accompanying the operation of this facility. The wastes are classified, cut, pressed and melted as occasion demands so that cement filling material is easily filled in containers, and solidified in the containers. As for the waste to be buried, at the time of its acceptance, 6 months or longer have elapsed since its generation in nuclear power stations, and the surface dose equivalent rate does not exceed 10 mSv/h. The acceptance plan and the expected number of burying, the total radioactivity of buried waste, and the location, geological and hydraulic features, the structure and facilities of waste burying facilities, the method of burying, the management of waste burying site and the evaluation of dose equivalent are reported. (K.I.)

  18. Current disposal planning for dry active wastes at Rokkasho Site

    In nuclear power stations, two kinds of low level radioactive wastes are generated: 'uniform solidified waste' in which waste liquid, spent resin and so on are uniformly solidified and 'solid waste' in which metals, lagging materials, plastics and others are solidified. In Rokkasho Low Level Radioactive Waste Burying Center, the burying facility for the first period for the uniform solidified waste started the operation in December, 1992, and this time as the second period plan, it has been planned to increase No. 2 waste burying facility for the solid waste. The kinds of the radioactive waste solidified in containers to be buried are the solid state radioactive waste generated by the operation of nuclear power stations and that generated accompanying the operation of this facility. The wastes are classified, cut, pressed and melted as occasion demands so that cement filling material is easily filled in containers, and solidified in the containers. As for the waste to be buried, at the time of its acceptance, 6 months or longer have elapsed since its generation in nuclear power stations, and the surface dose equivalent rate does not exceed 10 mSv/h. The acceptance plan and the expected number of burying, the total radioactivity of buried waste, and the location, geological and hydraulic features, the structure and facilities of waste burying facilities, the method of burying, the management of waste burying site and the evaluation of dose equivalent are reported. (K.I.)

  19. Identifying high dose activities in industrial site radiography

    Although the radiation doses received by industrial radiographers in the UK have progressively fallen over the last few years, with most now receiving less than 1 mSv/y, a few still receive, relative to the rest, much higher doses. As a percentage of all radiographers the number stays surprisingly constant from year to year. This paper describes a survey to identify the work causing these doses and suggest possible solutions. The UK Central Index of Dose Information was interrogated to identify the industrial radiography companies having staff (not necessarily the same person) with doses of greater than 5mSv/y in the last three years for which information was available. This was 15 in total. The people on the staff receiving these doses were identified and a questionnaire sent to the companies concerned requesting information about their work. A general questionnaire about the operation of the company was also included. With the agreement of the company these questionnaires were followed up by a visit to the company to interviews a number of the management and the radiographers if available. Both groups were generally very open about their problems and every discussion had a positive outcome. Several areas of work/reasons for the doses have been identified. These are: pipeline radiography, ultra sound radiographers working on nuclear reactors, complex plant work often with several teams in the area, inability to retreat from the wind out equipment due to height or access problems, site pressure to not follow the best practices and a lack of appreciation when a dose was being received or, alternatively, carelessness. Some o these problem areas are very difficult to resolve. However ways in which the Health and Safety can help influence the doses have been identified together with practical suggestions radiographers could adopt. These will be reported. (author)

  20. Activated G-protein releases cGMP from high affinity binding sites on PDE from toad rod outer segments (ROS)

    cGMP binding proteins in toad ROS were identified by direct photoaffinity labeling (PAL) with 32P-cGMP and quantified by retention of complexes on nitrocellulose filters. By PAL, high affinity sites were present on the α and β subunits of the cGMP-specific phosphodiesterase (PDE) which have MW/sub app/ of 94 and 90 kDa. A doublet was deduced from its photolabeling properties to represent PDE/sub γ/ photocrosslinked with PDE/sub α/ or PDE/sub β/, respectively. cGMP prebound to these high affinity sites was released by light-activated G-protein or its α subunit complexed with GTPγS; this inhibition of cGMP binding to PDE did not result from decreased cGMP availability due to enhanced hydrolysis. A low affinity cGMP binding component identified by PAL is tightly associated with ROS membranes. Apparent ATP/light-dependent stimulation of cGMP binding was shown to result from light activated cGMP hydrolysis in conjunction with ATP-promoted conversion of GMP to GDP/GTP and increased GDP/GTP binding. These findings coincide with a model for light-related regulation of cGMP binding and metabolism predicted from intact and cellfree kinetic measurements: in the dark state the cGMP hydrolic rate is constrained by the availability of cGMP because of its binding to high affinity sites on PDE. Light activated G-protein releases cGMP from these sites and allows for its redistribution to lower affinity sites represented by PDE catalytic site(s) and possible cGMP-dependent membrane cation channels

  1. School Pharmacist/School Environmental Hygienic Activities at School Site.

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  2. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  3. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    Qi Jian-Xun; Jiang Fan

    2011-01-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  4. 77 FR 74218 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    2012-12-13

    ... published a Notice of Availability (NOA) in the Federal Register (72 FR 62,672) of the Programmatic EIS for... Federal Register (77 FR 5560) of the Final EA for Commercial Wind Lease Issuance and Site Assessment... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the...

  5. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2010-11-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to...

  6. Poisoning Experiments Aimed at Discriminating Active and Less-Active Sites of Silica-Supported Tantalum Hydride for Alkane Metathesis

    Saggio, Guillaume

    2010-10-04

    Only 50% of the silica-supported tantalum hydride sites are active in the metathesis of propane. Indeed, more than 45% of the tantalum hydride can be eliminated by a selective oxygen poisoning of inactive sites with no significant decrease in the global turnover. Conversely, cyclopentane induces no such selective poisoning. Hence, the active tantalum hydride sites that show greater resistance to oxygen poisoning correspond to the νTa-H bands of higher wavenumbers, particularly that at 1860cm-1. These active tantalum hydride sites should correspond to tris- or monohydride species relatively far from silica surface oxygen atoms. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Recent progress in volcanism studies: Site characterization activities for the Yucca Mountain site characterization project

    Significant progress has been made on volcanism studies over the past calendar year. There are a number of major highlights from this work. Geochronology data have been obtained for the Lathrop Wells center using a range of isotopic, radiogenic, and age-calibrated methods. Initial work is encouraging but still insufficient to resolve the age of the center with confidence. Geologic mapping of the Sleeping Butte volcanic centers was completed and a report issued on the geology and chronology data. Twenty shallow trenches have been constructed in volcanic units of the Lathrop Wells volcanic center. Results of detailed studies of the trenches support a polycyclic eruptive history. New soil data from the trenches continue to support a late Pleistocene or Holocene age for many of the volcanic units at the center. Geochemical data (trace element and isotopic analysis) show that the volcanic units of the Lathrop Wells center cannot be related to one another by fractional crystallization of a single magma batch, supporting a polycyclic model of volcanism. Structural models using existing data are used to evaluate the probability of magmatic disruption of a potential repository. Several permissive models have been developed but none lead to significant differences in calculating the disruption ratio. Work was initiated on the eruptive and subsurface effects of magmatic activity on a repository. (author)

  8. Site specific rationale for technical impracticability of active groundwater restoration at a former manufactured gas plant site

    The National Contingency Plan (40 CFR Part 300 ) requires that remedial strategies must, at minimum, protect human health and the environment and meet applicable and relevant or appropriate requirements (ARARs). Where groundwater is impacted, maximum contaminant levels (MCLs) and maximum contaminant level goals (MCLGs) set under the Safe Drinking Water Act are often used as ARARs, whether or not the aquifer is a reasonably anticipated future source of drinking water. The US Environmental Protection Agency now recognizes the difficulty of groundwater restoration at sites where dense nonaqueous phase liquids are present, particularly in certain complex hydrogeological settings (EPA 1993). However, demonstration of impracticability generally does not occur until active remediation (e.g., pump and treat) has been shown to be ineffective. A case study of a former manufactured gas plant (MGP) is used to demonstrate how physical and chemical properties of the aquifer and coal tar, the major waste product from MGP sites, influence the feasibility of active restoration. Field characterization investigations, laboratory studies, and groundwater modeling are integrated into a demonstration following EPA guidelines. Laboratory studies included microbiological characterization and natural biodegradation and suggest that intrinsic bioremediation is occurring at this site. This work will be useful as EPA continues to develop presumptive remedies for cleanup under Superfund

  9. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta's K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports

  10. Coordination environment of the active-site metal ion of liver alcohol dehydrogenase.

    Makinen, M W; Yim, M B

    1981-01-01

    The coordination environment of the catalytically active metal ion of horse liver alcohol dehydrogenase (alcohol:NAD+ oxidoreductase, EC 1.1.1.1) has been investigated by electron paramagnetic resonance (EPR) methods with use of the active-site-specific Co2+-reconstituted enzyme. The EPR absorption spectrum of the metal-substituted enzyme is characteristic of a rhombically distorted environment. The spectrum of the enzyme--NAD+ complex shows approximate axial symmetry of the metal ion site, i...

  11. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and ...

  12. Molecular dynamics explorations of active site structure in designed and evolved enzymes

    Osuna Oliveras, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L.; Houk, Kendall N.

    2015-01-01

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explora...

  13. Active site dynamics of toluene hydroxylation by cytochrome P-450

    Rat liver cytochrome P-450 hydroxylates toluene to benzyl alcohol plus o-, m-, and p-cresol. Deuterated toluenes were incubated under saturating conditions with liver microsomes from phenobarbital-pretreated rats, and product yields and ratios were measured. Stepwise deuteration of the methyl leads to stepwise decreases in the alcohol/cresol ratio without changing the cresol isomer ratios. Extensive deuterium retention in the benzyl alcohols from PhCH2D and PhCHD2 suggests there is a large intrinsic isotope effect for benzylic hydroxylation. After replacement of the third benzylic H by D, the drop in the alcohol/cresol ratio was particularly acute, suggsting that metabolic switching from D to H within the methyl group was easier than switching from the methyl to the ring. Comparison of the alcohol/cresol ratio for PhCH3 vs PhCD3 indicated a net isotope effect of 6.9 for benzylic hydroxylation. From product yield data for PhCH3 and PhCD3, DV for benzyl alcohol formation is only 1.92, whereas DV for total product formation is 0.67 (i.e., inverse). From competitive incubations of PhCH3/PhCD3 mixtures D(V/K) isotope effects on benzyl alcohol formation and total product formation (3.6 and 1.23, respectively) are greatly reduced, implying strong commitment to catalysis. In contrast, D(V/K) for the alcohol/cresol ratio is 6.3, indicating that the majority of the intrinsic isotope effect is expressed through metabolic switching. Overall, these data are consistent with reversible formation of a complex between toluene and the active oxygen form of cytochrome P-450, which rearranges internally and reacts to form products faster than it dissociates back to release substrate

  14. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins. PMID:24635441

  15. XAFS Study of the Photo-Active Site of Mo/MCM-41

    An Mo/MCM-41 catalyst was prepared and used for study of propene and 1-butene photo-metathesis reactions. XAFS analysis revealed that hydrogen reduction leads to a decreased role for the Mo=O site. The Mo-O site plays an important role for the olefin photo-metathesis reaction on the H2 reduced Mo/MCM-41. From EXAFS analysis, the active site of photo-metathesis reaction is the Mo=O part for oxidized Mo/MCM-41, whereas it is the Mo-O site for reduced Mo/MCM-41

  16. Active sites for NO reduction over Fe-ZSM-5 catalysts.

    Schwidder, M; Santhosh Kumar, M; Brückner, A; Grünert, W

    2005-02-14

    A study of Fe-ZSM-5 catalysts with variable amounts of isolated, oligomeric and heavily aggregated Fe3+ oxo sites (as evidenced by UV-Vis and EPR spectroscopic data) and their catalytic properties in the selective catalytic reduction of NO by isobutane or by NH3 is presented, which allows development of a unified concept of the active Fe sites in these reactions, according to which isolated Fe sites catalyse both SCR reactions while oligomeric sites, though also involved in the selective reduction path, limit the catalyst performance by causing the total oxidation of the reductant. PMID:15685345

  17. Benzene Hydroxylation over FeZSM-5 Catalysts: Which Fe-sites Are Active?

    Yuranov, I.; Bulushev, D. A.; Renken, A.; Kiwi-Minsker, L.

    2004-01-01

    FeZSM-5 with a wide range of Fe content (0.015–2.1 wt%) were studied in the benzene hydroxylation to phenol with nitrous oxide (C6H6:N2O = 1:5) at low temperatures (98%) was obtained within 3 h without any deactivation of the catalyst. Three types of Fe(II) sites were formed in the zeolites extraframework due to activation and are attributed to: (1) Fe(II) sites in mononuclear species, (2) oligonuclear species with at least two oxygen-bridged Fe(II) sites, and (3) Fe(II) sites within Fe2O3 na...

  18. Concept for calculating dose rates from activated groundwater at accelerator sites

    Prolingheuer, N; Vanderborght, J; Schlögl, B; Nabbi, R; Moormann, R

    Licensing of particle accelerators requires the proof that the groundwater outside of the site will not be significantly contaminated by activation products formed below accelerator and target. In order to reduce the effort for this proof, a site independent simplified but conservative method is under development. The conventional approach for calculation of activation of soil and groundwater is shortly described on example of a site close to Forschungszentrum Juelich, Germany. Additionally an updated overview of a data library for partition coefficients for relevant nuclides transported in the aquifer at the site is presented. The approximate model for transport of nuclides with ground water including exemplary results on nuclide concentrations outside of the site boundary and of resulting effective doses is described. Further applications and developments are finally outlined.

  19. Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

    Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with [γ-32P]ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the 32P-labeled β-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total 32P radioactivity is found in site I and the rate of 32P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the β-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress

  20. Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

    Flores-Riveros, J.R.; Lane, M.D.

    1987-05-01

    Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with (..gamma..-/sup 32/P)ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the /sup 32/P-labeled ..beta..-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total /sup 32/P radioactivity is found in site I and the rate of /sup 32/P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the ..beta..-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress.

  1. Site-specific targeting of antibody activity in vivo mediated by disease-associated proteases

    Erster, Oran; Thomas, Jerry M; Hamzah, Juliana; Jabaiah, Abeer M.; Getz, Jennifer A.; Schoep, Tobias; Hall, Sejal S.; Ruoslahti, Erkki; Daugherty, Patrick S.

    2012-01-01

    As a general strategy to selectively target antibody activity in vivo, a molecular architecture was designed to render binding activity dependent upon proteases in disease tissues. A protease-activated antibody (pro-antibody) targeting vascular cell adhesion molecule 1 (VCAM-1), a marker of atherosclerotic plaques, was constructed by tethering a binding site-masking peptide to the antibody via a matrix metalloprotease (MMP) susceptible linker. Pro-antibody activation in vitro by MMP-1 yielded...

  2. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  3. Modeling Steroid 5alpha-reductase and Characterizing Its Potential Active Sites

    OU Min-Rui; LI Jun-Qian

    2012-01-01

    Steroid 5alpha-reductase of human is an enzyme in the biosynthetic pathway from testosterone (T) to dihydrotestosterone (DHT). Up to now, no crystal structure of this enzyme has been reported. However, knowledge of the tertiary structure and possible active sites is essential for understanding the catalysis mechanism and for the design of inhibitors. A model with putative active sites has been created and evaluated by using homology modeling and molecular docking techniques based on the bioinformatics knowledge. The homology model is optimized in Swiss PDB Viewer with MM method and substrate structures before docking are also optimized on HF/6-31G. The active site for the docking of NADP, T, DHT and Finasteride is located near the N-terminus of enzyme. Four active amino acids in the active site are identified as Ala26, Arg53, Arg176 and Lys177. Reaction procedure, binding pattern of active sites, the types of weak interaction and so on are also discussed.

  4. Effects of resource activities upon repository siting and waste containment with reference to bedded salt

    The primary consideration for the suitability of a nuclear waste repository site is the overall ability of the repository to safely contain radioactive waste. This report is a discussion of the past, present, and future effects of resource activities on waste containment. Past and present resource activities which provide release pathways (i.e., leaky boreholes, adjacent mines) will receive initial evaluation during the early stages of any repository site study. However, other resource activities which may have subtle effects on containment (e.g., long-term pumping causing increased groundwater gradients, invasion of saline water causing lower retardation) and all potential future resource activities must also be considered during the site evaluation process. Resource activities will affect both the siting and the designing of repositories. Ideally, sites should be located in areas of low resource activity and low potential for future activity, and repository design should seek to eliminate or minimize the adverse effects of any resource activity. Buffer zones should be created to provide areas in which resource activities that might adversely affect containment can be restricted or curtailed. This could mean removing large areas of land from resource development. The impact of these frozen assets should be assessed in terms of their economic value and of their effect upon resource reserves. This step could require a major effort in data acquisition and analysis followed by extensive numerical modeling of regional fluid flow and mass transport. Numerical models should be used to assess the effects of resource activity upon containment and should include the cumulative effects of different resource activities. Analysis by other methods is probably not possible except for relatively simple cases

  5. A caspase active site probe reveals high fractional inhibition needed to block DNA fragmentation.

    Méthot, Nathalie; Vaillancourt, John P; Huang, JingQi; Colucci, John; Han, Yongxin; Ménard, Stéphane; Zamboni, Robert; Toulmond, Sylvie; Nicholson, Donald W; Roy, Sophie

    2004-07-01

    Apoptotic markers consist of either caspase substrate cleavage products or phenotypic changes that manifest themselves as a consequence of caspase-mediated substrate cleavage. We have shown recently that pharmacological inhibitors of caspase activity prevent the appearance of two such apoptotic manifestations, alphaII-spectrin cleavage and DNA fragmentation, but that blockade of the latter required a significantly higher concentration of inhibitor. We investigated this phenomenon through the use of a novel radiolabeled caspase inhibitor, [(125)I]M808, which acts as a caspase active site probe. [(125)I]M808 bound to active caspases irreversibly and with high sensitivity in apoptotic cell extracts, in tissue extracts from several commonly used animal models of cellular injury, and in living cells. Moreover, [(125)I]M808 detected active caspases in septic mice when injected intravenously. Using this caspase probe, an active site occupancy assay was developed and used to measure the fractional inhibition required to block apoptosis-induced DNA fragmentation. In thymocytes, occupancy of up to 40% of caspase active sites had no effect on DNA fragmentation, whereas inhibition of half of the DNA cleaving activity required between 65 and 75% of active site occupancy. These results suggest that a high and persistent fractional inhibition will be required for successful caspase inhibition-based therapies. PMID:15067000

  6. Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

    Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole;

    2006-01-01

    to form high affinity metal ion sites in both the bidentate and potential tridentate settings. This indicates that the residues involved in the main ligand-binding pocket will have to move closer to each other during receptor activation. On the basis of the distance constraints from these activating metal...

  7. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    2012-07-03

    ... specific project proposals on those leases) in an identified Wind Energy Area (WEA) on the OCS offshore... Activities on the Atlantic OCS Offshore RI and MA'' to: Program Manager, Office of Renewable Energy Programs... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on...

  8. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    Parashar, Abhinav [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Venkatachalam, Avanthika [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India); Gideon, Daniel Andrew [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Manoj, Kelath Murali, E-mail: satyamjayatu@yahoo.com [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India)

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  9. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes

  10. Insight into the mechanism of phosphoenolpyruvate mutase catalysis derived from site-directed mutagenesis studies of active site residues.

    Jia, Y; Lu, Z; Huang, K; Herzberg, O; Dunaway-Mariano, D

    1999-10-26

    PEP mutase catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate in biosynthetic pathways leading to phosphonate secondary metabolites. A recent X-ray structure [Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., and Herzberg, O. (1999) Structure (in press)] of the Mytilus edulis enzyme complexed with the Mg(II) cofactor and oxalate inhibitor reveals an alpha/beta-barrel backbone-fold housing an active site in which Mg(II) is bound by the two carboxylate groups of the oxalate ligand and the side chain of D85 and, via bridging water molecules, by the side chains of D58, D85, D87, and E114. The oxalate ligand, in turn, interacts with the side chains of R159, W44, and S46 and the backbone amide NHs of G47 and L48. Modeling studies identified two feasible PEP binding modes: model A in which PEP replaces oxalate with its carboxylate group interacting with R159 and its phosphoryl group positioned close to D58 and Mg(II) shifting slightly from its original position in the crystal structure, and model B in which PEP replaces oxalate with its phosphoryl group interacting with R159 and Mg(II) retaining its original position. Site-directed mutagenesis studies of the key mutase active site residues (R159, D58, D85, D87, and E114) were carried out in order to evaluate the catalytic roles predicted by the two models. The observed retention of low catalytic activity in the mutants R159A, D85A, D87A, and E114A, coupled with the absence of detectable catalytic activity in D58A, was interpreted as evidence for model A in which D58 functions in nucleophilic catalysis (phosphoryl transfer), R159 functions in PEP carboxylate group binding, and the carboxylates of D85, D87 and E114 function in Mg(II) binding. These results also provide evidence against model B in which R159 serves to mediate the phosphoryl transfer. A catalytic motif, which could serve both the phosphoryl transfer and the C-C cleavage enzymes of the PEP mutase superfamily, is proposed. PMID:10571990

  11. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang; (NU Sinapore); (Nankai); (Oxford); (Chinese Aca. Sci.); (Tsinghua)

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  12. Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

    Phillips, J.; Warby, C; Whitby, F; Kushner, J; Hill, C

    2009-01-01

    Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

  13. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

    Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

    2012-05-01

    Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds. PMID:21877154

  14. Locomotor activity influences muscle architecture and bone growth but not muscle attachment site morphology

    Rabey, Karyne N.; Green, David J; Taylor, Andrea B.; Begun, David R.; Richmond, Brian G.; McFarlin, Shannon C.

    2014-01-01

    The ability to make behavioural inferences from skeletal remains is critical to understanding the lifestyles and activities of past human populations and extinct animals. Muscle attachment site (enthesis) morphology has long been assumed to reflect muscle strength and activity during life, but little experimental evidence exists to directly link activity patterns with muscle development and the morphology of their attachments to the skeleton. We used a mouse model to experimentally test how t...

  15. Nuclear waste: Issues concerning DOE's postponement of second repository siting activities

    In May 1986 the Department of Energy announced it was postponing site-specific work for a second nuclear waste repository because of progress made in siting the first repository and the uncertainty about when a second repository might be needed. A DOE draft report, which tentatively identified potential sites in seven different states, received considerable comment and objections by concerned states, Indian tribes, and individuals. Following the postponement decision, DOE initiated actions to redirect and restructure the second repository program, concentrating on technical issues rather than site-specific work. This reduction includes a phase-down of siting activities and the formulation of a Technology Development Program with an emphasis on cooperative efforts in international research

  16. Large zinc cation occupancy of octahedral sites in mechanically activated zinc ferrite powders

    The cation site occupancy of a mechanically activated nanocrystalline zinc ferrite powder was determined as (Zn0.552+Fe0.183+)tet[Zr0.452+Fe1.823+]octO4 through analysis of extended x-ray absorption fine structure measurements, showing a large redistribution of cations between sites compared to normal zinc ferrite samples. The overpopulation of cations in the octahedral sites was attributed to the ascendance in importance of the ionic radii over the crystal energy and bonding coordination in determining which interstitial sites are occupied in this structurally disordered powder. Slight changes are observed in the local atomic environment about the zinc cations, but not the iron cations, with respect to the spinel structure. The presence of Fe3+ on both sites is consistent with the measured room temperature magnetic properties. (c) 2000 American Institute of Physics

  17. The toponymy of communal activity: Anglo-Saxon assembly sites and their functions

    Baker, John

    2014-01-01

    The paper builds on earlier discussion of the multiple functions of medieval judicial assembly sites, providing a comprehensive evaluation of relevant English hundred-names, and making reference to associated microtoponymy. While religious, military, commercial, and recreational activities may all have occurred at assembly-sites, it can be hard to delineate the evidence so clearly along these lines, and attempts to do so may be anachronistic in some instances; nevertheless, the analysis of di...

  18. Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

    Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.; Gray, Kimberly A.; Notestein, Justin M. [NWU

    2015-06-04

    Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiOx domains are titrated on TiOx–SiO2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiOx, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H2O2 activation occurs. We use this method to determine the active site densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h-1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.

  19. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  20. Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

    Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

    2015-03-01

    Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed. PMID:25613522

  1. Stringency of the 2-His-1-Asp active-site motif in prolyl 4-hydroxylase.

    Kelly L Gorres

    Full Text Available The non-heme iron(II dioxygenase family of enzymes contain a common 2-His-1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C-H bonds. Prolyl 4-hydroxylase (P4H is an alpha-ketoglutarate-dependent iron(II dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His-1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change.

  2. Hard X-ray Morphological and Spectral Studies of The Galactic Center Molecular Cloud Sgr B2: Constraining Past Sgr A* Flaring Activity

    Zhang, Shuo; Mori, Kaya; Clavel, Maïca; Terrier, Régis; Ponti, Gabriele; Goldwurm, Andrea; Bauer, Franz E; Boggs, Steven E; Craig, William W; Christensen, Finn E; Harrison, Fiona A; Hong, Jaesub; Nynka, Melania; Stern, Daniel; Soldi, Simona; Tomsick, John A; Zhang, William W

    2015-01-01

    Galactic Center (GC) molecular cloud Sgr B2 is the best manifestation of an X-ray reflection nebula (XRN) reprocessing a past giant outburst from the supermassive black hole Sgr A*. Alternatively, Sgr B2 could be illuminated by low-energy cosmic ray electrons (LECRe) or protons (LECRp). In 2013, NuSTAR for the first time resolved Sgr B2 hard X-ray emission on sub-arcminute scales. Two prominent features are detected above 10 keV - a newly emerging cloud G0.66-0.13 and the central 90" radius region containing two compact cores Sgr B2(M) and Sgr B2(N) surrounded by diffuse emission. It is inconclusive whether the remaining level of Sgr B2 emission is still decreasing or has reached a constant background level. A decreasing Fe K$\\alpha$ emission can be best explained by XRN while a constant background emission can be best explained by LECRp. In the XRN scenario, the 3-79 keV Sgr B2 spectrum can well constrain the past Sgr A* outburst, resulting in an outburst spectrum with a peak luminosity of $L_{3-79\\rm~keV} \\...

  3. Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

    Wang, Lu; Boxer, Steven G; Markland, Thomas E

    2015-01-01

    Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

  4. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115.

    Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru

    2016-08-01

    Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst. PMID:27402448

  5. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity.

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-12-15

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser(696) and Ser(698) in the JM (juxtamembrane) region and probably Ser(886) and/or Ser(893) in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser(717) in the JM, and at Ser(733), Thr(752), Ser(783), Ser(864), Ser(911), Ser(958) and Thr(998) in the kinase domain. The LC-ESI-MS/MS spectra provided support that up to three sites (Thr(890), Ser(893) and Thr(894)) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr(890), Ser(893), Thr(894) and Thr(899), differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  6. Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

    Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

    2015-04-01

    On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

  7. Preliminary examination of the impacts of repository site characterization activities and facility construction and operation activities on Hanford air quality

    Glantz, C.S.; Ramsdell, J.V.

    1986-04-01

    Air quality impacts that would result from site characterization activities and from the construction and operation of a high-level nuclear wste repository at Hanford are estimated using two simple atmospheric dispersion models, HANCHI and CHISHORT. Model results indicate that pollutant concentrations would not exceed ambient air quality standards at any point outside the Hanford fenceline or at any publicly accessible location within the Hanford Site. The increase in pollutant concentrations in nearby communities due to site activities would be minimal. HANCHI and CHISHORT are documented in the appendices of this document. Further study of the repository's impact on air quality will be conducted when more detailed project plans and work schedules are available.

  8. Preliminary examination of the impacts of repository site characterization activities and facility construction and operation activities on Hanford air quality

    Air quality impacts that would result from site characterization activities and from the construction and operation of a high-level nuclear wste repository at Hanford are estimated using two simple atmospheric dispersion models, HANCHI and CHISHORT. Model results indicate that pollutant concentrations would not exceed ambient air quality standards at any point outside the Hanford fenceline or at any publicly accessible location within the Hanford Site. The increase in pollutant concentrations in nearby communities due to site activities would be minimal. HANCHI and CHISHORT are documented in the appendices of this document. Further study of the repository's impact on air quality will be conducted when more detailed project plans and work schedules are available

  9. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    Soares Alexei S

    2007-11-01

    Full Text Available Abstract Background Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. Results We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a ΔH of -13 ± 2 kJ/mol and a ΔS of -0.04 ± 0.01 kJ/(K*mol. The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. Conclusion We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the

  10. Threatened and endangered wildlife species of the Hanford Site related to CERCLA characterization activities

    Fitzner, R.E. [Pacific Northwest Lab., Richland, WA (United States); Weiss, S.G.; Stegen, J.A. [Westinghouse Hanford Co., Richland, WA (United States)

    1994-06-01

    The US Department of Energy`s (DOE) Hanford Site has been placed on the National Priorities List, which requires that it be remediated under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund. Potentially contaminated areas of the Hanford Site were grouped into operable units, and detailed characterization and investigation plans were formulated. The DOE Richland Operations Office requested Westinghouse Hanford Company (WHC) to conduct a biological assessment of the potential impact of these characterization activities on the threatened, endangered, and sensitive wildlife species of the Hanford Site. Additional direction for WHC compliances with wildlife protection can be found in the Environmental Compliance Manual. This document is intended to meet these requirements, in part, for the CERCLA characterization activities, as well as for other work comparable in scope. This report documents the biological assessment and describes the pertinent components of the Hanford Site as well as the planned characterization activities. Also provided are accounts of endangered, threatened, and federal candidate wildlife species on the Hanford Site and information as to how human disturbances can affect these species. Potential effects of the characterization activities are described with recommendations for mitigation measures.

  11. Utility experiences in redevelopment of formerly used sites -- Wisconsin Electric's risk management and economic development activities

    Wisconsin Electric Power Company, which recently celebrated its 100th anniversary, has actively promoted the redevelopment of its former sites as well as those of its customers. Serving Milwaukee and southeast Wisconsin, Wisconsin Electric's (WE) sites include former power plants, landfills, right-of-ways, and manufactured gas plant sites. In setting an example for others, as well as seeking to maximize the economic value of these sites, WE has either redeveloped or promoted the redevelopment of these sites by others. Examples include the East Wells Power Plant (now home of the Milwaukee Repertory Theater), the Lakeside Power Plant Site (now the home of Harnischfeger Corporation's headquarters), and the Commerce Street Power Plant located on the Milwaukee River near downtown Milwaukee. In each case the company evaluated the potential environmental liabilities against the unrealized asset value derived from facility location, site size, architectural uniqueness, or other characteristics. At the Commerce Street Power Plant, walking distance to the downtown Milwaukee business district combined with river frontage, were significant site values leveraged against a $5 million asbestos and lead-based paint removal project done to prepare the plant for marketing. More recently, WE has used its experience in promoting the redevelopment of the Menomonee River Valley, the original core of Milwaukee's industrial community, and in advancing a more practical regulatory approach to redeveloping older sites. Finally, the company is working with a non-profit community health clinic, community groups and local foundations in linking these redevelopment activities with the economic and physical health of inner city residents

  12. Constraining neutrinoless double beta decay

    A class of discrete flavor-symmetry-based models predicts constrained neutrino mass matrix schemes that lead to specific neutrino mass sum-rules (MSR). We show how these theories may constrain the absolute scale of neutrino mass, leading in most of the cases to a lower bound on the neutrinoless double beta decay effective amplitude.

  13. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S.; Drakou, Evangelia G.; Pantis, John D.

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity.

  14. Human activities in Natura 2000 sites: a highly diversified conservation network.

    Tsiafouli, Maria A; Apostolopoulou, Evangelia; Mazaris, Antonios D; Kallimanis, Athanasios S; Drakou, Evangelia G; Pantis, John D

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity. PMID:23571828

  15. Power-constrained supercomputing

    Bailey, Peter E.

    As we approach exascale systems, power is turning from an optimization goal to a critical operating constraint. With power bounds imposed by both stakeholders and the limitations of existing infrastructure, achieving practical exascale computing will therefore rely on optimizing performance subject to a power constraint. However, this requirement should not add to the burden of application developers; optimizing the runtime environment given restricted power will primarily be the job of high-performance system software. In this dissertation, we explore this area and develop new techniques that extract maximum performance subject to a particular power constraint. These techniques include a method to find theoretical optimal performance, a runtime system that shifts power in real time to improve performance, and a node-level prediction model for selecting power-efficient operating points. We use a linear programming (LP) formulation to optimize application schedules under various power constraints, where a schedule consists of a DVFS state and number of OpenMP threads for each section of computation between consecutive message passing events. We also provide a more flexible mixed integer-linear (ILP) formulation and show that the resulting schedules closely match schedules from the LP formulation. Across four applications, we use our LP-derived upper bounds to show that current approaches trail optimal, power-constrained performance by up to 41%. This demonstrates limitations of current systems, and our LP formulation provides future optimization approaches with a quantitative optimization target. We also introduce Conductor, a run-time system that intelligently distributes available power to nodes and cores to improve performance. The key techniques used are configuration space exploration and adaptive power balancing. Configuration exploration dynamically selects the optimal thread concurrency level and DVFS state subject to a hardware-enforced power bound

  16. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    Wang, Qin; Li, Yingjun; Liu, Baocang; Xu, Guangran; Zhang, Geng; Zhao, Qi; Zhang, Jun

    2015-11-01

    A series of well-dispersed bimetallic Pd@Pt nanodendrites uniformly supported on XC-72 carbon black are fabricated by using different capping agents. These capping agents are essential for the branched morphology control. However, the surfactant adsorbed on the nanodendrites surface blocks the access of reactant molecules to the active surface sites, and the catalytic activities of these bimetallic nanodendrites are significantly restricted. Herein, a facile reflux procedure to effectively remove the capping agent molecules without significantly affecting their sizes is reported for activating supported nanocatalysts. More significantly, the structure and morphology of the nanodendrites can also be retained, enhancing the numbers of active surface sites, catalytic activity and stability toward methanol and ethanol electro-oxidation reactions. The as-obtained hot water reflux-treated Pd@Pt/C catalyst manifests superior catalytic activity and stability both in terms of surface and mass specific activities, as compared to the untreated catalysts and the commercial Pt/C and Pd/C catalysts. We anticipate that this effective and facile removal method has more general applicability to highly active nanocatalysts prepared with various surfactants, and should lead to improvements in environmental protection and energy production.

  17. Immobilized low-activity waste site borehole 299-E17-21

    The Tank Waste Remediation System (TWRS) is the group at the Hanford Site responsible for the safe underground storage of liquid waste from previous Hanford Site operations, the storage and disposal of immobilized tank waste, and closure of underground tanks. The current plan is to dispose of immobilized low-activity tank waste (ILAW) in new facilities in the southcentral part of 200-East Area and in four existing vaults along the east side of 200-East Area. Boreholes 299-E17-21, B8501, and B8502 were drilled at the southwest corner of the ILAW site in support of the Performance Assessment activities for the disposal options. This report summarizes the initial geologic findings, field tests conducted on those boreholes, and ongoing studies. One deep (480 feet) borehole and two shallow (50 feet) boreholes were drilled at the southwest corner of the ILAW site. The primary factor dictating the location of the boreholes was their characterization function with respect to developing the geohydrologic model for the site and satisfying associated Data Quality Objectives. The deep borehole was drilled to characterize subsurface conditions beneath the ILAW site, and two shallow boreholes were drilled to support an ongoing environmental tracer study. The tracer study will supply information to the Performance Assessment. All the boreholes provide data on the vadose zone and saturated zone in a previously uncharacterized area

  18. Surface binding sites in carbohydrate active enzymes: An emerging picture of structural and functional diversity

    Svensson, Birte; Cockburn, Darrell

    2013-01-01

    universal and is in fact rare among some families of enzymes. In some cases an alternative to possessing a CBM is for the enzyme to bind to the substrate at a site on the catalytic domain, but away from the active site. Such a site is termed a surface (or secondary) binding site (SBS). SBSs have been...... identified in enzymes from a wide variety of families, though almost half are found in the α-amylase family GH13. The roles attributed to SBSs are not limited to targeting the enzyme to the substrate, but also include a variety of others such as guiding the substrate into the active site, altering enzyme...... specificity and acting as an allosteric site. Although SBSs share many roles with CBMs they may not simply be an alternative to CBMs, but rather complementary as SBSs and CBMs frequently co-occur in enzymes. Despite a relatively long history, it is only in recent years that SBSs have been studied in great...

  19. Immobilized low-activity waste site borehole 299-E17-21

    Reidel, S.P.; Reynolds, K.D.; Horton, D.G.

    1998-08-01

    The Tank Waste Remediation System (TWRS) is the group at the Hanford Site responsible for the safe underground storage of liquid waste from previous Hanford Site operations, the storage and disposal of immobilized tank waste, and closure of underground tanks. The current plan is to dispose of immobilized low-activity tank waste (ILAW) in new facilities in the southcentral part of 200-East Area and in four existing vaults along the east side of 200-East Area. Boreholes 299-E17-21, B8501, and B8502 were drilled at the southwest corner of the ILAW site in support of the Performance Assessment activities for the disposal options. This report summarizes the initial geologic findings, field tests conducted on those boreholes, and ongoing studies. One deep (480 feet) borehole and two shallow (50 feet) boreholes were drilled at the southwest corner of the ILAW site. The primary factor dictating the location of the boreholes was their characterization function with respect to developing the geohydrologic model for the site and satisfying associated Data Quality Objectives. The deep borehole was drilled to characterize subsurface conditions beneath the ILAW site, and two shallow boreholes were drilled to support an ongoing environmental tracer study. The tracer study will supply information to the Performance Assessment. All the boreholes provide data on the vadose zone and saturated zone in a previously uncharacterized area.

  20. POISONING OF ACTIVE SITES ON ZIEGLER-NATTA CATALYST FOR PROPYLENE POLYMERIZATION

    Kitti Tangjituabun; Sang Yull Kim; Yuichi Hiraoka; Toshiaki Taniike; Minoru Terano; Bunjerd Jongsomjit; Piyasan Praserthdam

    2008-01-01

    The effects of poisoning materials on catalytic activity and isospecificity of the supported Ziegler-Natta catalyst were investigated.A minor amount of simple structure of Lewis base,i.e.,methanol,acetone,ethyl acetate,was introduced into the catalyst slurry for partial poisoning catalytic active centers.It was found that the variations in deactivation power were in the order of methanol>acetone>ethyl acetate.The kinetic investigation via stopped-flow polymerization showed that poisoning compounds caused a decrease in activity through the reduction of the number of active sites whereas no effect on the degree of isotacticity was observed.

  1. Sphingosine-1-phosphate receptor 1 reporter mice reveal receptor activation sites in vivo

    Kono, Mari; Tucker, Ana E.; Tran, Jennifer; Bergner, Jennifer B.; Turner, Ewa M; Proia, Richard L.

    2014-01-01

    Activation of the GPCR sphingosine-1-phosphate receptor 1 (S1P1) by sphingosine-1-phosphate (S1P) regulates key physiological processes. S1P1 activation also has been implicated in pathologic processes, including autoimmunity and inflammation; however, the in vivo sites of S1P1 activation under normal and disease conditions are unclear. Here, we describe the development of a mouse model that allows in vivo evaluation of S1P1 activation. These mice, known as S1P1 GFP signaling mice, produce a ...

  2. Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.

    Saam, Jan; Ivanov, Igor; Walther, Matthias; Holzhütter, Hermann-Georg; Kuhn, Hartmut

    2007-08-14

    Cells contain numerous enzymes that use molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein, which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen-dependent enzymes, we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose, we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements. First, we computed the 3D free-energy distribution for oxygen, which led to identification of four oxygen channels in the protein. All channels connect the protein surface with a region of high oxygen affinity at the active site. This region is localized opposite to the nonheme iron providing a structural explanation for the reaction specificity of this lipoxygenase isoform. The catalytically most relevant path can be obstructed by L367F exchange, which leads to a strongly increased Michaelis constant for oxygen. The blocking mechanism is explained in detail by reordering the hydrogen-bonding network of water molecules. Our results provide strong evidence that the main route for oxygen access to the active site of the enzyme follows a channel formed by transiently interconnected cavities whereby the opening and closure are governed by side chain dynamics. PMID:17675410

  3. Active catalytic sites in the ammoxidation of propane and propene over V-Sb-O catalysts

    Buchholz, S.A.; Zanthoff, H.W. [Bochum Univ. (Germany). Lehrstuhl fuer Technische Chemie

    1998-12-31

    The ammoxidation of propane over VSb{sub y}O{sub x} catalysts (y=1, 2, 5) was investigated with respect to the role of different oxygen species in the selective and non selective reaction steps using transient experiments in the Temporal Analysis of Products (TAP) reactor. Only lattice oxygen is involved in the oxidation reactions. Using isotopic labelled oxygen it is shown that two different active sites exist on the surface. On site A, which can be reoxidized faster by gas phase oxygen compared to site B, mainly CO is formed. On site B CO{sub 2} and acrolein as well as NO and N{sub 2}O in the presence of ammonia in the feed gas are formed and reoxidation mainly occurs with bulk lattice oxygen. (orig.)

  4. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase. PMID:17850513

  5. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.

    Haibo Yu

    2007-02-01

    Full Text Available Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP, the recovery stroke in the conventional myosin has been shown to be dependent on the hydrolysis of ATP. To obtain a clearer mechanistic picture for such "mechanochemical coupling" in myosin, equilibrium active-site simulations with explicit solvent have been carried out to probe the behavior of the motor domain as functions of the nucleotide chemical state and conformation of the converter/relay helix. In conjunction with previous studies of ATP hydrolysis with different active-site conformations and normal mode analysis of structural flexibility, the results help establish an energetics-based framework for understanding the mechanochemical coupling. It is proposed that the activation of hydrolysis does not require the rotation of the lever arm per se, but the two processes are tightly coordinated because both strongly couple to the open/close transition of the active site. The underlying picture involves shifts in the dominant population of different structural motifs as a consequence of changes elsewhere in the motor domain. The contribution of this work and the accompanying paper [] is to propose the actual mechanism behind these "population shifts" and residues that play important roles in the process. It is suggested that structural flexibilities at both the small and large scales inherent to the motor domain make it possible to implement tight couplings between different structural motifs while maintaining small free-energy drops for processes that occur in the detached states, which is likely a feature shared among many molecular motors. The significantly different flexibility of the active site in different X-ray structures with variable level arm orientations supports the notation that external force sensed by the lever arm may transmit into the active site and influence the chemical steps (nucleotide

  6. Recent Experience Using Active Love Wave Techniques to Characterize Seismographic Station Sites

    Martin, A. J.; Yong, A.; Salomone, L.

    2014-12-01

    Active-source Love waves recorded by the multi-channel analysis of surface wave (MASLW) technique were recently analyzed in two site characterization projects. Between 2010 and 2011, the 2009 American Recovery and Reinvestment Act (ARRA) funded GEOVision to conduct geophysical investigations at 189 seismographic stations—185 in California and 4 in the Central Eastern U.S. (CEUS). The original project plan was to utilize active and passive Rayleigh wave-based techniques to obtain shear-wave velocity (VS) profiles to a minimum depth of 30 m and the time-averaged VS of the upper 30 meters (VS30). Early in the investigation it became evident that Rayleigh wave techniques, such as multi-channel analysis of surface waves (MASRW), were not effective at characterizing all sites. Shear-wave seismic refraction and MASLW techniques were therefore applied. The MASLW technique was deployed at a total of 38 sites, in addition to other methods, and used as the primary technique to characterize 22 sites, 5 of which were also characterized using Rayleigh wave techniques. In 2012, the Electric Power Research Institute funded characterization of 33 CEUS station sites. Based on experience from the ARRA investigation, both MASRW and MASLW data were acquired by GEOVision at 24 CEUS sites—the remaining 9 sites and 2 overlapping sites were characterized by University of Texas, Austin. Of the 24 sites characterized by GEOVision, 16 were characterized using MASLW data, 4 using both MASLW and MASRW data and 4 using MASRW data. Love wave techniques were often found to perform better, or at least yield phase velocity data that could be more readily modeled using the fundamental mode assumption, at shallow rock sites, sites with steep velocity gradients, and, sites with a thin, low velocity, surficial soil layer overlying stiffer sediments. These types of velocity structure often excite dominant higher modes in Rayleigh wave data, but not in Love wave data. At such sites, it may be possible

  7. Variants of the cell recognition site of fibronectin that retain attachment-promoting activity

    1985-01-01

    A tetrapeptide sequence, Arg-Gly-Asp-Ser, is the minimal structure recognized by cells in the large, adhesive glycoprotein fibronectin. We now have defined the structural requirements for this cell recognition site by testing several synthetic variants of the active tetrapeptide sequence. The conservative substitutions of lysine for arginine, alanine for glycine, or glutamic acid for aspartic acid each resulted in abrogation of the cell attachment-promoting activity characteristic of the natu...

  8. Screening Approach to the Activation of Soil and Contamination of Groundwater at Linear Proton Accelerator Sites

    Otto, Thomas

    The activation of soil and the contamination of groundwater at proton accelerator sites with the radionuclides 3H and 22Na are estimated with a Monte-Carlo calculation and a conservative soil- and ground water model. The obtained radionuclide concentrations show that the underground environment of future accelerators must be adequately protected against a migration of activation products. This study is of particular importance for the proton driver accelerator in the planned EURISOL facility.

  9. Study on the active sites of Cu-ZSM-5 in trichloroethylene catalytic combustion with air

    Cheng Hua Xu; Chuan Qi Liu; Yan Zhong; Xiu Zhou Yang; Jian Ying Liu; Ying Chun Yang; Zhi Xiang Ye

    2008-01-01

    The catalytic activity of Cu-ZSM-5 in trichloroethylene (TCE) combustion increases with the increasing skeletal Cu amount and however decreases with the increase of surface amorphous CuO,which is detected by infrared spectroscopy (IR) and diffuse reflectance ultraviolet-visible spectroscopy (DRS-UV-vis),therefore the skeletal Cu species are concluded to be the active sites for the TCE combustion.

  10. Remediation of uranium contaminated sites: clean-up activities in Serbia

    One of the serious environmental problems in Serbia represent sites contaminated with depleted uranium (DU) during past war activities. According to UNEP reports and our findings there are two types of contamination: (i) localized points of high, concentrated contamination where DU penetrators enter the soil, and (ii) low level of widespread DU contamination, which indicates that during the conflict DU dust was dispersed into the environment. Remediation of these sites is an urgent need because they represent a permanent threat to the population living in this area. Here we give a brief description of approaches commonly used in remediation of DU contaminated sites, and an overview of current clean-up activities performed in Serbia. (author)

  11. Identification and characterization of radioactively contaminated sites in Ukraine and planning for environmental restoration activities

    In the Pridniprovsk-Krivoy Rog region uranium, titanium, iron and manganese ores were mined and milled beginning in the 1950s. These activities have caused radioactive contamination of the environment at some sites. In recent times intensive works concerning the surveying of contaminated areas and substantiating the need for remediation have been initiated. The research methodologies applied and the results from radiation surveys are presented for the site of the first uranium mine in the Ukraine, for tailings originating from the Pridniprovsk Chemical Plant (PChP), for the recultivated dump-site of the former 'O'-mine, as well as for the wastes, raw materials and production of the Nicopol Ferro-Alloy Plant. The planning procedure for the remediation activities at the town of Zhovty Vody is described. (author)

  12. Active sites residues of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase (CPT-II).

    Nic a'Bháird, N; Yankovskaya, V; Ramsay, R R

    1998-01-01

    The carnitine acyltransferases which catalyse the reversible transfer of fatty acyl groups between carnitine and coenzyme A have been proposed to contain a catalytic histidine. Here, the chemical reactivity of active site groups has been used to demonstrate differences between the active sites of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase-II (CPT-II). Treatment of CPT-II with the histidine-selective reagent, diethyl pyrocarbonate (DEPC), resulted in simple linear pseudo-first-order kinetics. The reversal of the inhibition by hydroxylamine and the pKa (7.1) of the modified residue indicated that the residue was a histidine. The order of the inactivation kinetics showed that 1mol of histidine was modified per mol of CPT-II.When COT was treated with DEPC the kinetics of inhibition were biphasic with an initial rapid loss of activity followed by a slower loss of activity. The residue reacting in the faster phase of inhibition was not a histidine but possibly a serine. The modification of this residue did not lead to complete loss of activity suggesting that a direct role in catalysis is unlikely. It was deduced that the residue modified by DEPC in the slower phase was a lysine and indeed fluorodinitrobenzene (FDNB) inactivated COT with linear pseudo-first-order kinetics. The COT peptide containing the FDNB-labelled lysine was isolated and sequenced. Alignment of this sequence placed it 10 amino acids downstream of the putative active-site histidine. PMID:9480926

  13. Molecular Interactions Between the Active Sites of RGD (Arg-Gly-Asp with its Receptor (Integrine

    E. Jauregui

    2000-03-01

    Full Text Available A study of the molecular interactions between the active sites of RGD (Arg-Gly-Asp with it Receptor using simultaions is reported. Our calculations indicate that the guanidine-carboxylate complex is energetically favourd with respect to the guanidine-methyl tetrazole complex.

  14. 78 FR 8190 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    2013-02-05

    ... published the Notice in the Federal Register (77 FR 74218) inviting Federal, state, local government... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the Atlantic... Notice of Intent to Prepare an Environmental Assessment (EA) for Commercial Wind Leasing and...

  15. 77 FR 5830 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    2012-02-06

    ... (NOA) in the Federal Register (72 FR 62,672) of the Programmatic EIS for Alternative Energy Development... FR 30,616) of the EA for Issuance of Leases for Wind Resource Data Collection on the Outer... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the...

  16. 76 FR 40925 - Commercial Wind Lease Issuance and Site Characterization Activities on the Atlantic Outer...

    2011-07-12

    ... renewable energy leases (which includes reasonably foreseeable site characterization activities--geophysical...-Atlantic WEAs (76 FR 7226), which requested public input with regard to the identification of the important... Bureau of Ocean Energy Management, Regulation and Enforcement Commercial Wind Lease Issuance and...

  17. Dynamics of water molecules in the active-site cavity of human cytochromes P450

    Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars;

    2007-01-01

    We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot. In the...

  18. Organized Agents: Canadian Teacher Unions as Alternative Sites for Social Justice Activism

    Rottmann, Cindy

    2008-01-01

    Historically teachers' federations have been some of the major organizational sites for social justice leadership in K-12 public education. Despite this history of activism, social justice teacher unionism remains a relatively underdeveloped concept. This article merges four philosophical conceptions of social justice in education: liberal…

  19. Aberration-corrected imaging of active sites on industrial catalyst nanoparticles

    Gontard, Lionel Cervera; Chang, L-Y; Hetherington, CJD;

    2007-01-01

    Picture perfect: Information about the local topologies of active sites on commercial nanoparticles can be gained with atomic resolution through spherical-aberration-corrected transmission electron microscopy (TEM). A powder of Pt nanoparticles on carbon black was examined with two advanced TEM...

  20. Biosynthesis of selenosubtilisin: A novel way to target selenium into the active site of subtilisin

    LI Jing; LIU XiaoMan; JI YueTong; QI ZhenHui; GE Yan; XU JiaYun; LIU JunQiu; LUO GuiMin; SHEN JiaCong

    2008-01-01

    Glutathione peroxidase (GPx,EC1.11.1.9),an important anti-oxidative selenoenzyme,can catalyze the reduction of harmful hydroperoxides with concomitant glutathione,thereby protecting cells and other biological issues against oxidative damage.It captures considerable interest in redesign of its function for either the mechanism study or the pharmacological development as an antioxidant.In order to de-velop a general strategy for specifically targeting and operating selenium in active sites of enzymes,the catalytically essential residue selenocysteine (Sec) was first successfully bioincorporated into the catalytic center of subtilisin by using an auxotrophic expression system.The studies of the catalytic activity and the steady-state kinetics demonstrated that selenosubtilisin is an excellent GPx-like bio-catalyst.In comparison with the chemically modified method,biosynthesis exhibits obvious advan-tages:Sec could be site-directly incorporated into active sites of enzymes to overcome the non-speci-ficity generated by chemical modification.This study provides an important strategy for specifically targeting and operating selenium in the active site of an enzyme.

  1. 77 FR 3460 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2012-01-24

    ...This Notice announces the Department of Energy's (DOE) acceptance of claims in FY 2012 from eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of 1992. In FY 2009, Congress appropriated $70 million for Title X in the American Recovery and Reinvestment Act of 2009 (Recovery Act). Also in FY 2009, Congress provided $10 million......

  2. 78 FR 33908 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    2013-06-05

    ... identified Wind Energy Area (WEA) on the OCS offshore Rhode Island (RI) and Massachusetts (MA). The revised... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the.... BOEM may issue one or more commercial wind energy leases in the WEA. The competitive lease process...

  3. 40 CFR 35.6260 - Combining Cooperative Agreement sites and activities.

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Combining Cooperative Agreement sites and activities. 35.6260 Section 35.6260 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Contracts for Superfund Response Actions Combining Cooperative Agreements § 35.6260 Combining...

  4. The role of the catalysts with highly dispersed and isolated active sites in the selective oxidation of light hydrocarbons

    WANG Hongxuan; ZHAO Zhen

    2005-01-01

    This review summarizes the role of catalysts with highly dispersed and isolated active sites (active sites: supported atoms f≤0.5 % ) in the selective oxidation of light hydrocarbons, such as methane, ethane and propane, into oxygenatesand the epoxidation of olefins. The plausible structures of the highly dispersed and isolated active species, as well as their effects on the catalytic performances are discussed. The special physico-chemical properties and the functional mechanism of the catalysts with highly dispersed and isolated active sites, as well as the preparation, characterization of the catalysts with highly dispersed and isolated active sites and their applications in other types of reactions of lower hydrocarbons are summarized.

  5. Characterization and sequencing of the active site of 1-aminocyclopropane-1-carboxylate synthase

    The pyridoxal phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase the key enzyme in ethylene biosynthesis, is inactivated by its substrate S-adenosylmethionine (AdoMet). Apple ACC synthase was purified with an immunoaffinity gel, and its active site was probed with NaB3H4 or Ado[14C]Met. Peptide sequencing of both 3H- and 14C-labeled peptides revealed a common dodecapeptide of Ser-Leu-Ser-Xaa-Asp-Leu-Gly-Leu-Pro-Gly-Phe-Arg, where Xaa was the modified, radioactive residue in each case. Acid hydrolysis of the 3H-labeled enzyme released radioactive N-pyridoxyllysine, indicating that the active-site peptide contained lysine at position 4. Mass spectrometry of the 14C-labeled peptide indicated a protonated molecular ion at m/z 1390.6, from which the mass of Xaa was calculated to be 229, a number that is equivalent to the mass of a lysine residue alkylated by the 2-aminobutyrate portion of AdoMet, as we previously proposed. These results indicate that the same active-site lysine binds the PLP and convalently links to the 2-aminobutyrate portion of AdoMet during inactivation. The active site of tomato ACC synthase was probed in the same manner with Ado [14C]Met. Sequencing of the tomato active-site peptide revealed two highly conserved dodecapeptides; the minor peptide possessed a sequence identical to that of the apple enzyme, whereas the major peptide differed from the minor peptide in that methionine replaced leucine at position 6

  6. Active sites for methane activation in MgO and Li doped MgO

    Kwapień, Karolina

    2012-01-01

    Die vorliegende Dissertation präsentiert eine detaillierte quantenchemische Untersuchung der H-Abstraktion von Methan durch MgO und Li dotiertes MgO. Motiviert wurde die durch das UniCat-Excellenz-Cluster, welches sich zum Ziel gesetzt hat, die oxidative Kupplung von Methan (OCM) im Detail zu verstehen. Basierend auf der Hypothese, dass Li+O•– Spezies für den H-Abstraktion Schritt verantwortlich sind, wurden kleine kationische MgO- und Li dotierte MgO-Cluster (die O•– Sites modellieren) unt...

  7. A split active site couples cap recognition by Dcp2 to activation

    Floor, Stephen N.; Jones, Brittnee N.; Hernandez, Gail A.; Gross, John D.

    2010-01-01

    Decapping by Dcp2 is an essential step in 5′-3′ mRNA decay. In yeast, decapping requires an open-to-closed transition in Dcp2, though the link between closure and catalysis remains elusive. Here we show using NMR that cap binds conserved residues on both the catalytic and regulatory domains of Dcp2. Lesions in the cap-binding site on the regulatory domain reduce the catalytic step two orders of magnitude and block formation of the closed state whereas Dcp1 enhances the catalytic step by a fac...

  8. Integral Public Activities as a Support to the Site Selection Process for LILW Repository

    The first site selection process for low and intermediate level radioactive waste (LILW) repository took place between 1990 and 1993 in Slovenia was stopped unsuccessfully with very strong public opposition at local level, followed by political withdrawal on national level. As one of the consequences ARAO started to develop new approach to the site selection based also on the findings from sociology, psychology and other human sciences. The recommendations on public involvement and transparency were so strong that ARAO started with first limited public relation (PR) activities which later grew to the PR process which supports all technical activities in ARAO. Presently the PR process covers communication, information and research activities and assures careful planning, prompt responds and involvement of the highest responsible persons at ARAO. Integral public relation activities are divided in several parts. Majority of activities support the on-going site selection process where activities are presently focused on functioning of local partnerships developed as a basic communication tool to involve as much citizens and public as possible on local level. Presently two local partnerships are working in Krsko and Brezice community with clear role to enhance public involvement according to Aarchus convention. Each of the partnerships is organized in a specific way adjusted to the local needs. Communication activities are organized also for different other projects and are preparing the necessary basis for the work with different groups of stake holders and in different situations. As a foundation very broad information material, such as books, leaflets, reports, magazines, video cassettes, CD and DVD on the radioactive waste management is prepared and used for different purposes. We also try to be proactive with web pages and have a well organized visitors' center. Improvement of public relation process is achieved through constant survey and feed-back information

  9. Number of active transcription factor binding sites is essential for the Hes7 oscillator

    de Angelis Martin

    2006-02-01

    Full Text Available Abstract Background It is commonly accepted that embryonic segmentation of vertebrates is regulated by a segmentation clock, which is induced by the cycling genes Hes1 and Hes7. Their products form dimers that bind to the regulatory regions and thereby repress the transcription of their own encoding genes. An increase of the half-life of Hes7 protein causes irregular somite formation. This was shown in recent experiments by Hirata et al. In the same work, numerical simulations from a delay differential equations model, originally invented by Lewis, gave additional support. For a longer half-life of the Hes7 protein, these simulations exhibited strongly damped oscillations with, after few periods, severely attenuated the amplitudes. In these simulations, the Hill coefficient, a crucial model parameter, was set to 2 indicating that Hes7 has only one binding site in its promoter. On the other hand, Bessho et al. established three regulatory elements in the promoter region. Results We show that – with the same half life – the delay system is highly sensitive to changes in the Hill coefficient. A small increase changes the qualitative behaviour of the solutions drastically. There is sustained oscillation and hence the model can no longer explain the disruption of the segmentation clock. On the other hand, the Hill coefficient is correlated with the number of active binding sites, and with the way in which dimers bind to them. In this paper, we adopt response functions in order to estimate Hill coefficients for a variable number of active binding sites. It turns out that three active transcription factor binding sites increase the Hill coefficient by at least 20% as compared to one single active site. Conclusion Our findings lead to the following crucial dichotomy: either Hirata's model is correct for the Hes7 oscillator, in which case at most two binding sites are active in its promoter region; or at least three binding sites are active, in which

  10. Transcriptional activities of mammalian genomes at sites of recombination with foreign DNA

    The nucleotide sequences of several sites of recombination between adenovirus DNA and hamster, mouse, or human cell DNAs were determined. These sites of recombination had been cloned from adenovirus type 2 (Ad2)- or type 12 (Ad12)-transformed cells, from Ad12-induced tumor cells, or from a symmetric recombinant between Ad12 DNA and human cell DNA. One important precondition for the generation of recombinants between host and foreign DNAs might be the establishment of a chromatin configuration that permits access of foreign DNA and of the recombination machinery to cellular DNA. Such favorable chromatin structures might arise during cellular DNA replication or transcription or both. As a first approach toward investigating these more complex problems of foreign DNA insertion. The authors determined transcriptional activities of cellular DNA sequences at viral junction sites. The results presented demonstrate that the cellular DNA sequences involved in linkage to viral DNA at five completely different sites in DNA from three different species are transcribed into RNAs even in cells which have not been transformed or infected by adenovirus. These results are consistent with the notion that at least some of the cellular DNA sequences at sites of insertion of adenovirus (foreign) DNA are transcriptionally active and thus provide an opportunity for recombination

  11. Role of active sites in the reaction of methanol to olefin over modified ZSM-5 zeolite

    ZSM-5 zeolites were modified with metals Mg, K, Ca, Ba and La by an incipient impregnation and characterized by X-ray diffraction, N/sub 2/ adsorption and temperature - programmed desorption of NH/sub 3/ and CO/sub 2/. The obtained samples were investigated for their selectivity and catalytic stability in the methanol-to-olefin (MTO) reaction. The catalytic performance was influenced by the properties of active sites on the catalyst, which was indicated by the changes of the light olefin selectivity and catalytic stability in the methanol conversion. Correlating the reaction evaluation with the catalyst characterization, it can be seen that the catalyst with too strong basic sites shows an inferior catalytic performance. In addition, steam treatment further increased the catalytic performance, especially for Ca modified ZSM-5. It may be concluded that basic sites must suitably match with acidic sites for a special ZSM-5 in the methanol conversion and the formed active sites were relative with the modification metal based on the obtained results. (author)

  12. Ionizing Groups at the Active Site of the Alkaline Phosphatase from Ostrea cucullate

    CHEN Qiao; WANG Qin; LIAO Jinhua; CHEN Qingxi

    2006-01-01

    The ionizing groups at the active site of alkaline phosphatase (ALP, EC 3.1.3.1) from Ostrea cucullate were studied using kinetic methods. The ionization constant, pKe, of the ionizing groups at the active site of the enzyme was found to be 10.11 at 37.0℃ and the organic solvent, dioxin, had no effect on the pKe. The standard dissociation enthalpy (△Ho) was determined to be 10.57 kcal/mol (1 cal=4.18 J). The results show that the dissociation group of the enzyme active center is the з-NH3+ of lysine. Chemical modification of the enzyme by acetic anhydride and succinic anhydride demonstrates that the amino group is one of the enzyme's functional groups.

  13. Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    Parker, Shane M

    2014-01-01

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few {\\mu}Eh or less) with M = 128 in both cases, which is in contrast to conventional ab initio density matrix renormalization group.

  14. Communication: Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    Parker, Shane M.; Shiozaki, Toru [Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208 (United States)

    2014-12-07

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE{sub h} or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.

  15. Communication: Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μEh or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation

  16. Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome.

    El Sayyed, Hafez; Le Chat, Ludovic; Lebailly, Elise; Vickridge, Elise; Pages, Carine; Cornet, Francois; Cosentino Lagomarsino, Marco; Espéli, Olivier

    2016-05-01

    Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle. PMID:27171414

  17. Regulatory inspection activities on nuclear power plant sites during construction in the United Kingdom

    The work of regulatory inspection of the construction of the plant on the site is performed not only by the inspector who has been allocated to inspection duties for that site but also by the specialist staff who are involved with the safety assessment of the plant. The coordination of this work is described in the paper and examples are given of inspection activities associated with the enforcement requirements of license conditions as well as those related to the inspection of the plant itself

  18. Technical basis for classification of low-activity waste fraction from Hanford site tanks

    Petersen, C.A., Westinghouse Hanford

    1996-07-17

    The overall objective of this report is to provide a technical basis to support a U.S. Nuclear Regulatory Commission determination to classify the low-activity waste from the Hanford Site single-shell and double-shell tanks as `incidental` wastes after removal of additional radionuclides and immobilization.The proposed processing method, in addition to the previous radionuclide removal efforts, will remove the largest practical amount of total site radioactivity, attributable to high-level wastes, for disposal in a deep geologic repository. The remainder of the waste would be considered `incidental` waste and could be disposed onsite.

  19. Kinetic model of ethopropazine interaction with horse serum butyrylcholinesterase and its docking into the active site.

    Golicnik, Marko; Sinko, Goran; Simeon-Rudolf, Vera; Grubic, Zoran; Stojan, Jure

    2002-02-01

    The action of a potent tricyclic cholinesterase inhibitor ethopropazine on the hydrolysis of acetylthiocholine and butyrylthiocholine by purified horse serum butyrylcholinesterase (EC 3.1.1.8) was investigated at 25 and 37 degrees C. The enzyme activities were measured on a stopped-flow apparatus and the analysis of experimental data was done by applying a six-parameter model for substrate hydrolysis. The model, which was introduced to explain the kinetics of Drosophila melanogaster acetylcholinesterase [Stojan et al. (1998) FEBS Lett. 440, 85-88], is defined with two dissociation constants and four rate constants and can describe both cooperative phenomena, apparent activation at low substrate concentrations and substrate inhibition by excess of substrate. For the analysis of the data in the presence of ethopropazine at two temperatures, we have enlarged the reaction scheme to allow primarily its competition with the substrate at the peripheral site, but the competition at the acylation site was not excluded. The proposed reaction scheme revealed, upon analysis, competitive effects of ethopropazine at both sites; at 25 degrees C, three enzyme-inhibitor dissociation constants could be evaluated; at 37 degrees C, only two constants could be evaluated. Although the model considers both cooperative phenomena, it appears that decreased enzyme sensitivity at higher temperature, predominantly for the ligands at the peripheral binding site, makes the determination of some expected enzyme substrate and/or inhibitor complexes technically impossible. The same reason might also account for one of the paradoxes in cholinesterases: activities at 25 degrees C at low substrate concentrations are higher than at 37 degrees C. Positioning of ethopropazine in the active-site gorge by molecular dynamics simulations shows that A328, W82, D70, and Y332 amino acid residues stabilize binding of the inhibitor. PMID:11811945

  20. Assessment of national systems for obtaining local acceptance of nuclear waste management siting activities

    On behalf of the United States Department of Energy (DOE), International Energy Associates Limited (IEAL) of Washington, D.C. has conducted surveys and analyses of fourteen countries' plans and approaches for dealing with the problems of obtaining local siting acceptance for nuclear waste management facilities. It was determined that the following elements of the formal systems generally facilitate and/or expedite waste management siting decisions: (1) a clear-cut pro-nuclear power position on the part of the government; (2) a willingness on the part of the central government to exert (with prudence and restraint) its pre-emptive rights in nuclear matters; (3) political structures in which the heads of regional or provincial governments are appointed by the central government; (4) national laws that link reactor licensing with a detailed plan for waste management; (5) an established and stable policy with regard to reprocessing. In contrast, it was determined that the following elements of the formal system generally hinder waste management siting activities: (1) historically strong local land used veto laws; (2) the use of national referenda for making nuclear decisions; (3) requirements for public hearings. The informal approaches fall into the following five categories: (1) political: e.g. assertion of will by political leaders, activities to enlist support of local politicians, activities to broaden involvement in decision-making; (2) economic: e.g. emphasis on normal benefits, provision for additional economic benefits; (3) siting: e.g. at or near existing nuclear facilities, on government or utility property, at multiple locations to spread the political burden; (4) timing: e.g. decoupling drilling activities from ultimate repository site decision, deliberate deferral to (long-range) future; (5) education: e.g. creation of special government programmes, enlisting of media support

  1. Linde FUSRAP Site Remediation: Engineering Challenges and Solutions of Remedial Activities on an Active Industrial Facility - 13506

    The Linde FUSRAP Site (Linde) is located in Tonawanda, New York at a major research and development facility for Praxair, Inc. (Praxair). Successful remediation activities at Linde combines meeting cleanup objectives of radiological contamination while minimizing impacts to Praxair business operations. The unique use of Praxair's property coupled with an array of active and abandoned utilities poses many engineering and operational challenges; each of which has been overcome during the remedial action at Linde. The U.S. Army Corps of Engineers - Buffalo District (USACE) and CABRERA SERVICES, INC. (CABRERA) have successfully faced engineering challenges such as relocation of an aboveground structure, structural protection of an active water line, and installation of active mechanical, electrical, and communication utilities to perform remediation. As remediation nears completion, continued success of engineering challenges is critical as remaining activities exist in the vicinity of infrastructure essential to business operations; an electrical substation and duct bank providing power throughout the Praxair facility. Emphasis on engineering and operations through final remediation and into site restoration will allow for the safe and successful completion of the project. (authors)

  2. Lightweight cryptography for constrained devices

    Alippi, Cesare; Bogdanov, Andrey; Regazzoni, Francesco

    2014-01-01

    Lightweight cryptography is a rapidly evolving research field that responds to the request for security in resource constrained devices. This need arises from crucial pervasive IT applications, such as those based on RFID tags where cost and energy constraints drastically limit the solution...... complexity, with the consequence that traditional cryptography solutions become too costly to be implemented. In this paper, we survey design strategies and techniques suitable for implementing security primitives in constrained devices....

  3. Active-site titration analysis of surface influence on immobilized Candida antarctica Lipase B activity

    Matrix morphology and surface polarity effects were investigated for Candida antarctica lipase B immobilization. Measurements of the amount of lipase immobilized (bicinchoninic acid method) and the catalyst’s tributyrin hydrolysis activity, coupled with a determination of the lipase’s functional fr...

  4. RCRA and CERCLA requirements affecting cleanup activities at a federal facility superfund site

    The Fernald Environmental Management Project (FEMP) achieved success on an integrated groundwater monitoring program which addressed both RCRA and CERCLA requirements. The integrated plan resulted in a cost savings of approximately $2.6 million. At present, the FEMP is also working on an integrated closure process to address Hazardous Waste Management Units (HWMUs) at the site. To date, Ohio EPA seems willing to discuss an integrated program with some stipulations. If an integrated program is implemented, a cost savings of several million dollars will be realized since the CERCLA documents can be used in place of a RCRA closure plan. The success of an integrated program at the FEMP is impossible without the support of DOE and the regulators. Since DOE is an owner/operator of the facility and Ohio EPA regulates hazardous waste management activities at the FEMP, both parties must be satisfied with the proposed integration activities. Similarly, US EPA retains CERCLA authority over the site along with a signed consent agreement with DOE, which dictates the schedule of the CERCLA activities. Another federal facility used RCRA closure plans to satisfy CERCLA activities. This federal facility was in a different US EPA Region than the FEMP. While this approach was successful for this site, an integrated approach was required at the FEMP because of the signed Consent Agreement and Consent Decree. For federal facilities which have a large number of HWMUs along with OUs, an integrated approach may result in a timely and cost-effective cleanup

  5. Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase.

    Kiss, András L; Palló, Anna; Náray-Szabó, Gábor; Harmat, Veronika; Polgár, László

    2008-05-01

    It is widely accepted that the catalytic activity of serine proteases depends primarily on the Asp-His-Ser catalytic triad and other residues within the vicinity of this motif. Some of these residues form the oxyanion binding site that stabilizes the tetrahedral intermediate by hydrogen bonding to the negatively charged oxyanion. In acylaminoacyl peptidase from the thermophile Aeropyrum pernix, the main chain NH group of Gly369 is one of the hydrogen bond donors forming the oxyanion binding site. The side chain of His367, a conserved residue in acylaminoacyl peptidases across all species, fastens the loop holding Gly369. Determination of the crystal structure of the H367A mutant revealed that this loop, including Gly369, moves away considerably, accounting for the observed three orders of magnitude decrease in the specificity rate constant. For the wild-type enzyme ln(k(cat)/K(m)) vs. 1/T deviates from linearity indicating greater rate enhancement with increasing temperature for the dissociation of the enzyme-substrate complex compared with its decomposition to product. In contrast, the H367A variant provided a linear Arrhenius plot, and its reaction was associated with unfavourable entropy of activation. These results show that a residue relatively distant from the active site can significantly affect the catalytic activity of acylaminoacyl peptidase without changing the overall structure of the enzyme. PMID:18325786

  6. Progress report on decommissioning activities at the Fernald Environmental Management Project (FEMP) site

    NONE

    1998-07-01

    The Fernald Environmental Management Project (FEMP), is located about 18 miles northwest of Cincinnati, Ohio. Between 1953 and 1989, the facility, then called the Feed Material Production Center or FMPC, produced uranium metal products used in the eventual production of weapons grade material for use by other US Department of Energy (DOE) sites. In 1989, FMPC`s production was suspended by the federal government in order to focus resources on environmental restoration versus defense production. In 1992, Fluor Daniel Fernald assumed responsibility for managing all cleanup activities at the FEMP under contract to the DOE. In 1990, as part of the remediation effort, the site was divided into five operable units based on physical proximity of contaminated areas, similar amounts of types of contamination, or the potential for a similar technology to be used in cleanup activities. This report continues the outline of the decontamination and decommissioning (D and D) activities at the FEMP site Operable Unit 3 (OU3) and provides an update on the status of the decommissioning activities. OU3, the Facilities Closure and Demolition Project, involves the remediation of more than 200 uranium processing facilities. The mission of the project is to remove nuclear materials stored in these buildings, then perform the clean out of the buildings and equipment, and decontaminate and dismantle the facilities.

  7. Progress report on decommissioning activities at the Fernald Environmental Management Project (FEMP) site

    The Fernald Environmental Management Project (FEMP), is located about 18 miles northwest of Cincinnati, Ohio. Between 1953 and 1989, the facility, then called the Feed Material Production Center or FMPC, produced uranium metal products used in the eventual production of weapons grade material for use by other US Department of Energy (DOE) sites. In 1989, FMPC's production was suspended by the federal government in order to focus resources on environmental restoration versus defense production. In 1992, Fluor Daniel Fernald assumed responsibility for managing all cleanup activities at the FEMP under contract to the DOE. In 1990, as part of the remediation effort, the site was divided into five operable units based on physical proximity of contaminated areas, similar amounts of types of contamination, or the potential for a similar technology to be used in cleanup activities. This report continues the outline of the decontamination and decommissioning (D and D) activities at the FEMP site Operable Unit 3 (OU3) and provides an update on the status of the decommissioning activities. OU3, the Facilities Closure and Demolition Project, involves the remediation of more than 200 uranium processing facilities. The mission of the project is to remove nuclear materials stored in these buildings, then perform the clean out of the buildings and equipment, and decontaminate and dismantle the facilities

  8. Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site

    Misquitta Stephanie A

    2004-02-01

    Full Text Available Abstract Background Glutaminyl cyclase (QC forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP and mutated the apparent active site residues to assess their role in QC catalysis. Results The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence of the disulfide. Mutagenesis of the six active site residues present in both 1AMP and QC reveal essential roles for the two histidines (140 and 330, QC numbering and the two glutamates (201 and 202, while the two aspartates (159 and 248 appear to play no catalytic role. ICP-MS analysis shows less than stoichiometric zinc (0.3:1 in the purified enzyme. Conclusions We conclude that human pituitary glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site residues. In contrast to the aminopeptidase, however, QC does not appear to require zinc for enzymatic activity.

  9. Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum

    Udatha, D.B.R.K. Gupta; Madsen, Karina Marie; Panagiotou, Gianni; Olsson, Lisbeth

    2015-01-01

    The catalytic residues in carbohydrate esterase enzyme families constitute a highly conserved triad: serine, histidine and aspartic acid. This catalytic triad is generally located in a very sharp turn of the protein backbone structure, called the nucleophilic elbow and identified by the consensus...... sequence GXSXG. An esterase from Sorangium cellulosum Soce56 that contains five nucleophilic elbows was cloned and expressed in Escherichia coli and the function of each nucleophilic elbowed site was characterized. In order to elucidate the function of each nucleophilic elbow, site directed mutagenesis was...... used to generate variants with deactivated nucleophilic elbows and the functional promiscuity was analyzed. In silico analysis together with enzymological characterization interestingly showed that each nucleophilic elbow formed a local active site with varied substrate specificities and affinities. To...

  10. Role of a cysteine residue in the active site of ERK and the MAPKK family

    Kinases of mitogen-activated protein kinase (MAPK) cascades, including extracellular signal-regulated protein kinase (ERK), represent likely targets for pharmacological intervention in proliferative diseases. Here, we report that FR148083 inhibits ERK2 enzyme activity and TGFβ-induced AP-1-dependent luciferase expression with respective IC50 values of 0.08 and 0.05 μM. FR265083 (1'-2' dihydro form) and FR263574 (1'-2' and 7'-8' tetrahydro form) exhibited 5.5-fold less and no activity, respectively, indicating that both the α,β-unsaturated ketone and the conformation of the lactone ring contribute to this inhibitory activity. The X-ray crystal structure of the ERK2/FR148083 complex revealed that the compound binds to the ATP binding site of ERK2, involving a covalent bond to Sγ of ERK2 Cys166, hydrogen bonds with the backbone NH of Met108, Nζ of Lys114, backbone C=O of Ser153, Nδ2 of Asn154, and hydrophobic interactions with the side chains of Ile31, Val39, Ala52, and Leu156. The covalent bond motif in the ERK2/FR148083 complex assures that the inhibitor has high activity for ERK2 and no activity for other MAPKs such as JNK1 and p38MAPKα/β/γ/δ which have leucine residues at the site corresponding to Cys166 in ERK2. On the other hand, MEK1 and MKK7, kinases of the MAPKK family which also can be inhibited by FR148083, contain a cysteine residue corresponding to Cys166 of ERK2. The covalent binding to the common cysteine residue in the ATP-binding site is therefore likely to play a crucial role in the inhibitory activity for these MAP kinases. These findings on the molecular recognition mechanisms of FR148083 for kinases with Cys166 should provide a novel strategy for the pharmacological intervention of MAPK cascades

  11. Spitzer observations of Abell 1763 - II: Constraining the nature of activity in the cluster-feeding filament with VLA and XMM-Newton data

    Edwards, Louise O V; Frayer, David T; Neto, Gastao B Lima; Durret, Florence

    2010-01-01

    The Abell 1763 superstructure at z=0.23 contains the first galaxy filament to be directly detected using mid-infrared observations. Our previous work has shown that the frequency of starbursting galaxies, as characterized by 24{\\mu}m emission is much higher within the filament than at either the center of the rich galaxy cluster, or the field surrounding the system. New VLA and XMM-Newton data are presented here. We use the radio and X-ray data to examine the fraction and location of active galaxies, both active galactic nuclei (AGN) and starbursts. The radio far-infrared correlation, X-ray point source location, IRAC colors, and quasar positions are all used to gain an understanding of the presence of dominant AGN. We find very few MIPS-selected galaxies that are clearly dominated by AGN activity. Most radio selected members within the filament are starbursts. Within the supercluster, 3 of 8 spectroscopic members detected both in the radio and in the mid-infrared are radio-bright AGN. They are found at or ne...

  12. Soil pollution with trace elements at selected sites in Romania studied by instrumental neutron activation analysis

    Instrumental neutron activation analysis (INAA) was used to determine concentrations of 42 elements in samples of surface soil collected at seven sites polluted from various anthropogenic activities and a control site in a relatively clean area. Elements studied were Ag, Al, As, Au, Ba, Br, Ca, Cd, Ce, Co, Cr, Cs, Eu, Fe, Gd, Hf, Hg, K, La, Lu, Mg, Mn, Mo, Na, Nd, Ni, Rb, Sb, Sc, Se, Sm, Sr, Ta, Tb, Th, Ti, U, V, W, Yb, Zn, and Zr. The results are compared with data for trace elements atmospheric deposition in lichen transplants from the same sites. The most severe soil contamination was observed at Copsa Mica from non-ferrous metallurgy. Appreciable soil contamination was also indicated at Baia Mare (non-ferrous mining and metallurgy), Deva (coal-fired power plant, cement and building materials industry), Galati (ferrous metallurgy), Magurele and Afumati (general urban pollution), and Oradea (chemical and light industries). In most cases excessive levels of toxic metals in soils matched correspondingly high values in lichen transplants. Compared to Romanian norms, legal upper limits were exceeded for Zn and Cd at Copsa Mica. Also, As and Sb occurred in excessive levels at given sites. (orig.)

  13. Assessment of Tritium Activity in Groundwater at the Nuclear Objects Sites in Lithuania

    Vigilija Cidzikienė

    2014-01-01

    Full Text Available The assessment of nuclear objects sites in Lithuania, including groundwater characterization, took place in the last few years. Tritium activity in groundwater is a very useful tool for determining how groundwater systems function. Natural and artificial tritium was measured in 8 wells in different layers (from 1.5 to 15 meters depth. The results were compared with other regions of Lithuania also. The evaluated tritium activities varied from 1.8 to 6.4 Bq/L at nuclear objects sites in Lithuania and they are coming to background level (1.83 Bq/L and other places in Lithuania. The data show, that groundwater at the nuclear power objects sites is not contaminated with artificial tritium. In this work, the vertical tritium transfer from soil water to the groundwater well at nuclear objects site was estimated. The data show that the main factor for vertical tritium transfer to the well depends on the depth of wells.

  14. Structure/function correlations over binuclear non-heme iron active sites.

    Solomon, Edward I; Park, Kiyoung

    2016-09-01

    Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed. PMID:27369780

  15. Soil pollution with trace elements at selected sites in Romania studied by instrumental neutron activation analysis

    Pantelica, A. [Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH), Magurele, Ilfov County (Romania); Carmo Freitas, M. do [Technological and Nuclear Institute (ITN), Sacavem (Portugal); Ene, A. [Dunarea de Jos Univ. of Galati (Romania). Dept. of Chemistry, Physics and Environment; Steinnes, E. [Norwegian Univ. of Science and Technology, Trondheim (Norway). Dept. of Chemistry

    2013-03-01

    Instrumental neutron activation analysis (INAA) was used to determine concentrations of 42 elements in samples of surface soil collected at seven sites polluted from various anthropogenic activities and a control site in a relatively clean area. Elements studied were Ag, Al, As, Au, Ba, Br, Ca, Cd, Ce, Co, Cr, Cs, Eu, Fe, Gd, Hf, Hg, K, La, Lu, Mg, Mn, Mo, Na, Nd, Ni, Rb, Sb, Sc, Se, Sm, Sr, Ta, Tb, Th, Ti, U, V, W, Yb, Zn, and Zr. The results are compared with data for trace elements atmospheric deposition in lichen transplants from the same sites. The most severe soil contamination was observed at Copsa Mica from non-ferrous metallurgy. Appreciable soil contamination was also indicated at Baia Mare (non-ferrous mining and metallurgy), Deva (coal-fired power plant, cement and building materials industry), Galati (ferrous metallurgy), Magurele and Afumati (general urban pollution), and Oradea (chemical and light industries). In most cases excessive levels of toxic metals in soils matched correspondingly high values in lichen transplants. Compared to Romanian norms, legal upper limits were exceeded for Zn and Cd at Copsa Mica. Also, As and Sb occurred in excessive levels at given sites. (orig.)

  16. The active sites in the heterogeneous Baeyer-Villiger oxidation of cyclopentanone by hydrotalcite catalysts

    Ueno, Shinji; Ebitani, Kohki; Ookubo, Akira; Kaneda, Kiyotomi

    1997-11-01

    The active sites of hydrotalcites, [ Mg1-x2+Alx3+( OH) 2] x+[ Ax/nn-·m H 2O ] x-, A″ n-; CO 32-, Cl -, etc., were studied in the heterogeneous Baeyer-Villiger oxidation of cyclopentanone to δ-valerolactone with a combination oxidant system of molecular oxygen and benzaldehyde (O 2/benzaldehyde) in a 1,2-dichloroethane solvent. The hydrotalcites with different basicity were prepared by changing element ratios of Al 3+ to Mg 2+ in the Brucite-like layer and by changing anionic compounds (CO 32-, Cl -, and SO 42-) in the interlayer. The basicities of hydrotalcites were evaluated by measuring the calorimetric heats of benzoic acid adsorption and the zeta-potential of potassium chloride and by the indicator titration method. Yields of δ-valerolactone were almost proportional to the basicities of hydrotalcites, i.e., the heats of benzoic acid adsorption on hydrotalcites, which suggests that basic sites of hydrotalcites are active sites for the oxidation. Yields of δ-valerolactone were also dependent on the basicities of hydrotalcites using m-chloroperbenzoic acid ( m-CPBA) as an oxidant instead of O 2/benzaldehyde. Basic sites of hydrotalcites play an important role in the oxygen transfer from perbenzoic acid to ketone.

  17. 78 FR 21352 - Update on Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2013-04-10

    ... on Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY... reimbursement for cleanup work performed by licensees at eligible uranium and thorium processing sites in... licensees of eligible uranium and thorium processing sites. If licensees submit claims in FY 2013,...

  18. Characterization of the interactions between the active site of a protein tyrosine kinase and a divalent metal activator

    Ayrapetov Marina K

    2005-11-01

    Full Text Available Abstract Background Protein tyrosine kinases are important enzymes for cell signalling and key targets for anticancer drug discovery. The catalytic mechanisms of protein tyrosine kinase-catalysed phosphorylation are not fully understood. Protein tyrosine kinase Csk requires two Mg2+ cations for activity: one (M1 binds to ATP, and the other (M2 acts as an essential activator. Results Experiments in this communication characterize the interaction between M2 and Csk. Csk activity is sensitive to pH in the range of 6 to 7. Kinetic characterization indicates that the sensitivity is not due to altered substrate binding, but caused by the sensitivity of M2 binding to pH. Several residues in the active site with potential of binding M2 are mutated and the effect on metal activation studied. An active mutant of Asn319 is generated, and this mutation does not alter the metal binding characteristics. Mutations of Glu236 or Asp332 abolish the kinase activity, precluding a positive or negative conclusion on their role in M2 coordination. Finally, the ability of divalent metal cations to activate Csk correlates to a combination of ionic radius and the coordination number. Conclusion These studies demonstrate that M2 binding to Csk is sensitive to pH, which is mainly responsible for Csk activity change in the acidic arm of the pH response curve. They also demonstrate critical differences in the metal activator coordination sphere in protein tyrosine kinase Csk and a protein Ser/Thr kinase, the cAMP-dependent protein kinase. They shed light on the physical interactions between a protein tyrosine kinase and a divalent metal activator.

  19. Synthesis of supported bimetallic nanoparticles with controlled size and composition distributions for active site elucidation

    Hakim, Sikander H.; Sener, Canan; Alba Rubio, Ana C.; Gostanian, Thomas M.; O' neill, Brandon J; Ribeiro, Fabio H.; Miller, Jeffrey T.; Dumesic, James A

    2015-08-01

    Elucidation of active sites in supported bimetallic catalysts is complicated by the high level of dispersity in the nanoparticle size and composition that is inherent in conventional methods of catalyst preparation. We present a synthesis strategy that leads to highly dispersed, bimetallic nanoparticles with uniform particle size and composition by means of controlled surface reactions. We demonstrate the synthesis of three systems, RhMo, PtMo, and RhRe, consisting of a highly reducible metal with an oxophilic promoter. These catalysts are characterized by FTIR, CO chemisorption, STEM/EDS, TPR, and XAS analysis. The catalytic properties of these bimetallic nanoparticles were probed for the selective CO hydrogenolysis of (hydroxymethyl)tetrahydropyran to produce 1,6 hexanediol. Based on the characterization results and reactivity trends, the active sites in the hydrogenolysis reaction are identified to be small ensembles of the more noble metal (Rh, Pt) adjacent to highly reduced moieties of the more oxophilic metal (Mo, Re).

  20. Use of the Multi-Agency Radiological Laboratory Analytical Protocols Manual (MARLAP) for site cleanup activities

    MARLAP is being developed as a multi-agency guidance manual for project managers and radioanalytical laboratories. The document uses a performance based approach and will provide guidance and a framework to assure that laboratory radioanalytical data meets the specific project or program needs and requirements. MARLAP supports a wide range of data collection activities including site characterization and compliance demonstration activities. Current participants include: US Environmental Protection Agency (EPA), US Department of Energy (DOE), US Nuclear Regulatory Commission (NRC), US Department of Defense (DoD), US National Institutes of Standards and Technology (NIST), US Geologic Survey (USGS), US Food and Drug Administration (FDA), Commonwealth of Kentucky, and the State of California. MARLAP is the radioanalytical laboratory counterpart to the Multi-Agency Radiological Survey and Site Investigation Manual (MARSSIM). MARLAP is currently in a preliminary draft stage. (author)

  1. Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

    Wang, P-H; De Sancho, D; Best, R B; Blumberger, J

    2016-01-01

    The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates. PMID:27497172

  2. Chemistry related to the actives sites of the [Fe]- and [FeFe]-hydrogenases

    Hill, Amanda D.

    2016-01-01

    Hydrogenases are an important group of enzymes found in a range of microorganisms. There are three phylogenetically distinct classes of hydrogenase all of which feature iron-containing complexes. The work contained in this thesis has two main focuses: the synthesis and characterization of novel mimics of the [Fe]-hydrogenase active site, and spectroscopic studies on the interaction of iron-sulfur clusters with CO and CN− relevant to the biosynthesis of the H-cluster of [FeFe]-hydrogenase. ...

  3. Interaction of mining activities and aquatic environment: A review from Greek mine sites.

    Vasileiou, Eleni; Kallioras, Andreas

    2016-04-01

    In Greece a significant amount of mineral and ore deposits have been recorded accompanied by large industrial interest and a long mining history. Today many active and/or abandoned mine sites are scattered within the country; while mining activities take place in different sites for exploiting various deposits (clay, limestone, slate, gypsum, kaolin, mixed sulphide ores (lead, zinc, olivine, pozzolan, quartz lignite, nickel, magnesite, aluminum, bauxite, gold, marbles etc). The most prominent recent ones are: (i) the lignite exploitation that is extended in the area of Ptolemais (Western Macedonia) and Megalopolis (Central Peloponnese); and (ii) the major bauxite deposits located in central Greece within the Parnassos-Ghiona geotectonic zone and on Euboea Island. In the latter area, significant ores of magnesite were exploited and mixed sulphide ores. Centuries of intensive mining exploitation and metallurgical treatment of lead-silver deposits in Greece, have also resulted in significant abandoned sites, such as the one in Lavrion. Mining activities in Lavrio, were initiated in ancient times and continued until the 1980s, resulting in the production of significant waste stockpiles deposited in the area, crucial for the local water resources. Ιn many mining sites, environmental pressures are also recorded after the mine closure to the aquatic environment, as the surface waters flow through waste dump areas and contaminated soils. This paper aims to the geospatial visualization of the mining activities in Greece, in connection to their negative (surface- and/or ground-water pollution; overpumping due to extensive dewatering practices) or positive (enhanced groundwater recharge; pit lakes, improvement of water budget in the catchment scale) impacts on local water resources.

  4. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2011-05-26

    ...This Notice announces revisions to the Department of Energy (DOE) acceptance of claims in FY 2011 from eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of 1992. In our Federal Register Notice of November 24, 2010 (75 FR 71677), the Department announced the closing date for the submission of claims in FY 2011 as April 29,......

  5. Identification of the provenience of Majolica from sites in the Caribbean using neutron activation analysis

    Olin, J.S.; Sayre, E.V.

    1975-01-01

    Tin-enamelled earthenware pottery from five early Spanish Colonial sites in the Dominican Republic and Venezuela were sampled and analyzed by neutron activation analysis in an attempt to determine whether these sherds had a common source. The tentative conclusion was that although several sources were indicated for the specimens analyzed the overall similarity in composition indicated that these sources were probably closely related. (JSR)

  6. Measurement of human tissue-type plasminogen activator by a two-site immunoradiometric assay

    A two-site immunoradiometric assay for human extrinsic (tissue-type) plasminogen activator was developed by using rabbit antibodies raised against plasminogen activator purified from human melanoma cell culture fluid. Samples of 100 μl containing 1 to 100 ng/ml plasminogen activator were incubated in the wells of polyvinyl chloride microtiter plates coated with antibody. The amount of bound extrinsic plasminogen activator was quantitated by the subsequent binding of 125I-labeled affinospecific antibody. The mean level of plasma samples taken at rest was 6.6 +/- 2.9 ng/ml (n = 54). This level increased approximately threefold by exhaustive physical exercise, venous occlusion, or infusion of DDAVP. Extrinsic plasminogen activator in plasma is composed of a fibrin-adsorbable and active component (1.9 +/- 1.1 ng/ml, n = 54, in resting conditions) and an inactive component that does not bind to a fibrin clot (probably extrinsic plasminogen activator-proteinase inhibitor complexes). The fibrin-adsorbable fraction increased approximately fivefold to eightfold after physical exercise, venous occlusion, or DDAVP injections. Potential applications of the immunoradiometric assay are illustrated by the measurement of extrinsic plasminogen activator in different tissue extracts, body fluids, and cell culture fluids and in oocyte translation products after injection with mRNA for plasminogen activator

  7. Days of dismantling activities of installations and rehabilitation of contaminated sites in France

    The objective of these days, organized by the section environment of the French society of radiation protection, is to present a panorama of the activities of nuclear installations dismantling and contaminated sites rehabilitation in France, by leaning in the same time on practical cases and by stating the French rule and the national and international recommendations on the subject. These days have also for object to approach the stakes associated with the sectors of waste management and the materials generated by these activities and in a more general way, the stakes to come for the different actors of the dismantling and the rehabilitation. (N.C.)

  8. Comparative active-site mutation study of human and Caenorhabditis elegans thymidine kinase 1

    Skovgaard, Tine; Uhlin, Ulla; Munch-Petersen, Birgitte

    2012-01-01

    ligands. To improve our understanding of TK1 substrate specificity, we performed a detailed, mutation-based comparative structure-function study of the active sites of two thymidine kinases: HuTK1 and Caenorhabditis elegans TK1 (CeTK1). Specifically, mutations were introduced into the hydrophobic pocket...... surrounding the substrate base. In CeTK1, some of these mutations led to increased activity with deoxycytidine and deoxyguanosine, two unusual substrates for TK1-like kinases. In HuTK1, mutation of T163 to S resulted in a kinase with a 140-fold lower K(m) for the antiviral nucleoside analogue 3'-azido-3...

  9. Reaction of argininosuccinase with bromomesaconic acid: role of an essential lysine in the active site

    We have undertaken studies on bovine liver argininosuccinase (L-argininosuccinate arginine-lyase with the active site-directed reagent bromo[U-14C]mesaconic acid, an analogue of fumaric acid. Reactivity, measured by enzyme inactivation, followed pseudo-first-order kinetics, and the rate increased with reagent concentration. Argininosuccinate completely protected the enzyme against inactivation, but neither arginine nor fumarate was protective. A plot of the degree of inactivation as a function of alkyl groups incorporated was extrapolated to 4 mol per mol of enzyme, or 1 mol per active site. After large-scale alkylation of the enzyme (and digestion with trypsin), two 14C-labeled tryptic peptides were isolated. These were chemically sequenced by the Edman method. The amino acid sequences proved to be identical with regions of the deduced amino acid sequences or argininosuccinases from human and yeast sources The 14C-labeled tryptic peptide in the active site region had the sequence Gly-Leu-Glu-Xaa-Ala-Gly-Leu-Leu-Thr-Lys; Xaa represents an unknown phenylthiohydantoin derivative detected in cycle 4. The corresponding amino acid was identified as lysine-51 on the basis of sequence similarity with human and yeast amino acid sequences in this region. The reaction of the enzyme with the alkylating agent and the specific protection against inactivation by argininosuccinate suggest that this lysine residue has an essential role in the binding of argininosuccinate to the enzyme and, consequently, is essential for catalysis

  10. Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.

    Xu, Kehan; Dedic, Emil; Brodersen, Ditlev E

    2016-07-01

    The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonuclease and has been shown to target initiator tRNA(fMet) in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892-899. © 2016 Wiley Periodicals, Inc. PMID:26833558

  11. Methods for Determining the Activity Concentration Calibration Factor for Ventilation Duct in Cyclotron Sites

    Cyclotrons are commonly used for production of radioactive isotopes for nuclear medicine purposes. The nuclear process requires installation of a ventilation stack. According to the regulations in many countries, the released activity should be monitored and controlled in order to limit air pollution. This requires a stuck radiation detector and determining a converting factor that will translate the radiation detector reading into activity concentration units. Calibrating the conversion factor is done mainly by releasing a known amount of activity. Having a preliminary estimation of the conversion factor, during the site construction stage, is an important option for the duct configuration design, in order to achieve the required detection sensitivity. An algorithm for estimating the stack concentration calibration factor in positron emitting isotopes producing sites was developed. The algorithm which is described in this article is based on three independent methods that consist of MCNP simulations analytical calculations and experimental setup with controlled static calibration releases of gaseous 18F which was produced especially for this purpose by the cyclotron site in Soreq Nuclear Research Center Israel. The specified methods applied on few stack sections with different shapes and sizes

  12. Radiological audit of remedial action activities at the processing site, transfer site, and Cheney disposal site Grand Junction, Colorado: Audit date, August 9--11, 1993. Final report

    1993-08-01

    The Uranium Mill Tailing Remedial Action (UMTRA) Project`s Technical Assistance Contractor (TAC) performed a radiological audit of the Remedial Action Contractor (RAC), MK-Ferguson and CWM Federal Environmental Services, Inc., at the processing site, transfer site, and Cheney disposal site in Grand Junction, Colorado. Jim Hylko and Bill James of the TAC conducted this audit August 9 through 11, 1993. Bob Cornish and Frank Bosiljevec represented the US Department of Energy (DOE). This report presents one programmatic finding, eleven site-specific observations, one good practice, and four programmatic observations.

  13. Hyperbolicity and Constrained Evolution in Linearized Gravity

    Matzner, R A

    2005-01-01

    Solving the 4-d Einstein equations as evolution in time requires solving equations of two types: the four elliptic initial data (constraint) equations, followed by the six second order evolution equations. Analytically the constraint equations remain solved under the action of the evolution, and one approach is to simply monitor them ({\\it unconstrained} evolution). Since computational solution of differential equations introduces almost inevitable errors, it is clearly "more correct" to introduce a scheme which actively maintains the constraints by solution ({\\it constrained} evolution). This has shown promise in computational settings, but the analysis of the resulting mixed elliptic hyperbolic method has not been completely carried out. We present such an analysis for one method of constrained evolution, applied to a simple vacuum system, linearized gravitational waves. We begin with a study of the hyperbolicity of the unconstrained Einstein equations. (Because the study of hyperbolicity deals only with th...

  14. Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

    Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele; Goedken, Eric R.; Gum, Rebecca J.; Borhani, David W.; Argiriadi, Maria; Groebe, Duncan R.; Jia, Yong; Clampit, Jill E.; Haasch, Deanna L.; Smith, Harriet T.; Wang, Sanyi; Song, Danying; Coen, Michael L.; Cloutier, Timothy E.; Tang, Hua; Cheng, Xueheng; Quinn, Christopher; Liu, Bo; Xin, Zhili; Liu, Gang; Fry, Elizabeth H.; Stoll, Vincent; Ng, Teresa I.; Banach, David; Marcotte, Doug; Burns, David J.; Calderwood, David J.; Hajduk, Philip J. (Abbott)

    2012-03-02

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in

  15. Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation.

    Yamano, Koji; Queliconi, Bruno B; Koyano, Fumika; Saeki, Yasushi; Hirokawa, Takatsugu; Tanaka, Keiji; Matsuda, Noriyuki

    2015-10-16

    Damaged mitochondria are eliminated through autophagy machinery. A cytosolic E3 ubiquitin ligase Parkin, a gene product mutated in familial Parkinsonism, is essential for this pathway. Recent progress has revealed that phosphorylation of both Parkin and ubiquitin at Ser(65) by PINK1 are crucial for activation and recruitment of Parkin to the damaged mitochondria. However, the mechanism by which phosphorylated ubiquitin associates with and activates phosphorylated Parkin E3 ligase activity remains largely unknown. Here, we analyze interactions between phosphorylated forms of both Parkin and ubiquitin at a spatial resolution of the amino acid residue by site-specific photo-crosslinking. We reveal that the in-between-RING (IBR) domain along with RING1 domain of Parkin preferentially binds to ubiquitin in a phosphorylation-dependent manner. Furthermore, another approach, the Fluoppi (fluorescent-based technology detecting protein-protein interaction) assay, also showed that pathogenic mutations in these domains blocked interactions with phosphomimetic ubiquitin in mammalian cells. Molecular modeling based on the site-specific photo-crosslinking interaction map combined with mass spectrometry strongly suggests that a novel binding mechanism between Parkin and ubiquitin leads to a Parkin conformational change with subsequent activation of Parkin E3 ligase activity. PMID:26260794

  16. A kinetic description for sodium and potassium effects on (Na+ plus K+)-adenosine triphosphatase: a model for a two-nonequivalent site potassium activation and an analysis of multiequivalent site models for sodium activation.

    Lindenmayer, G E; Schwartz, A; Thompson, H K

    1974-01-01

    1. Dissociation constants for sodium and potassium of a site that modulates the rate of ouabain-(Na(+)+K(+))-ATPase interaction were applied to models for potassium activation of (Na(+)+K(+))-ATPase. The constants for potassium (0.213 mM) and for sodium (13.7 mM) were defined, respectively, as activation constant, K(a) and inhibitory constant, K(i).2. Tests of the one- and the two-equivalent site models, that describe sodium and potassium competition, revealed that neither model adequately predicts the activation effects of potassium in the presence of 100 or 200 mM sodium.3. The potassium-activation data, obtained at low potassium and high sodium, were explained by a two-nonequivalent site model where the dissociation constants of the first site are 0.213 mM for potassium and 13.7 mM for sodium. The second site was characterized by dissociation constants of 0.091 mM for potassium and 74.1 mM for sodium.4. The two-nonequivalent site model adequately predicted the responses to concentrations of potassium between 0.25 and 5 mM in the presence of 100-500 mM sodium. At lower sodium concentrations the predicted responses formed an upper limit for the function of observed activities. This limit was reached at lower concentrations of potassium and higher concentrations of sodium, which inferred saturation of the sodium-activation sites with sodium.5. Sodium-activation data were corrected for sodium interaction with potassium-activation sites by use of the two-nonequivalent site model for potassium activation. Tests of equivalent site models suggested that the corrected data for sodium activation may be most consistent with a model that has three-equivalent sites. Other multiequivalent site models (n = 2, 4, 5 or 6), however, cannot be statistically eliminated as possibilities. The three-equivalent site activation model was characterized by dissociation constants of 1.39 mM for sodium and 11.7 mM for potassium. The system theoretically would be half-maximally activated by

  17. Morphometric, acoustic and lithofacies characterization of mud volcanoes in the Eastern Mediterranean: Toward a new approach and classification to constrain the regional distribution and activity of mud volcanoes?

    Flore, Mary; Sébastien, Migeon; Elia, d'Acremont; Alain, Rabaute; Silvia, Ceramicola; Daniel, Praeg; Christian, Blanpied

    2015-04-01

    On continental margins, several types of seabed features recording fluid circulation within the sediment column have already been recognized, including mud volcanoes, pockmarks, carbonates pavements and/or mounds and brine lakes. They can be associated to (a) thermogenic or biogenic fluids migrating along tectonic conduits, (b) dissociation of gas hydrates, or (c) dewatering of turbidite channels and mass-transport deposits. Although fluid-escape structures have been analyzed for the last two decades using diverse and complementary data, many questions are still debated about their morphologies/architectures, origin and formation, their temporal dynamic and the impact of the geodynamical context on their location/formation. In the Eastern Mediterranean, fluid seepages and in particular mud volcanoes, were identified in three geodynamical contexts including active margins (Calabrian accretionary prism and Mediterranean ridge) and highly-sedimented passive margin (Nil deep-sea fan). In this study, we follow a new approach allowing to (1) better quantify a broad set of morphological parameters that characterize the seabed fluid-escape structures, (2) propose an advance classification of these structures, the final goal being to test whether one or several morphological types of fluid-escape structures can be characteristic of one tectonic and sedimentological setting in the Eastern Mediterranean basin. To achieve this classification based on geophysical and geological analysis (morphometry, reflectivity, seismic r and lithofacies features), we used a broad homogenous dataset at the scale of the Eastern Mediterranean, including multibeam bathymetry, acoustic backscatter, 2D/3D seismic reflection, and sediment cores description and analysis. More than 500 mud volcano-like structures were identified based on one criterion or on the association of several criteria, while 40 of them were clearly proved to be mud volcanoes by coring. These structures exhibit different

  18. Three-dimensional representations of salt-dome margins at four active strategic petroleum reserve sites.

    Rautman, Christopher Arthur; Stein, Joshua S.

    2003-01-01

    Existing paper-based site characterization models of salt domes at the four active U.S. Strategic Petroleum Reserve sites have been converted to digital format and visualized using modern computer software. The four sites are the Bayou Choctaw dome in Iberville Parish, Louisiana; the Big Hill dome in Jefferson County, Texas; the Bryan Mound dome in Brazoria County, Texas; and the West Hackberry dome in Cameron Parish, Louisiana. A new modeling algorithm has been developed to overcome limitations of many standard geological modeling software packages in order to deal with structurally overhanging salt margins that are typical of many salt domes. This algorithm, and the implementing computer program, make use of the existing interpretive modeling conducted manually using professional geological judgement and presented in two dimensions in the original site characterization reports as structure contour maps on the top of salt. The algorithm makes use of concepts of finite-element meshes of general engineering usage. Although the specific implementation of the algorithm described in this report and the resulting output files are tailored to the modeling and visualization software used to construct the figures contained herein, the algorithm itself is generic and other implementations and output formats are possible. The graphical visualizations of the salt domes at the four Strategic Petroleum Reserve sites are believed to be major improvements over the previously available two-dimensional representations of the domes via conventional geologic drawings (cross sections and contour maps). Additionally, the numerical mesh files produced by this modeling activity are available for import into and display by other software routines. The mesh data are not explicitly tabulated in this report; however an electronic version in simple ASCII format is included on a PC-based compact disk.

  19. Functional properties of the two redox-active sites in yeast protein disulphide isomerase in vitro and in vivo

    Westphal, V; Darby, N J; Winther, Jakob R.

    1999-01-01

    Protein folding catalysed by protein disulphide isomerase (PDI) has been studied both in vivo and in vitro using different assays. PDI contains a CGHC active site in each of its two catalytic domains (a and a'). The relative importance of each active site in PDI from Saccharomyces cerevisiae (y...

  20. How peer-review constrains cognition

    Cowley, Stephen

    2015-01-01

    ‘cognition’ describes enabling conditions for flexible behavior, the practices of peer-review thus constrain knowledge-making. To pursue cognitive functions of peer-review, however, manuscripts must be seen as ‘symbolizations’, replicable patterns that use technologically enabled activity. On this bio-cognitive...... came to be re-aggregated: agonistic review drove reformatting of argument structure, changes in rhetorical ploys and careful choice of wordings. For this reason, the paper’s knowledge-claims can be traced to human activity that occurs in distributed cognitive systems. Peer-review is on the frontline in...

  1. Targeting mechanisms at sites of complement activation for imaging and therapy.

    Holers, V Michael

    2016-06-01

    The complement system plays a key role in many acute injury states as well as chronic autoimmune and inflammatory diseases. Localized complement activation and alternative pathway-mediated amplification on diverse target surfaces promote local recruitment of pro-inflammatory cells and elaboration of other mediators. Despite a general understanding of the architecture of the system, though, many of the mechanisms that underlie site-specific complement activation and amplification in vivo are incompletely understood. In addition, there is no capability yet to measure the level of local tissue site-specific complement activation in patients without performing biopsies to detect products using immunohistochemical techniques. Herein is reviewed emerging evidence obtained through clinical research studies of human rheumatoid arthritis along with translational studies of its disease models which demonstrate that several parallel mechanisms are involved in site-specific amplification of activation of the complement system in vivo. Among these processes are de-regulation of the alternative pathway, effector pathway-catalyzed amplification of proximal complement activation, recognition of injury-associated ligands by components of the lectin pathway, and engagement of pathogenic natural antibodies that recognize a limited set of injury-associated neoepitopes. Studies suggest that each of these inter-related processes can play key roles in amplification of complement-dependent injury on self-tissues in vivo. These findings, in addition to development of an imaging strategy described herein designed to quantitatively measure local complement C3 fixation, have relevance to therapeutic and diagnostic strategies targeting the complement system. PMID:25979851

  2. Modeling emissions and dispersion of contaminants from cleanup activities at a mixed waste site to estimate air impacts and risks

    The transport and dispersion of contaminants via the air pathway is a major concern during cleanup of contaminated sites. Impacts to air quality and human health during cleanup were evaluated for the Weldon Spring site by using site-specific information for source areas, activities, and receptor locations. In order to ensure protection of human health and the environment, results are being used to focus on those cleanup activities for which release controls should be emphasized

  3. Comparative analysis of the impact of geological activity on astronomical sites of the Canary Islands, Hawaii and Chile

    Eff-Darwich, A.; Garcia-Lorenzo, B.; Rodriguez-Losada, J. A.; de la Nuez, J.; Hernandez-Gutierrez, L. E.; Romero-Ruiz, M. C.

    2009-01-01

    An analysis of the impact of seismic and volcanic activity was carried out at selected astronomical sites, namely the observatories of El Teide (Tenerife, Canary Islands), Roque de los Muchachos (La Palma, Canary Islands), Mauna Kea (Hawaii) and Paranal (Chile) and the candidate site of Cerro Ventarrones (Chile). Hazard associated to volcanic activity is low or negligible at all sites, whereas seismic hazard is very high in Chile and Hawaii. The lowest geological hazard in both seismic and vo...

  4. Carbon sources and biogeochemical processes in Monticchio maar lakes, Mt Vulture volcano (southern Italy): New geochemical constrains of active degassing of mantle derived fluids

    Caracausi, A.; Nuccio, P. M.; Favara, R.; Grassa, F.

    2012-04-01

    Since the catastrophic releases of carbon dioxide from the African volcanic lakes Nyos and Monoun in the 1980s, the scientific community draw attention towards all those crater lakes able to accumulate massive amount of CO2, which could be catastrophically released following overturn of their deep waters. This implies a quantification of the gas accumulation rate into the lakes and the knowledge of recharge processes and their evolution in time. In fact the gaseous recharge in a lake occurs at alarming rates, when an active degassing of hazardous nature volatiles occurs into the lakes and the structure and dynamic of the lake permit the accumulation of gases into the water. The Monticchio lakes, LPM and LGM, occupies two maar craters formed during the last volcanic activity of Mt. Vulture occurred ˜ 140 000 years ago. LPM is a permanently stratified lake, with a thick deep volume of stagnant water and a shallower layer affected by seasonal overturn. On the contrary LGM is a monomittic lake with a complete overturn of the water during winter time. The major dissolved volatiles are methane and CO2. Dissolved helium is in trace amounts and its isotopic signature ranges between 6.1 and 5.3 Ra (Ra is the atmospheric 3He/4He isotopic ratio). These values are within the range of those measured in the olivine fluid inclusions (both of mantle xenoliths and dispersed in the pyroclastics) of LPM maar ejecta. During three years of investigations we observed that dissolved methane in the deep waters of LGM drastically decreases in wintertime as consequence of the complete overturn of the water. The isotopic signature of methane in the deepest portions of LGM (both sediment and water) is quite stable with time and highlights a biogenic origin, being produced both by acetate fermentation and by CO2-reduction in variable proportions. In contrast, a higher contribution of methane produced via CO2 reduction characterizes sediments at shallower depths. At LPM, there is a great

  5. Constraining UV continuum slopes of active galactic nuclei with cloudy models of broad-line region extreme-ultraviolet emission lines

    Moloney, Joshua [CASA, Department of Astrophysical and Planetary Sciences, University of Colorado, Boulder, CO 80309 (United States); Michael Shull, J., E-mail: joshua.moloney@colorado.edu, E-mail: michael.shull@colorado.edu [Also at Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA, UK. (United Kingdom)

    2014-10-01

    Understanding the composition and structure of the broad-line region (BLR) of active galactic nuclei (AGNs) is important for answering many outstanding questions in supermassive black hole evolution, galaxy evolution, and ionization of the intergalactic medium. We used single-epoch UV spectra from the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope to measure EUV emission-line fluxes from four individual AGNs with 0.49 ≤ z ≤ 0.64, two AGNs with 0.32 ≤ z ≤ 0.40, and a composite of 159 AGNs. With the CLOUDY photoionization code, we calculated emission-line fluxes from BLR clouds with a range of density, hydrogen ionizing flux, and incident continuum spectral indices. The photoionization grids were fit to the observations using single-component and locally optimally emitting cloud (LOC) models. The LOC models provide good fits to the measured fluxes, while the single-component models do not. The UV spectral indices preferred by our LOC models are consistent with those measured from COS spectra. EUV emission lines such as N IV λ765, O II λ833, and O III λ834 originate primarily from gas with electron temperatures between 37,000 K and 55,000 K. This gas is found in BLR clouds with high hydrogen densities (n {sub H} ≥ 10{sup 12} cm{sup –3}) and hydrogen ionizing photon fluxes (Φ{sub H} ≥ 10{sup 22} cm{sup –2} s{sup –1}).

  6. Altered binding of thioflavin t to the peripheral anionic site of acetylcholinesterase after phosphorylation of the active site by chlorpyrifos oxon or dichlorvos

    The peripheral anionic site of acetylcholinesterase, when occupied by a ligand, is known to modulate reaction rates at the active site of this important enzyme. The current report utilized the peripheral anionic site specific fluorogenic probe thioflavin t to determine if the organophosphates chlorpyrifos oxon and dichlorvos bind to the peripheral anionic site of human recombinant acetylcholinesterase, since certain organophosphates display concentration-dependent kinetics when inhibiting this enzyme. Incubation of 3 nM acetylcholinesterase active sites with 50 nM or 2000 nM inhibitor altered both the Bmax and Kd for thioflavin t binding to the peripheral anionic site. However, these changes resulted from phosphorylation of Ser203 since increasing either inhibitor from 50 nM to 2000 nM did not alter further thioflavin t binding kinetics. Moreover, the organophosphate-induced decrease in Bmax did not represent an actual reduction in binding sites, but instead likely resulted from conformational interactions between the acylation and peripheral anionic sites that led to a decrease in the rigidity of bound thioflavin t. A drop in fluorescence quantum yield, leading to an apparent decrease in Bmax, would accompany the decreased rigidity of bound thioflavin t molecules. The organophosphate-induced alterations in Kd represented changes in binding affinity of thioflavin t, with diethylphosphorylation of Ser203 increasing Kd, and dimethylphosphorylation of Ser203 decreasing Kd. These results indicate that chlorpyrifos oxon and dichlorvos do not bind directly to the peripheral anionic site of acetylcholinesterase, but can affect binding to that site through phosphorylation of Ser203

  7. Numerical PDE-constrained optimization

    De los Reyes, Juan Carlos

    2015-01-01

    This book introduces, in an accessible way, the basic elements of Numerical PDE-Constrained Optimization, from the derivation of optimality conditions to the design of solution algorithms. Numerical optimization methods in function-spaces and their application to PDE-constrained problems are carefully presented. The developed results are illustrated with several examples, including linear and nonlinear ones. In addition, MATLAB codes, for representative problems, are included. Furthermore, recent results in the emerging field of nonsmooth numerical PDE constrained optimization are also covered. The book provides an overview on the derivation of optimality conditions and on some solution algorithms for problems involving bound constraints, state-constraints, sparse cost functionals and variational inequality constraints.

  8. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-01-01

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser696 and Ser698 in the JM (juxtamembrane) region and probably Ser886 and/or Ser893 in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser717 in the JM, and at Ser733, Thr752, Ser783, Ser864, Ser911, Ser958 and Thr9...

  9. Cernavoda Unit 2: - BOP 3D model proposal for a possible organization of site activities

    The scope of this activity is to define characteristics and advantages of the 3D model of Cernavoda BOP to this set up at site for engineering and construction activities. This model will provide a modern and proven tool able to strongly support the site activities with particular regard to the following: 1. engineering activities, - plant arrangement 'double check' for resolution of clashing; - easy management of future design changes; - real time plant configuration updating as soon as any design modification is approved and integrated in the model; - preparation of high quality documentation for procurement, construction and commissioning; - prompt availability of the as built configuration of the plant as soon as the last modification is frozen; 2. material procurement activities, - definition of the priorities in the construction material procurement according to the construction planning by area; - inventory list of equipment, pipes, fittings, valves, cable trays and ventilation ducts to be installed in each construction area; 3. construction activities, - definition of construction sequences, with particular reference in the congested areas, for piping cable trays (electrical and C-and-I) and ventilations ducts; - definition of piping spools by construction contractors; - follow-up of the activities in each area (i.e. construction, painting, insulation, flushing, pressure testing, etc); 4. turn-over and commissioning, - check of the progress. The success of this approach is based on the following: i) proper management of the remote workstations providing easy and reliable access to the model; ii) subdivision of the Integrated Building in construction areas, whose detail design may be allotted to Romanian organizations with multidisciplinary tasks; iii) integration in the model of the remote developed engineering in order to validate the details of the design. (authors)

  10. O2 activation by binuclear Cu sites: Noncoupled versus exchange coupled reaction mechanisms

    Chen, Peng; Solomon, Edward I.

    2004-09-01

    Binuclear Cu proteins play vital roles in O2 binding and activation in biology and can be classified into coupled and noncoupled binuclear sites based on the magnetic interaction between the two Cu centers. Coupled binuclear Cu proteins include hemocyanin, tyrosinase, and catechol oxidase. These proteins have two Cu centers strongly magnetically coupled through direct bridging ligands that provide a mechanism for the 2-electron reduction of O2 to a µ-2:2 side-on peroxide bridged species. This side-on bridged peroxo-CuII2 species is activated for electrophilic attack on the phenolic ring of substrates. Noncoupled binuclear Cu proteins include peptidylglycine -hydroxylating monooxygenase and dopamine -monooxygenase. These proteins have binuclear Cu active sites that are distant, that exhibit no exchange interaction, and that activate O2 at a single Cu center to generate a reactive CuII/O2 species for H-atom abstraction from the C-H bond of substrates. O2 intermediates in the coupled binuclear Cu enzymes can be trapped and studied spectroscopically. Possible intermediates in noncoupled binuclear Cu proteins can be defined through correlation to mononuclear CuII/O2 model complexes. The different intermediates in these two classes of binuclear Cu proteins exhibit different reactivities that correlate with their different electronic structures and exchange coupling interactions between the binuclear Cu centers. These studies provide insight into the role of exchange coupling between the Cu centers in their reaction mechanisms.

  11. Tricyclic covalent inhibitors selectively target Jak3 through an active site thiol.

    Goedken, Eric R; Argiriadi, Maria A; Banach, David L; Fiamengo, Bryan A; Foley, Sage E; Frank, Kristine E; George, Jonathan S; Harris, Christopher M; Hobson, Adrian D; Ihle, David C; Marcotte, Douglas; Merta, Philip J; Michalak, Mark E; Murdock, Sara E; Tomlinson, Medha J; Voss, Jeffrey W

    2015-02-20

    The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases. PMID:25552479

  12. Exploring the active site structure of photoreceptor proteins by Raman optical activity

    Unno, Masashi

    2015-03-01

    Understanding protein function at the atomic level is a major challenge in a field of biophysics and requires the combined efforts of structural and functional methods. We use photoreceptor proteins as a model system to understand in atomic detail how a chromophore and a protein interact to sense light and send a biological signal. A potential technique for investigating molecular structures is Raman optical activity (ROA), which is a spectroscopic method with a high sensitivity to the structural details of chiral molecules. However, its application to photoreceptor proteins has not been reported. Thus we have constructed ROA spectrometer using near-infrared (NIR) laser excitation at 785 nm. The NIR excitation enables us to measure ROA spectra for a variety of biological samples, including photoreceptor proteins, without fluorescence from the samples. In the present study, we have applied the NIR-ROA to bacteriorhodopsin (BR) and photoactive yellow protein (PYP). BR is a light-driven proton pump and contains a protonated Schiff base of retinal as a chromophore. PYP is a blue light receptor, and this protein has the 4-hydroxycinnamyl chromophore, which is covalently linked to Cys69 through a thiolester bond. We have successfully obtained the ROA spectra of the chromophore within a protein environment. Furthermore, calculations of the ROA spectra utilizing density functional theory provide detailed structural information, such as data on out-of-plane distortions of the chromophore. The structural information obtained from the ROA spectra includes the positions of hydrogen atoms, which are usually not detected in the crystal structures of biological samples.

  13. Integral communication activities in support of the repository site selection in Slovenia

    The siting and licensing of a radioactive waste repository requires a complete public consensus that is very difficult to obtain. The main reasons for the public reluctance to accept the radioactive waste repository are the feeling of being ignored in the decision making process and inadequate understanding of radioactivity. Therefore communication and information activities, as early as possible in the siting process, are very important for reducing the potential conflicts of interests between the local community and the investor of the radioactive waste repository on the potential repository sites. ARAO communication activities are based on research on public opinion and public knowledge about radioactive waste management. Communication strategies that provide two-way communication channels, such as interactive web pages, workshops, study circles, visitors' centre, are preferred. Different educational materials (leaflets, CD-ROMs, articles in the local newspapers, yearly magazine, and posters) are also being produced. Collaboration with non-governmental environmental organizations has also proved to be helpful in confidence building, as well as in informing the public. It is also very important for establishing competent public participation in the decision making process. (author)

  14. Stress-induced enhancement of leukocyte trafficking into sites of surgery or immune activation

    Viswanathan, Kavitha; Dhabhar, Firdaus S.

    2005-04-01

    Effective immunoprotection requires rapid recruitment of leukocytes into sites of surgery, wounding, infection, or vaccination. In contrast to immunosuppressive chronic stressors, short-term acute stressors have immunoenhancing effects. Here, we quantify leukocyte infiltration within a surgical sponge to elucidate the kinetics, magnitude, subpopulation, and chemoattractant specificity of an acute stress-induced increase in leukocyte trafficking to a site of immune activation. Mice acutely stressed before sponge implantation showed 200-300% higher neutrophil, macrophage, natural killer cell, and T cell infiltration than did nonstressed animals. We also quantified the effects of acute stress on lymphotactin- (LTN; a predominantly lymphocyte-specific chemokine), and TNF-- (a proinflammatory cytokine) stimulated leukocyte infiltration. An additional stress-induced increase in infiltration was observed for neutrophils, in response to TNF-, macrophages, in response to TNF- and LTN, and natural killer cells and T cells in response to LTN. These results show that acute stress initially increases trafficking of all major leukocyte subpopulations to a site of immune activation. Tissue damage-, antigen-, or pathogen-driven chemoattractants subsequently determine which subpopulations are recruited more vigorously. Such stress-induced increases in leukocyte trafficking may enhance immunoprotection during surgery, vaccination, or infection, but may also exacerbate immunopathology during inflammatory (cardiovascular disease or gingivitis) or autoimmune (psoriasis, arthritis, or multiple sclerosis) diseases. chemokine | psychophysiological stress | surgical sponge | wound healing | lymphotactin

  15. Synthesis and characterization of (18)F-labeled active site inhibited factor VII (ASIS).

    Erlandsson, Maria; Nielsen, Carsten H; Jeppesen, Troels E; Kristensen, Jesper B; Petersen, Lars C; Madsen, Jacob; Kjaer, Andreas

    2015-05-15

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an (18)F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[(18)F]fluorobenzoate, and the [(18)F]ASIS was purified on a PD-10 desalting column. The radiochemical yield was 25 ± 6%, the radiochemical purity was >97%, and the pseudospecific radioactivity was 35 ± 9 GBq/µmol. The binding efficacy was evaluated in pull-down experiments, which monitored the binding of unlabeled ASIS and [(18)F]ASIS to TF and to a specific anti-factor VII antibody (F1A2-mAb). No significant difference in binding efficacy between [(18)F]ASIS and ASIS could be detected. Furthermore, [(18)F]ASIS was relatively stable in vitro and in vivo in mice. In conclusion, [(18)F]ASIS has for the first time been successfully synthesized as a possible positron emission tomography tracer to image TF expression levels. In vivo positron emission tomography studies to evaluate the full potential of [(18)F]ASIS are in progress. PMID:25820758

  16. Benzodiazepines: rat pinealocyte binding sites and augmentation of norepinephrine-stimulated N-acetyltransferase activity

    Matthew, E.; Parfitt, A.G.; Sugden, D.; Engelhardt, D.L.; Zimmerman, E.A.; Klein, D.C.

    1984-02-01

    Studies of (/sup 3/H)diazepam binding to intact rat pineal cells were carried out in tissue culture preparations. The binding was saturable, reversible and proportional to the number of cells used. Scatchard analysis resulted in a linear plot (Kd . 23 nM, maximum binding sites (Bmax) . 1.56 pmol/mg of protein for cells in monolayer culture; Kd . 7 nM, Bmax . 1.3 pmol/mg of protein for cells in suspension culture). Inhibition constants (Ki) for clonazepam (500 nM), flunitrazepam (38 nM) and Ro-5-4864 (5 nM) indicated that the binding sites were probably of the ''peripheral'' type. In addition, the effects of diazepam on norepinephrine-stimulated N-acetyltransferase (NAT) activity were studied in organ culture and dissociated cell culture. Diazepam (10-50 microM) both prolonged and increased the magnitude of the norepinephrine-induced increase in NAT activity but did not affect the initial rate of rise of enzyme activity. The effect was dose-dependent and was also seen with clonazepam, flunitrazepam and Ro-5-4864, but not with Ro-15-1788. Diazepam, by itself, at these concentrations, had no effect on NAT, but enzyme activity was increased by higher concentrations (0.1-1 mM). Although a relationship between the (/sup 3/H)diazepam binding sites described here and the effect of benzodiazepines on NAT cannot be established from these studies, the data suggest that the benzodiazepines may alter melatonin levels through their action on NAT.

  17. Benzodiazepines: rat pinealocyte binding sites and augmentation of norepinephrine-stimulated N-acetyltransferase activity

    Studies of [3H]diazepam binding to intact rat pineal cells were carried out in tissue culture preparations. The binding was saturable, reversible and proportional to the number of cells used. Scatchard analysis resulted in a linear plot [Kd . 23 nM, maximum binding sites (Bmax) . 1.56 pmol/mg of protein for cells in monolayer culture; Kd . 7 nM, Bmax . 1.3 pmol/mg of protein for cells in suspension culture]. Inhibition constants (Ki) for clonazepam (500 nM), flunitrazepam (38 nM) and Ro-5-4864 (5 nM) indicated that the binding sites were probably of the ''peripheral'' type. In addition, the effects of diazepam on norepinephrine-stimulated N-acetyltransferase (NAT) activity were studied in organ culture and dissociated cell culture. Diazepam (10-50 microM) both prolonged and increased the magnitude of the norepinephrine-induced increase in NAT activity but did not affect the initial rate of rise of enzyme activity. The effect was dose-dependent and was also seen with clonazepam, flunitrazepam and Ro-5-4864, but not with Ro-15-1788. Diazepam, by itself, at these concentrations, had no effect on NAT, but enzyme activity was increased by higher concentrations (0.1-1 mM). Although a relationship between the [3H]diazepam binding sites described here and the effect of benzodiazepines on NAT cannot be established from these studies, the data suggest that the benzodiazepines may alter melatonin levels through their action on NAT

  18. Affinity labeling and characterization of the active site histidine of glucosephosphate isomerase

    N-bromoacetylethanolamine phosphate was found to act as a specific affinity label for the active center of glucosephosphate isomerase. The inactivation process followed pseudo-first order kinetics, was irreversible, and exhibited rate saturation kinetics with minimal half-lives of inactivation of 4.5 and 6.3 min for the enzyme isolated from human placenta and rabbit muscle, respectively. The pH dependence of the inactivation process closely paralleled the pH dependence of the overall catalytic process with pK/sub a/ values at pH 6.4 and 9.0. The stoichiometry of labeling of either enzyme, as determined with N-bromo[14C2]acetylethanolamine phosphate, was 1 eq of the affinity label/subunit of enzyme. After acid hydrolysis and amino acid analysis of the radioactive affinity-labeled human enzyme, only radioactive 3-carboxymethyl histidine was found. In the case of the rabbit enzyme, the only radioactive derivative obtained was 1-carboxymethyl histidine. Active site tryptic peptides were isolated by solvent extraction, thin layer peptide fingerprinting, and ion exchange chromatography before and after removal of the phosphate from the active site peptide. Amino acid analysis of the labeled peptides from the two species were very similar. Using high sensitivity methods for sequence analysis, the primary structure of the active site was established as Val-Leu-His-Ala-Glu-Asn-Val-Asp (Gly,Thr,Ser) Glu-Ile (Thr-Gly-His-Lys-Glx)-Tyr-Phe. Apparent sequence homology between the catalytic center of glucosephosphate isomerase and triosephosphate isomerase suggest that the two enzymes may have evolved from a common ancestral gene

  19. Improved oxygen reduction activity on Pt3Ni(111) via increased surface site availability.

    Stamenkovic, Vojislav R; Fowler, Ben; Mun, Bongjin Simon; Wang, Guofeng; Ross, Philip N; Lucas, Christopher A; Marković, Nenad M

    2007-01-26

    The slow rate of the oxygen reduction reaction (ORR) in the polymer electrolyte membrane fuel cell (PEMFC) is the main limitation for automotive applications. We demonstrated that the Pt3Ni(111) surface is 10-fold more active for the ORR than the corresponding Pt(111) surface and 90-fold more active than the current state-of-the-art Pt/C catalysts for PEMFC. The Pt3Ni(111) surface has an unusual electronic structure (d-band center position) and arrangement of surface atoms in the near-surface region. Under operating conditions relevant to fuel cells, its near-surface layer exhibits a highly structured compositional oscillation in the outermost and third layers, which are Pt-rich, and in the second atomic layer, which is Ni-rich. The weak interaction between the Pt surface atoms and nonreactive oxygenated species increases the number of active sites for O2 adsorption. PMID:17218494

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

    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.

  1. Chemotactic Activity of Cyclophilin A in the Skin Mucus of Yellow Catfish (Pelteobagrus fulvidraco and Its Active Site for Chemotaxis

    Farman Ullah Dawar

    2016-08-01

    Full Text Available Fish skin mucus is a dynamic barrier for invading pathogens with a variety of anti-microbial enzymes, including cyclophilin A (CypA, a multi-functional protein with peptidyl-prolyl cis/trans isomerase (PPIase activity. Beside various other immunological functions, CypA induces leucocytes migration in vitro in teleost. In the current study, we have discovered several novel immune-relevant proteins in yellow catfish skin mucus by mass spectrometry (MS. The CypA present among them was further detected by Western blot. Moreover, the CypA present in the skin mucus displayed strong chemotactic activity for yellow catfish leucocytes. Interestingly, asparagine (like arginine in mammals at position 69 was the critical site in yellow catfish CypA involved in leucocyte attraction. These novel efforts do not only highlight the enzymatic texture of skin mucus, but signify CypA to be targeted for anti-inflammatory therapeutics.

  2. Active site studies of Escherichia coli 2-keto-4-hydroxyglutarate aldolase

    Vlahos, C.J.

    1987-01-01

    The data presented delineate the complete amino acid sequence of E. coli KHG aldolase and also identify Lys-133, Glu-45, and Arg-49 as aminoacyl residues required for catalytic activity. Incubation of E. coli KHG aldolase with (/sup 14/C)pyruvate in the presence of NaCNBH/sub 3/ results in the incorporation of one mol of /sup 14/C per mol of enzyme subunit. Digestion of this enzyme-adduct with trypsin, followed by purification of the peptides, allowed for the isolation of a unique radioactive peptide. Its amino acid sequence showed that the pyruvate-binding (i.e., Schiff-base forming) lysine residue is located at position 133 in the intact enzyme. E. coli KHG aldolase activity is lost when the enzyme is reacted with bromopyruvate; saturation kinetics are observed. The substrates, pyruvate and KHG, protect the enzyme from inactivation. Both facts suggest that the reagent is active-site specific. Incubation of the aldolase with (3-/sup 14/C)bromopyruvate is associated with a concomitant loss of enzymatic activity and esterification of Glu-45; if the enzyme is denatured in the presence of excess bromopyruvate, Cys-159 and Cys-180 are also alkylated. Blocking the active-site lysine residue with pyruvate prevents Glu-45 from being esterified but does not eliminate alkylation of these two cysteine residues. Woodward's Reagent K was also found to inactivate the aldolase under conditions that are usually specific for carboxyl group modification. This aldolase is also inactivated by 1,2-cyclohexanedione. Loss of enzymatic activity occurs concomitantly with modification of one arginine residue per enzyme subunit. Treatment of the aldolase with the arginine-specific reagent, 4-(oxyacetyl)phenoxyacetic acid, followed by digestion with trypsin allowed for the isolation of a unique peptide and the identification of Arg-49 as the specific residue involved.

  3. Three dimensional visualization in support of Yucca Mountain Site characterization activities

    An understanding of the geologic and hydrologic environment for the proposed high-level nuclear waste repository at Yucca Mountain, NV is a critical component of site characterization activities. Conventional methods allow visualization of geologic data in only two or two and a half dimensions. Recent advances in computer workstation hardware and software now make it possible to create interactive three dimensional visualizations. Visualization software has been used to create preliminary two-, two-and-a-half-, and three-dimensional visualizations of Yucca Mountain structure and stratigraphy. The three dimensional models can also display lithologically dependent or independent parametric data. Yucca Mountain site characterization studies that will be supported by this capability include structural, lithologic, and hydrologic modeling, and repository design

  4. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  5. The active site of oxidative phosphorylation and the origin of hyperhomocysteinemia in aging and dementia.

    McCully, Kilmer S

    2015-01-01

    The active site of oxidative phosphorylation and adenosine triphosphate (ATP) synthesis in mitochondria is proposed to consist of two molecules of thioretinamide bound to cobalamin, forming thioretinaco, complexed with ozone, oxygen, nicotinamide adenine dinucleotide. and inorganic phosphate, TR2CoO3O2NAD(+)H2PO4(-). Reduction of the pyridinium nitrogen of the nicotinamide group by an electron from electron transport complexes initiates polymerization of phosphate with adenosine diphosphate, yielding nicotinamide riboside and ATP bound to thioretinaco ozonide oxygen. A second electron reduces oxygen to hydroperoxyl radical, releasing ATP from the active site. A proton gradient is created within F1F0 ATPase complexes of mitochondria by reaction of protons with reduced nicotinamide riboside and with hydroperoxyl radical, yielding reduced nicotinamide riboside and hydroperoxide. The hyperhomocysteinemia of aging and dementia is attributed to decreased synthesis of adenosyl methionine by thioretinaco ozonide and ATP, causing decreased allosteric activation of cystathionine synthase and decreased allosteric inhibition of methylenetetrahydrofolate reductase and resulting in dysregulation of methionine metabolism. PMID:25887881

  6. Bagging constrained equity premium predictors

    Hillebrand, Eric; Lee, Tae-Hwy; Medeiros, Marcelo

    2014-01-01

    regression coefficient and positivity of the forecast. Bagging constrained estimators can have smaller asymptotic mean-squared prediction errors than forecasts from a restricted model without bagging. Monte Carlo simulations show that forecast gains can be achieved in realistic sample sizes for the stock...

  7. The Constrained Bottleneck Transportation Problem

    Peerayuth Charnsethikul; Saeree Svetasreni

    2007-01-01

    Two classes of the bottleneck transportation problem with an additional budget constraint are introduced. An exact approach was proposed to solve both problem classes with proofs of correctness and complexity. Moreover, the approach was extended to solve a class of multi-commodity transportation network with a special case of the multi-period constrained bottleneck assignment problem.

  8. Constrained Clustering With Imperfect Oracles.

    Zhu, Xiatian; Loy, Chen Change; Gong, Shaogang

    2016-06-01

    While clustering is usually an unsupervised operation, there are circumstances where we have access to prior belief that pairs of samples should (or should not) be assigned with the same cluster. Constrained clustering aims to exploit this prior belief as constraint (or weak supervision) to influence the cluster formation so as to obtain a data structure more closely resembling human perception. Two important issues remain open: 1) how to exploit sparse constraints effectively and 2) how to handle ill-conditioned/noisy constraints generated by imperfect oracles. In this paper, we present a novel pairwise similarity measure framework to address the above issues. Specifically, in contrast to existing constrained clustering approaches that blindly rely on all features for constraint propagation, our approach searches for neighborhoods driven by discriminative feature selection for more effective constraint diffusion. Crucially, we formulate a novel approach to handling the noisy constraint problem, which has been unrealistically ignored in the constrained clustering literature. Extensive comparative results show that our method is superior to the state-of-the-art constrained clustering approaches and can generally benefit existing pairwise similarity-based data clustering algorithms, such as spectral clustering and affinity propagation. PMID:25622327

  9. PCR-based site-specific mutagenesis of peptide antibiotics FALL-39 and its biologic activities

    Yun-xia YANG; Yun FENG; Bo-yao WANG; Qi WU

    2004-01-01

    AIM: To construct PGEX-1λT-FALL-39 expression vector and its mutant vector, and study the relationship of function and structure. METHODS: A cDNA encoding mature FALL-39 was cloned from SPCA- 1 cell mRNA and the prokaryotic expression vector PGEX- 1λT-FALL-39 was constructed. Two kinds of polymerase chain reaction (PCR) for the site-direction mutagenesis were used to construct FALL-39 mutant expression vector, FALL-39-Lys-32 and FALL-39-Lys-24. Minimal effective concentration, minimal inhibitory concentration, and minimal bactericidal concentration were used to assay the antibacterial activities of these peptides. Effects of different solution on the antibacterial activity of FALL-39 and FALL-39-Lys-32 were observed by CFU determination. The hemolytic effects of these peptides were also examined on human red blood cells. RESULTS: Two site-specific mutants FALL-39-Lys-32 and FALL-39-Lys24 were obtained by PCR-induced mutagenesis. In comparison with two-step PCR which required two pairs of primers, one step PCR which required one pair of primers is a simple and efficient method for the PCR based site-specific mutagenesis. Using the prokaryotic expression system, the E coli-based products of recombinant FALL39 and its mutant peptides were also obtained. The antibacterial assay showed that FALL-39-Lys-32 and FALL-39-Lys24 were more potential in the antibacterial activity against E coli ML35p and Pseltdomonas aeruginosa ATCC27853 than that of FALL-39, and no increase in hemolysis was observed at the antibacterial concentrations. The antibacterial activity of FALL-39-Lys-32 against E coli was more potent than that of FALL-39 in NaCl-containing LB medium, while its activity was almost the same as FALL-39 in SO2-4 containing Medium E. CONCLUSION: PCR-based mutagensis is a useful model system for studying the structure and function relationship of antimicrobial peptides. Keeping α-helical conformation of FALL-39 and increasing net positive charge can increase the

  10. Water molecule network and active site flexibility of apo protein tyrosine phosphatase 1B

    Pedersen, A.K.; Peters, Günther H.J.; Møller, K.B.;

    2004-01-01

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including...... the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 Angstrom apo PTP1B structure has been obtained, showing four highly coordinated water molecules...

  11. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions

    Walkiewicz, Katarzyna W.

    2015-06-17

    The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein ‘nanomachines’ to become activated in a site-specific manner.

  12. Determination of blood Cd in subjects living near dismessed mines and active industrial sites

    Madeddu, Roberto Beniamino; Tolu, Paola; Asara, Yolande; Farace, Cristiano; Forte, Giovanni; Bocca, Beatrice

    2012-01-01

    The environmental exposure to Cd in 265 subjects living in a South-Western area of Sardinia (Sulcis-Iglesiente) with a great history of mining activities and large industrial settings was assessed. Individuals living near the industrial plants had geometric means (GM) of blood Cd (0.79 μg/l) significantly higher than controls (0.47 μg/l) and than residents of the mining sites (0.54 μg/l). Demographic and lifestyle variables were also investigated and data show...

  13. Application of instrumental neutron activation analysis to study ceramic fragments from Damascus Castle site, Syria

    Thirty-three archaeological ceramic fragment samples from Damascus Castle archaeological site, Damascus city, Syria, were analyzed using instrumental neutron activation analysis (INAA). 36 elements were determined. These elemental concentrations have been processed using two multivariate statistical methods, cluster and factor analysis in order to determine similarities and correlation between the various samples. Factor analysis confirms that 84.8% of the ceramics samples classified by cluster analysis are correctly classified by cluster analysis. The results provided persuasive evidence that Castle pottery used at least four different clay sources. Moreover, by means of systematic local analysis it will be clear whether these sources are local or not. (author)

  14. Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.

    Chung, Ivy Yeuk Wah; Paetzel, Mark

    2013-05-01

    Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water. PMID:23511637

  15. Non-native ligands define the active site of Pennisetum glaucum (L.) R. Br dehydroascorbate reductase.

    Krishna Das, Bhaba; Kumar, Amit; Maindola, Priyank; Mahanty, Srikrishna; Jain, S K; Reddy, Mallireddy K; Arockiasamy, Arulandu

    2016-05-13

    Dehydroascorbate reductase (DHAR), a member of the glutathione-S-transferase (GST) family, reduces dehydroascorbate (DHA) to ascorbate (AsA; Vitamin-C) in a glutathione (GSH)-dependent manner and in doing so, replenishes the critical AsA pool of the cell. To understand the enzyme mechanism in detail, we determined the crystal structure of a plant DHAR from Pennisetum glaucum (PgDHAR) using Iodide-Single Anomalous Dispersion (SAD) and Molecular replacement methods, in two different space groups. Here, we show PgDHAR in complex with two non-native ligands, viz. an acetate bound at the G-site, which resembles the γ-carboxyl moiety of GSH, and a glycerol at the H-site, which shares the backbone of AsA. We also show that, in the absence of bound native substrates, these non-native ligands help define the critical 'hook points' in the DHAR enzyme active site. Further, our data suggest that these non-native ligands can act as the logical bootstrapping points for iterative design of inhibitors/analogs for DHARs. PMID:27067046

  16. Active urea transport by the skin of Bufo viridis: Amiloride- and phloretin-sensitive transport sites

    Urea is actively transported inwardly (Ji) across the skin of the green toad Bufo viridis. Ji is markedly enhanced in toads adapted to hypertonic saline. The authors studied urea transport across the skin of Bufo viridis under a variety of experimental conditions, including treatment with amiloride and phloretin, agents that inhibit urea permeability in the bladder of Bufo marinus. Amiloride (10-4 M) significantly inhibited Ji in both adapted and unadapted animals and was unaffected by removal of sodium from the external medium. Phloretin (10-4 M) significantly inhibited Ji in adapted animals by 23-46%; there was also a reduction in Ji in unadapted toads at 10-4 and 5 x 10-4 M phloretin. A dose-response study revealed that the concentration of phloretin causing half-maximal inhibition (K1/2) was 5 x 10-4 M for adapted animals. Ji was unaffected by the substitution of sucrose for Ringer solution or by ouabain. They conclude (1) the process of adaptation appears to involve an increase in the number of amiloride- and phloretin-inhibitable urea transport sites in the skin, with a possible increase in the affinity of the sites for phloretin; (2) the adapted skin resembles the Bufo marinus urinary bladder with respect to amiloride and phloretin-inhibitable sites; (3) they confirm earlier observations that Ji is independent of sodium transport

  17. Prioritizing conservation activities using reserve site selection methods and population viability analysis.

    Newbold, Stephen C; Siikamäki, Juha

    2009-10-01

    In recent years a large literature on reserve site selection (RSS) has developed at the interface between ecology, operations research, and environmental economics. Reserve site selection models use numerical optimization techniques to select sites for a network of nature reserves for protecting biodiversity. In this paper, we develop a population viability analysis (PVA) model for salmon and incorporate it into an RSS framework for prioritizing conservation activities in upstream watersheds. We use spawner return data for three closely related salmon stocks in the upper Columbia River basin and estimates of the economic costs of watershed protection from NOAA to illustrate the framework. We compare the relative cost-effectiveness of five alternative watershed prioritization methods, based on various combinations of biological and economic information. Prioritization based on biological benefit-economic cost comparisons and accounting for spatial interdependencies among watersheds substantially outperforms other more heuristic methods. When using this best-performing prioritization method, spending 10% of the cost of protecting all upstream watersheds yields 79% of the biological benefits (increase in stock persistence) from protecting all watersheds, compared to between 20% and 64% for the alternative methods. We also find that prioritization based on either costs or benefits alone can lead to severe reductions in cost-effectiveness. PMID:19831069

  18. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    Warren, Ean; Bekins, Barbara A.

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  19. The influence of a small amount of active sites on the adsorption kinetics of nitrogen on ruthenium

    Recently, Dahl et al. [S. Dahl, A. Logadottir, R.C. Egeberg, J.H. Larsen, I. Chorkendorff, E. Toernqvist, J.K. Norskov, Phys. Rev. Lett. 83 (1999) 1814; S. Dahl, E. Toernqvist, I. Chorkendorff, J. Catal. 192 (2000) 381] have proposed very interesting hypothesis that the rate of dissociation and adsorption of nitrogen on Ru(0 0 0 1) facet is totally dominated by the presence of a small amount of step sites on Ru(0 0 0 1) terraces. Following this idea, a kinetic model, based on applying the Statistical Rate Theory approach, was developed in order to explain if such mechanism is able to explain the observed features of the system N2/Ru(0 0 0 1). As a result, it was stated that the activation barrier for adsorption on the active (step) sites is equal to 36 kJ/mol; in turn, the adsorption energy of nitrogen atoms on the active sites is 43 kJ/mol. It implies that the rate of adsorption via the active sites is much faster than direct adsorption on the three-fold hollow sites; moreover, the occupation of the active sites is always close to zero at the investigated temperatures, so they are not blocked and may act as an indirect channel for adsorption. Thus, the rate of nitrogen adsorption on Ru(0 0 0 1) surface is governed by the rate of diffusion of nitrogen atoms from the active sites into the three-fold hollow sites. The analysis of thermodesorption spectra revealed an important role of repulsive interactions between the N atoms adsorbed on the hollow sites, the associated interaction parameter between nearest neighbors was estimated to be 5 kJ/mol. The presence of small amount of gold on Ru(0 0 0 1), apart of blocking the active sites, seems to remove the repulsion between nitrogen atoms

  20. Novel autophosphorylation sites of Src family kinases regulate kinase activity and SH2 domain-binding capacity.

    Weir, Marion E; Mann, Jacqueline E; Corwin, Thomas; Fulton, Zachary W; Hao, Jennifer M; Maniscalco, Jeanine F; Kenney, Marie C; Roman Roque, Kristal M; Chapdelaine, Elizabeth F; Stelzl, Ulrich; Deming, Paula B; Ballif, Bryan A; Hinkle, Karen L

    2016-04-01

    Src family tyrosine kinases (SFKs) are critical players in normal and aberrant biological processes. While phosphorylation importantly regulates SFKs at two known tyrosines, large-scale phosphoproteomics have revealed four additional tyrosines commonly phosphorylated in SFKs. We found these novel tyrosines to be autophosphorylation sites. Mimicking phosphorylation at the C-terminal site to the activation loop decreased Fyn activity. Phosphomimetics and direct phosphorylation at the three SH2 domain sites increased Fyn activity while reducing phosphotyrosine-dependent interactions. While 68% of human SH2 domains exhibit conservation of at least one of these tyrosines, few have been found phosphorylated except when found in cis to a kinase domain. PMID:27001024

  1. Comparative analysis of the impact of geological activity on astronomical sites of the Canary Islands, Hawaii and Chile

    Eff-Darwich, A; Rodriguez-Losada, J A; de la Nuez, J; Hernandez-Gutierrez, L E; Romero-Ruiz, M C

    2009-01-01

    An analysis of the impact of seismic and volcanic activity was carried out at selected astronomical sites, namely the observatories of El Teide (Tenerife, Canary Islands), Roque de los Muchachos (La Palma, Canary Islands), Mauna Kea (Hawaii) and Paranal (Chile) and the candidate site of Cerro Ventarrones (Chile). Hazard associated to volcanic activity is low or negligible at all sites, whereas seismic hazard is very high in Chile and Hawaii. The lowest geological hazard in both seismic and volcanic activity was found at Roque de los Muchachos observatory, in the island of La Palma.

  2. Acetylene is an active-site-directed, slow-binding, reversible inhibitor of Azotobacter vinelandii hydrogenase

    The inhibition of purified and membrane-bound hydrogenase from Azotobacter vinelandii by dihydrogen-free acetylene was investigated. The inhibition was a time-dependent process which exhibited first-order kinetics. Both H2 and CO protected against the inhibition by acetylene. K/sub protect(app)/ values of 0.41 and 24 μM were derived for these gases, respectively. Both H2-oxidizing activity and the tritium exchange capacity of the purified enzyme were inhibited at the same rate by acetylene. Removal of acetylene reversed the inhibition for both the purified and the membrane-associated form of the enzyme. The purified hydrogenases from both Rhizobium japonicum and Alcaligenes eutrophus H16 were also inhibited by acetylene in a time-dependent fashion. These findings suggest that acetylene is an active-site-directed, slow-binding, reversible inhibitor of some membrane-bound hydrogenases from aerobic bacteria

  3. Active site coupling in PDE:PKA complexes promotes resetting of mammalian cAMP signaling.

    Krishnamurthy, Srinath; Moorthy, Balakrishnan Shenbaga; Xin Xiang, Lim; Xin Shan, Lim; Bharatham, Kavitha; Tulsian, Nikhil Kumar; Mihalek, Ivana; Anand, Ganesh S

    2014-09-16

    Cyclic 3'5' adenosine monophosphate (cAMP)-dependent-protein kinase (PKA) signaling is a fundamental regulatory pathway for mediating cellular responses to hormonal stimuli. The pathway is activated by high-affinity association of cAMP with the regulatory subunit of PKA and signal termination is achieved upon cAMP dissociation from PKA. Although steps in the activation phase are well understood, little is known on how signal termination/resetting occurs. Due to the high affinity of cAMP to PKA (KD ∼ low nM), bound cAMP does not readily dissociate from PKA, thus begging the question of how tightly bound cAMP is released from PKA to reset its signaling state to respond to subsequent stimuli. It has been recently shown that phosphodiesterases (PDEs) can catalyze dissociation of bound cAMP and thereby play an active role in cAMP signal desensitization/termination. This is achieved through direct interactions with the regulatory subunit of PKA, thereby facilitating cAMP dissociation and hydrolysis. In this study, we have mapped direct interactions between a specific cyclic nucleotide phosphodiesterase (PDE8A) and a PKA regulatory subunit (RIα isoform) in mammalian cAMP signaling, by a combination of amide hydrogen/deuterium exchange mass spectrometry, peptide array, and computational docking. The interaction interface of the PDE8A:RIα complex, probed by peptide array and hydrogen/deuterium exchange mass spectrometry, brings together regions spanning the phosphodiesterase active site and cAMP-binding sites of RIα. Computational docking combined with amide hydrogen/deuterium exchange mass spectrometry provided a model for parallel dissociation of bound cAMP from the two tandem cAMP-binding domains of RIα. Active site coupling suggests a role for substrate channeling in the PDE-dependent dissociation and hydrolysis of cAMP bound to PKA. This is the first instance, to our knowledge, of PDEs directly interacting with a cAMP-receptor protein in a mammalian system, and

  4. Crystal Structure of Liganded Rat Peroxisomal Multifunctional Enzyme Type 1: A FLEXIBLE MOLECULE WITH TWO INTERCONNECTED ACTIVE SITES*

    Kasaragod, Prasad; Venkatesan, Rajaram; Kiema, Tiila R.; Hiltunen, J. Kalervo; Wierenga, Rik K.

    2010-01-01

    The crystal structure of the full-length rat peroxisomal multifunctional enzyme, type 1 (rpMFE1), has been determined at 2.8 Å resolution. This enzyme has three catalytic activities and two active sites. The N-terminal part has the crotonase fold, which builds the active site for the Δ3,Δ2-enoyl-CoA isomerase and the Δ2-enoyl-CoA hydratase-1 catalytic activities, and the C-terminal part has the (3S)-hydroxyacyl-CoA dehydrogenase fold and makes the (3S)-hydroxyacyl-CoA dehydrogenase active sit...

  5. Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors.

    Dossi, Kyriaki; Tsirkone, Vicky G; Hayes, Joseph M; Matousek, Josef; Poucková, Pavla; Soucek, Josef; Zadinova, Marie; Zographos, Spyros E; Leonidas, Demetres D

    2009-11-01

    Bovine seminal ribonuclease (BS-RNase) is a 27kDa homodimeric enzyme and a member of the pancreatic RNase A superfamily. It is the only RNase with a quaternary structure and it is a mixture of two dimeric forms. In the most abundant form the active site is formed by the swapping of the N-terminal segments. BS-RNase is a potent antitumor agent with severe side effects such as aspermatogenicity, and immunosuppression. As a first step towards the design of potent inhibitors of this enzyme we mapped its active site through the study of the binding of uridine 2'-phosphate (U2'p), uridine 3'-phosphate (U3'p), uridine 5'-diphosphate (UDP), cytidine 3'-phosphate (C3'p), and cytidine 5-phosphate (C5'p), by kinetics, and X-ray crystallography. These phosphonucleotides are potent inhibitors with C3'p being the most potent with a K(i) value of 22 microM. Absorption, distribution, metabolism, and excretion pharmacokinetic property predictions reveal U2'p, U3'p, and C5'p as the most promising with respect to oral bioavailability. In vivo studies on the aspermatogenic effect have shown that C3'p and C5'p inhibit significantly this biological action of BS-RNase. PMID:19643512

  6. Identification of the active site histidine in Staphylococcus hyicus lipase using chemical modification and mass spectrometry.

    Boots, J W; van Dongen, W D; Verheij, H M; de Haas, G H; Haverkamp, J; Slotboom, A J

    1995-04-01

    Staphylococcus hyicus lipase is a serine hydrolase. In order to identify the active site histidine of S. hyicus lipase we have chemically modified S. hyicus lipase with 1-bromo-octan-2-one. The enzyme is rapidly inactivated by this inhibitor with a half-time of 578 s at pH 6.5 and 30 degrees C. Addition of the enzyme's cofactor calcium increases the inactivation rate approx. 2-fold. When n-hexadecylphosphocholine, a non-hydrolysable substrate analogue, is added the inactivation rate decreases about 3-fold, suggesting that a residue in the active site of S. hyicus lipase is involved in the inactivation reaction. Inactivation of S. hyicus lipase with 14C-labelled 1-bromo-octan-2-one shows that 1.4 moles of inhibitor per mole of lipase are incorporated. The results of an electrospray mass spectrometric study of the inactivated enzyme are consistent with this finding. In order to identify the modified residue, both the inactivated and the unmodified lipase were digested with cyanogen bromide followed by trypsin. The resulting peptides were analysed using HPLC and fast atom bombardment mass spectrometry. The results allow the modified residue to be assigned to the peptide Gly597-Lys612. Collision induced dissociation mass spectrometry allowed the modified residue to be identified as His-600. From these results we conclude that this residue forms part of the catalytic triad of S. hyicus lipase. PMID:7711054

  7. The role of active site aromatic residues in substrate degradation by the human chitotriosidase.

    Eide, Kristine Bistrup; Stockinger, Linn Wilhelmsen; Lewin, Anna Sofia; Tøndervik, Anne; Eijsink, Vincent G H; Sørlie, Morten

    2016-02-01

    Human chitotriosidase (HCHT) is a glycoside hydrolase family 18 chitinase synthesized and secreted in human macrophages thought be an innate part of the human immune system. It consists of a catalytic domain with the (β/α)8 TIM barrel fold having a large area of solvent-exposed aromatic amino acids in the active site and an additional family 14 carbohydrate-binding module. To gain further insight into enzyme functionality, especially the effect of the active site aromatic residues, we expressed two variants with mutations in subsites on either side of the catalytic acid, subsite -3 (W31A) and +2 (W218A), and compared their catalytic properties on chitin and high molecular weight chitosans. Exchange of Trp to Ala in subsite -3 resulted in a 12-fold reduction in extent of degradation and a 20-fold reduction in kcat(app) on chitin, while the values are 5-fold and 10-fold for subsite +2. Moreover, aromatic residue mutation resulted in a decrease of the rate of chitosan degradation contrasting previous observations for bacterial family 18 chitinases. Interestingly, the presence of product polymers of 40 sugar moieties and higher starts to disappear already at 8% degradation for HCHT50-W31A. Such behavior contrast that of the wild type and HCHT-W218A and resembles the action of endo-nonprocessive chitinases. PMID:26621384

  8. Active sites of two orthologous cytochromes P450 2E1: Differences revealed by spectroscopic methods

    Cytochromes P450 2E1 of human and minipig origin were examined by absorption spectroscopy under high hydrostatic pressure and by resonance Raman spectroscopy. Human enzyme tends to denature to the P420 form more easily than the minipig form; moreover, the apparent compressibility of the heme active site (as judged from a redshift of the absorption maximum with pressure) is greater than that of the minipig counterpart. Relative compactness of the minipig enzyme is also seen in the Raman spectra, where the presence of planar heme conformation was inferred from band positions characteristic of the low-spin heme with high degree of symmetry. In this respect, the CYP2E1 seems to be another example of P450 conformational heterogeneity as shown, e.g., by Davydov et al. for CYP3A4 [Biochem. Biophys. Res. Commun. 312 (2003) 121-130]. The results indicate that the flexibility of the CYP active site is likely one of its basic structural characteristics

  9. Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site.

    Song, Xiangfei; Wang, Yefei; Zhang, Shujun; Yan, Shihai; Li, Tong; Yao, Lishan

    2015-07-27

    An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex. PMID:26114648

  10. On-site characterization and verification for removal of cesium contamination along an active rail spur

    A rapid, cost-effective sampling and analysis approach was used to conduct on-site analysis of soil and ballast for 137Cs contamination along an active rail spur in Oak Ridge, Tennessee. Savings in time and analytical costs were realized for both the characterization and cleanup phases of this project. For characterization, a procedure was developed to conduct gamma-logging of shallow boreholes. Portable gamma radiation survey instruments consisting of a 5- by 5-cm NaI detector coupled to a digital ratemeter/scaler with a single-channel analyzer were calibrated to a 137Cs source, then used for both surface and subsurface gamma radiation surveys. A correlation was made between the direct radiation measurements and 137Cs concentrations in surface and subsurface soil and ballast. Borehole logs of gamma-ray activity as a function of depth were used to estimate vertical profiles of the subsurface distribution of 137Cs. Information from these surveys was used to develop accurate 3-dimensional isopleths of contaminated areas, including estimates of waste volumes. After a remedial alternative was selected, on-site analytical methods were again used to verify that the cleanup level was achieved. Samples from excavated areas were analyzed for 137Cs by comparative gamma-ray counting using a multi-channel pulse height analyzer and a 3-in. diameter by 2-in. thick NaI crystal. The counting system was housed in a mobile field laboratory. To better direct ongoing excavation, a correlation factor between samples analyzed by gamma spectroscopy and measurements made by field instruments was determined. In both the characterization and the cleanup phases, sample results were verified by independent off-site laboratory analyses

  11. Accommodation of GDP-Linked Sugars in the Active Site of GDP-Perosamine Synthase

    Cook, Paul D.; Carney, Amanda E.; Holden, Hazel M. (UW)

    2009-01-12

    Perosamine (4-amino-4,6-dideoxy-d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 {angstrom} resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K{sub m} for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k{sub cat} was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy-d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.

  12. Research in Support of Remediation Activities at the Savannah River Site

    The USDOE Savannah River Site (SRS), an 803-km2 (310-mile2) facility located south of Aiken, SC on the upper Atlantic Coastal Plain and bounded to the west by the Savannah River, was established in the 1950s for the production and refinement of nuclear materials. To fulfill this mission during the past 50 years SRS has operated five nuclear reactors, two large chemical separation areas, waste disposal facilities (landfills, waste ponds, waste tanks, and waste stabilization), and a large number of research and logistics support facilities. Contaminants of concern (COC) resulting from site operations include chlorinated solvents, radionuclides, metals, and metalloids, often found as complex mixtures that greatly complicate remediation efforts when compared with civilian industries. The objective of this article is to provide a description of the lithology and hydrostratigraphy of the SRS, as well as a brief history of site operations and research activities as a preface to the current special section of Vadose Zone Journal (VZJ) dedicated to SRS, focusing mainly on issues that are unique to the USDOE complex. Contributions to the special section reflect a diverse range of topics, from hydrologic tracer experiments conducted both within the vadose and saturated zones to studies specifically aimed at identifying geochemical processes controlling the migration and partitioning of specific contaminants (e.g., TCE, 137Cs, U, and Pu) in SRS subsurface environments. Addressing the diverse environmental challenges of the SRS provides a unique opportunity to conduct both fundamental and applied research across a range of experimental scales. Hence, the SRS has been a pioneering force in several areas of environmental research and remediation, often through active interdisciplinary collaboration with researchers from other USDOE facilities, academic and federal institutions, and commercial entities

  13. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200.

    Kovaleva, Elena G; Rogers, Melanie S; Lipscomb, John D

    2015-09-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species. PMID:26267790

  14. The "Simeiz-Katzively" co-location site of space geodesy techniques: current state and future activity

    Yatskiv, Y.; Odynets, P.; Volvach, O.

    2014-12-01

    Two Satellite Laser Ranging (SLR) stations, two Global Navigation Satellite System (GNSS) stations and Very Long Base Interferometry (VLBI) station are placed on the "Simeiz-Katzively" co-location site. The activity of these space geodesy techniques in 2010-2012 is presented. Special attention is paid on results of new local tie surveys at this co-location site.

  15. Examining guidelines for the site selection for geological disposal. Research activities principle for future risk assessment and quality assurance

    A draft for the committee in charge of nuclear safety regulations regarding geological disposal of high-level radioactive wastes from nuclear facilities is presented. The report particularly concerns with a line of policy or principle at the stage of investigation activities for the site selection and site characterization. IAEA guidelines are consulted. (S. Ohno)

  16. Rate of hydrolysis in ATP synthase is fine-tuned by  -subunit motif controlling active site conformation

    Beke-Somfai, T.

    2013-01-23

    Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. F(o)F(1) ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F(1) performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central γ-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-Å-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to γ-subunit position, the active site conformation is fine-tuned mainly by small α-subunit changes. Quantum mechanics-based results confirm that the sub-Ångström gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.

  17. Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77

    Cockburn, Darrell; Wilkens, Casper; Ruzanski, Christian;

    2014-01-01

    Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half ...

  18. The active site of hen egg-white lysozyme: flexibility and chemical bonding

    Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C

  19. Microquake activity associated with underground nuclear testing at the Nevada Test Site

    In the fall of 1976, the Los Alamos Close-In Seismic Network was added to the existing strong motion net deployed around each nuclear test conducted by Los Alamos. Six to ten stations, including both accelerometers and seismometers, are installed within a two-DOB (depth of burial) circle around SGZ (surface ground zero) and operated until the major portion of the microquake activity ceases, usually within 48 hours. Epicentral locations are determined and local magnitudes are calculated from event durations. Four primary conclusions have been reached on the basis of the data analyzed to date: (1) major faults bounding the immediate site of a nuclear test confine the observed microquake activity to the structural block in which the test is conducted; (2) microquake epicenters are generally distributed around the cavity created by the nuclear test with the peak occurrence generally occurring about three cavity radii away from the working point; (3) magnitudes of locatable microquakes apparently distribute randomly over the entire region of activity; and (4) the microquake activity as a function of time appears to be controlled by the collapse phenomenology

  20. Constrained Multiobjective Biogeography Optimization Algorithm

    Hongwei Mo

    2014-01-01

    Full Text Available Multiobjective optimization involves minimizing or maximizing multiple objective functions subject to a set of constraints. In this study, a novel constrained multiobjective biogeography optimization algorithm (CMBOA is proposed. It is the first biogeography optimization algorithm for constrained multiobjective optimization. In CMBOA, a disturbance migration operator is designed to generate diverse feasible individuals in order to promote the diversity of individuals on Pareto front. Infeasible individuals nearby feasible region are evolved to feasibility by recombining with their nearest nondominated feasible individuals. The convergence of CMBOA is proved by using probability theory. The performance of CMBOA is evaluated on a set of 6 benchmark problems and experimental results show that the CMBOA performs better than or similar to the classical NSGA-II and IS-MOEA.

  1. Trends in PDE constrained optimization

    Benner, Peter; Engell, Sebastian; Griewank, Andreas; Harbrecht, Helmut; Hinze, Michael; Rannacher, Rolf; Ulbrich, Stefan

    2014-01-01

    Optimization problems subject to constraints governed by partial differential equations (PDEs) are among the most challenging problems in the context of industrial, economical and medical applications. Almost the entire range of problems in this field of research was studied and further explored as part of the Deutsche Forschungsgemeinschaft (DFG) priority program 1253 on “Optimization with Partial Differential Equations” from 2006 to 2013. The investigations were motivated by the fascinating potential applications and challenging mathematical problems that arise in the field of PDE constrained optimization. New analytic and algorithmic paradigms have been developed, implemented and validated in the context of real-world applications. In this special volume, contributions from more than fifteen German universities combine the results of this interdisciplinary program with a focus on applied mathematics.   The book is divided into five sections on “Constrained Optimization, Identification and Control”...

  2. Constrained ballistics and geometrical optics

    Epstein, Marcelo

    2014-01-01

    The problem of constant-speed ballistics is studied under the umbrella of non-linear non-holonomic constrained systems. The Newtonian approach is shown to be equivalent to the use of Chetaev's rule to incorporate the constraint within the initially unconstrained formulation. Although the resulting equations are not, in principle, obtained from a variational statement, it is shown that the trajectories coincide with those of geometrical optics in a medium with a suitably chosen refractive inde...

  3. Bagging Constrained Equity Premium Predictors

    Tae-Hwy Lee; Eric Hillebrand; Marcelo Medeiros

    2013-01-01

    The literature on excess return prediction has considered a wide array of estimation schemes, among them unrestricted and restricted regression coefficients. We consider bootstrap aggregation (bagging) to smooth parameter restrictions. Two types of restrictions are considered: positivity of the regression coefficient and positivity of the forecast. Bagging constrained estimators can have smaller asymptotic mean-squared prediction errors than forecasts from a restricted model without bagging. ...

  4. Human uroporphyrinogen III synthase: NMR-based mapping of the active site.

    Cunha, Luis; Kuti, Miklos; Bishop, David F; Mezei, Mihaly; Zeng, Lei; Zhou, Ming-Ming; Desnick, Robert J

    2008-05-01

    Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex. PMID:18004775

  5. Relevance of Co, Ag-ferrierite catalysts acidity and cation siting to CH4-NOx-SCR activity

    The influence of acidity on Ag.Co exchanged ferrierite obtained from different parent forms was tested in CH4-DeNOx reaction. Ag and Co cation siting distribution and residual zeolite acidity were evaluated by means of a quantitative evaluation of catalyst acidity through NH3-TPD experiments and a detailed structural catalyst characterization by Rietveld refinement. A new nomenclature for the cation sites in hydrated and dehydrated cation exchange ferrierites was introduced for sake of clarity. The sites relative populations obtained by the UV-Vis spectra did not agree with the values given by the Rietveld refinement and the SCR. activity scale since the high abundance of Co cations in the retained most active position. Co2a, was shown by the less active catalyst obtained from the Na,K form. It was concluded that SCR activity does not only depend on Co and Ag siting within the zeolite framework but also by the presence of residual acidity evidenced on the most active catalysts. CH4 combustion tests showed that the presence of residual acidity appears relevant to SCR catalytic performances, likely related to its ability in methane activation. The importance of the coexistence of Co and zeolitic, acid sites for the HC-SCR suggested that SCR reaction could proceed on a dual site.

  6. Multiple-site mutations of phage Bp7 endolysin improves its activities against target bacteria

    Can; Zhang; Yuanchao; Wang; Huzhi; Sun; Huiying; Ren

    2015-01-01

    The widespread use of antibiotics has caused serious drug resistance. Bacteria that were once easily treatable are now extremely difficult to treat. Endolysin can be used as an alternative to antibiotics for the treatment of drug-resistant bacteria. To analyze the antibacterial activity of the endolysin of phage Bp7(Bp7e), a 489-bp DNA fragment of endolysin Bp7e was PCR-amplified from a phage Bp7 genome and cloned, and then a p ET28a-Bp7e prokaryotic expression vector was constructed. Two amino acids were mutated(L99A, M102E) to construct p ET28a-Bp7Δe, with p ET28a-Bp7e as a template. Phylogenetic analysis suggested that BP7e belongs to a T4-like phage endolysin group. Bp7e and its mutant Bp7Δe were expressed in Escherichia coli BL21(DE3) as soluble proteins. They were purified by affinity chromatography, and then their antibacterial activities were analyzed. The results demonstrated that the recombinant proteins Bp7e and Bp7Δe showed obvious antibacterial activity against Micrococcus lysodeikticus but no activity against Staphylococcus aureus. In the presence of malic acid, Bp7e and Bp7Δe exhibited an effect on most E. coli strains which could be lysed by phage Bp7, but no effect on Salmonella paratyphi or Pseudomonas aeruginosa. Moreover, Bp7Δe with double-site mutations showed stronger antibacterial activity and a broader lysis range than Bp7e.

  7. Biochemical characterization of mutants in the active site residues of the β-galactosidase enzyme of Bacillus circulans ATCC 31382

    Bultema, Jelle B; Bas J.H. Kuipers; Lubbert Dijkhuizen

    2014-01-01

    The Bacillus circulans ATCC 31382 β-galactosidase (BgaD) is a retaining-type glycosidase of glycoside hydrolase family 2 (GH2). Its commercial enzyme preparation, Biolacta N5, is used for commercial-scale production of galacto-oligosaccharides (GOS). The BgaD active site and catalytic amino acid residues have not been studied. Using bioinformatic routines we identified two putative catalytic glutamates and two highly conserved active site histidines. The site-directed mutants E447N, E532Q, an...

  8. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

    Gittel, Antje; Barta, Jiri; Kohoutova, Iva;

    2014-01-01

    its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen...... site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure...

  9. Assessment of national systems for obtaining local acceptance of waste management siting and routing activities

    Paige, H.W.; Lipman, D.S.; Owens, J.E.

    1980-07-01

    There is a rich mixture of formal and informal approaches being used in our sister nuclear democracies in their attempts to deal with the difficulties of obtaining local acceptance for siting of waste management facilities and activities. Some of these are meeting with a degree of success not yet achieved in the US. Although this survey documents and assesses many of these approaches, time did not permit addressing in any detail their relevance to common problems in the US. It would appear the US could benefit from a periodic review of the successes and failures of these efforts, including analysis of their applicability to the US system. Of those countries (Germany, Sweden, Switzerland, Japan, Belgium, and the US) who are working to a time table for the preparation of a high-level waste (HLW) repository, Germany is the only country to have gained local siting acceptance for theirs. With this (the most difficult of siting problems) behind them they appear to be in the best overall condition relative to waste management progress and plans. This has been achieved without a particularly favorable political structure, made up for by determination on the part of the political leadership. Of the remaining three countries studied (France, UK and Canada) France, with its AVM production facility, is clearly the world leader in the HLW immobilization aspect of waste management. France, Belgium and the UK appear to have the least favorable political structures and environments for arriving at waste management decisions. US, Switzerland and Canada appear to have the least favorable political structures and environments for arriving at waste management decisions.

  10. In Situ Probing of the Active Site Geometry of Ultrathin Nanowires for the Oxygen Reduction Reaction.

    Liu, Haiqing; An, Wei; Li, Yuanyuan; Frenkel, Anatoly I; Sasaki, Kotaro; Koenigsmann, Christopher; Su, Dong; Anderson, Rachel M; Crooks, Richard M; Adzic, Radoslav R; Liu, Ping; Wong, Stanislaus S

    2015-10-01

    To create truly effective electrocatalysts for the cathodic reaction governing proton exchange membrane fuel cells (PEMFC), namely the oxygen reduction reaction (ORR), necessitates an accurate and detailed structural understanding of these electrocatalysts, especially at the nanoscale, and to precisely correlate that structure with demonstrable performance enhancement. To address this key issue, we have combined and interwoven theoretical calculations with experimental, spectroscopic observations in order to acquire useful structural insights into the active site geometry with implications for designing optimized nanoscale electrocatalysts with rationally predicted properties. Specifically, we have probed ultrathin (∼2 nm) core-shell Pt∼Pd9Au nanowires, which have been previously shown to be excellent candidates for ORR in terms of both activity and long-term stability, from the complementary perspectives of both DFT calculations and X-ray absorption spectroscopy (XAS). The combination and correlation of data from both experimental and theoretical studies has revealed for the first time that the catalytically active structure of our ternary nanowires can actually be ascribed to a PtAu∼Pd configuration, comprising a PtAu binary shell and a pure inner Pd core. Moreover, we have plausibly attributed the resulting structure to a specific synthesis step, namely the Cu underpotential deposition (UPD) followed by galvanic replacement with Pt. Hence, the fundamental insights gained into the performance of our ultrathin nanowires from our demonstrated approach will likely guide future directed efforts aimed at broadly improving upon the durability and stability of nanoscale electrocatalysts in general. PMID:26402364

  11. Natural resource management activities at the Savannah River Site. Environmental Assessment

    1993-07-01

    This environmental assessment (EA) reviews the environmental consequences of ongoing natural resource management activities on the Savannah River Site (SRS). Appendix A contains the Natural Resources Management Plant (NRMP). While several SRS organizations have primary responsibilities for different elements of the plan, the United States Department of Agriculture (USDA), Forest Service, Savannah River Forest Station (SRFS) is responsible for most elements. Of the river scenarios defined in 1985, the High-Intensity Management alternative established the upper bound of environmental consequences; it represents a more intense level of resource management than that being performed under current resource management activities. This alternative established compliance mechanisms for several natural resource-related requirements and maximum practical timber harvesting. Similarly, the Low-Intensity Management alternative established the lower bound of environmental consequences and represents a less intense level of resource management than that being performed under current resource management activities. This alternative also established compliance mechanisms, but defined a passively managed natural area. The Proposed Action of this EA describes the current level of multiple-natural resource management. This EA reviews the proposed action, and the high and low intensity alternative scenarios.

  12. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    Cao, Huiluo

    2015-07-21

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  13. Analysis of the activity of virus internal ribosome entry site in silkworm Bombyx mori

    Lupeng Ye; Lanfang Zhuang; Jisheng Li; Zhengying You; Jianshe Liang; Hao Wei; Jianrong Lin

    2013-01-01

    Internal ribosome entry site (IRES) has been widely used in genetic engineering; however,the application in silkworm (Bombyx mori) has hardly been reported.In this study,the biological activity of partial sequence of Encephalomyocardltis virus (EMCV) IRES,Rhopalosiphum padi virus (RhPV)IRES,and the hybrid of IRES of EMCV and RhPV were investigated in Spodoptera frugiperda (Sf9) cell line and silkworm tissues.The hybrid IRES of EMCV and RhPV showed more effective than EMCV IRES or RhPV IRES in promoting downstream gene expression in insect and silkworm.The activities of all IRESs in middle silk gland of silkworm were higher than those in the fat body and posterior silk gland.The hybrid IRES of EMCV and RhPV was integrated into silkworm genome by transgenic technology to test biological activity of IRES.Each of the positive transgenic individuals had significant expression of report gene EGFP.These results suggested that IRES has a potential to be used in the genetic engineering research of silkworm.

  14. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    Huiluo eCao

    2015-07-01

    Full Text Available The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of ammonia oxidizing archaea in different habitats (water versus sediment potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  15. Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations

    Prostasin or human channel-activating protease 1 has been reported to play a critical role in the regulation of extracellular sodium ion transport via its activation of the epithelial cell sodium channel. Here, the structure of the extracellular portion of the membrane associated serine protease has been solved to high resolution in complex with a nonselective d-FFR chloromethyl ketone inhibitor, in an apo form, in a form where the apo crystal has been soaked with the covalent inhibitor camostat and in complex with the protein inhibitor aprotinin. It was also crystallized in the presence of the divalent cation Ca+2. Comparison of the structures with each other and with other members of the trypsin-like serine protease family reveals unique structural features of prostasin and a large degree of conformational variation within specificity determining loops. Of particular interest is the S1 subsite loop which opens and closes in response to basic residues or divalent ions, directly binding Ca+2 cations. This induced fit active site provides a new possible mode of regulation of trypsin-like proteases adapted in particular to extracellular regions with variable ionic concentrations such as the outer membrane layer of the epithelial cell.

  16. Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India and their antimicrobial activities

    Salam eNimaichand

    2015-05-01

    Full Text Available Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups, Micromonospora (4, Amycolatopsis (3, Arthrobacter (3, Kitasatospora (2, Janibacter (1, Nocardia (1, Pseudonocardia (1 and Rhodococcus (1. Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS. The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

  17. AKAP9 regulates activation-induced retention of T lymphocytes at sites of inflammation.

    Herter, Jan M; Grabie, Nir; Cullere, Xavier; Azcutia, Veronica; Rosetti, Florencia; Bennett, Paul; Herter-Sprie, Grit S; Elyaman, Wassim; Luscinskas, Francis W; Lichtman, Andrew H; Mayadas, Tanya N

    2015-01-01

    The mechanisms driving T cell homing to lymph nodes and migration to tissue are well described but little is known about factors that affect T cell egress from tissues. Here, we generate mice with a T cell-specific deletion of the scaffold protein A kinase anchoring protein 9 (AKAP9) and use models of inflammatory disease to demonstrate that AKAP9 is dispensable for T cell priming and migration into tissues and lymph nodes, but is required for T cell retention in tissues. AKAP9 deficiency results in increased T cell egress to draining lymph nodes, which is associated with impaired T cell re-activation in tissues and protection from organ damage. AKAP9-deficient T cells exhibit reduced microtubule-dependent recycling of TCRs back to the cell surface and this affects antigen-dependent activation, primarily by non-classical antigen-presenting cells. Thus, AKAP9-dependent TCR trafficking drives efficient T cell re-activation and extends their retention at sites of inflammation with implications for disease pathogenesis. PMID:26680259

  18. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme

    Berezniak, Tomasz [University of Heidelberg; Zahran, Mai [ORNL; Imhof, Petra [University of Heidelberg; Jaeschke, Andres [Free University of Berlin; Smith, Jeremy C [ORNL

    2010-10-01

    The Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme, accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition, a reaction with broad application in organic chemistry. Here, the Diels-Alderase ribozyme is examined via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. The simulations indicate that the catalytic pocket is highly dynamic. At low Mg(2+) ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of Mg(2+) ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high Mg(2+) cation concentration exhibits a double minimum, with a barrier to opening of approximately 5.5 kJ/mol and the closed state approximately 3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the Mg(2+) ion concentration

  19. In Operando Identification of Geometrical-Site-Dependent Water Oxidation Activity of Spinel Co3O4.

    Wang, Hsin-Yi; Hung, Sung-Fu; Chen, Han-Yi; Chan, Ting-Shan; Chen, Hao Ming; Liu, Bin

    2016-01-13

    Spinel Co3O4, comprising two types of cobalt ions: one Co(2+) in the tetrahedral site (Co(2+)(Td)) and the other two Co(3+) in the octahedral site (Co(3+)(Oh)), has been widely explored as a promising oxygen evolution reaction (OER) catalyst for water electrolysis. However, the roles of two geometrical cobalt ions toward the OER have remained elusive. Here, we investigated the geometrical-site-dependent OER activity of Co3O4 catalyst by substituting Co(2+)(Td) and Co(3+)(Oh) with inactive Zn(2+) and Al(3+), respectively. Following a thorough in operando analysis by electrochemical impedance spectroscopy and X-ray absorption spectroscopy, it was revealed that Co(2+)Td site is responsible for the formation of cobalt oxyhydroxide (CoOOH), which acted as the active site for water oxidation. PMID:26710084

  20. Redox activity of airborne particulate matter at different sites in the Los Angeles Basin

    Epidemiologic studies have shown associations between ambient particulate matter (PM) and adverse health outcomes including increased mortality, emergency room visits, and time lost from school and work. The mechanisms of PM-related health effects are still incompletely understood, but a hypothesis under investigation is that many of the adverse health effects may derive from oxidative stress, initiated by the formation of reactive oxygen species (ROS) within affected cells. While the adverse effects from PM have historically been associated with the airborne concentration of PM and more recently fine-particle PM, we considered it relevant to develop an assay to quantitatively measure the ability of PM to catalyze ROS generation as the initial step in the induction of oxidative stress. This ability of PM could then be related to different sources, chemical composition, and physical and spatial/temporal characteristics in the ambient environment. The measurement of ROS-forming ability in relation to sources and other factors will have potential relevance to control of redox-active PM. If oxidative stress represents a relevant mechanism of toxicity from PM, the measurement of redox activity represents a first step in the elucidation of the subsequent downstream processes. We have developed an assay for PM redox activity, utilizing the reduction of oxygen by dithiothreitol which serves as an electron source. We have found that PM will catalyze the reduction of oxygen and have examined the distribution and chemical characteristics of the redox activity of PM fractions collected in different sites in the Los Angeles Basin. Samples of concentrated coarse, fine, and ultrafine PM, obtained with aerosol concentrators, were studied with regard to their chemical properties and redox activity. Redox activity was highest in the ultrafine fraction, in agreement with results indicating ultrafines were the most potent toward inducing that heme oxygenase expression and depleting

  1. Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity.

    Anderson, Kyle W; Mast, Natalia; Hudgens, Jeffrey W; Lin, Joseph B; Turko, Illarion V; Pikuleva, Irina A

    2016-05-27

    Cytochrome P450 46A1 (CYP46A1) is a microsomal enzyme and cholesterol 24-hydroxylase that controls cholesterol elimination from the brain. This P450 is also a potential target for Alzheimer disease because it can be activated pharmacologically by some marketed drugs, as exemplified by efavirenz, the anti-HIV medication. Previously, we suggested that pharmaceuticals activate CYP46A1 allosterically through binding to a site on the cytosolic protein surface, which is different from the enzyme active site facing the membrane. Here we identified this allosteric site for efavirenz on CYP46A1 by using a combination of hydrogen-deuterium exchange coupled to MS, computational modeling, site-directed mutagenesis, and analysis of the CYP46A1 crystal structure. We also mapped the binding region for the CYP46A1 redox partner oxidoreductase and found that the allosteric and redox partner binding sites share a common border. On the basis of the data obtained, we propose the mechanism of CYP46A1 allostery and the pathway for the signal transmission from the P450 allosteric site to the active site. PMID:27056331

  2. Synthesis, Purification and Characterization of Ferredoxins with Re-Designed Active Sites

    Kristensen, Jytte

    Iron-sulfur proteins with cuboidal [Fe4S4] clusters exhibit a remarkable functional diversity. Insights on the factors determining the function of the protein can be obtained by modifications of the metal site by incorporation of metals other than iron in the active site of the protein. This......, purification and characteri¬za¬tion of the two new proteins were carried out. The P. furiosus ferredoxin was studied as a reference for the two artificial proteins. The P. furiosus [Fe3S4] and [Fe4S4] ferre¬doxins were studied with cyclic voltam¬¬me¬try as re¬fe¬rence for the work on the artificial proteins....... The effects of different buffer systems and additives were tested to find the optimal conditions for electro¬chemi¬cal charac¬te¬ri¬za¬tion. Different buffer systems did not have a significant effect, but the voltammo¬grams were strongly dependent on the NaCl content as NaCl had an attenua¬ting effect...

  3. Fluconazole Binding and Sterol Demethylation in Three CYP51 Isoforms Indicate Differences in Active Site Topology

    Bellamine, A.; Lepesheva, Galina I.; Waterman, Mike (Vanderbilt)

    2010-11-16

    14{alpha}-Demethylase (CYP51) is a key enzyme in all sterol biosynthetic pathways (animals, fungi, plants, protists, and some bacteria), catalyzing the removal of the C-14 methyl group following cyclization of squalene. Based on mutations found in CYP51 genes from Candida albicans azole-resistant isolates obtained after fluconazole treatment of fungal infections, and using site-directed mutagenesis, we have found that fluconazole binding and substrate metabolism vary among three different CYP51 isoforms: human, fungal, and mycobacterial. In C. albicans, the Y132H mutant from isolates shows no effect on fluconazole binding, whereas the F145L mutant results in a 5-fold increase in its IC{sub 50} for fluconazole, suggesting that F145 (conserved only in fungal 14{alpha}-demethylases) interacts with this azole. In C. albicans, F145L accounts, in part, for the difference in fluconazole sensitivity reported between mammals and fungi, providing a basis for treatment of fungal infections. The C. albicans Y132H and human Y145H CYP51 mutants show essentially no effect on substrate metabolism, but the Mycobacterium tuberculosis F89H CYP51 mutant loses both its substrate binding and metabolism. Because these three residues align in the three isoforms, the results indicate that their active sites contain important structural differences, and further emphasize that fluconazole and substrate binding are uncoupled properties.

  4. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase.

    Cyril Moccand

    Full Text Available The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2 that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5'-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5'-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.

  5. 76 FR 51391 - Commercial Wind Lease Issuance and Site Characterization Activities on the Atlantic Outer...

    2011-08-18

    ....605- 285.618. After the lessee has collected sufficient site characterization and assessment data, the...), reasonably foreseeable site characterization scenarios within these lease areas (including geophysical... from leasing, site characterization, and site assessment in and around the Call Area described...

  6. The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

    Gopal, B.; Madan, Lalima L.; Betz, Stephen F.; Kossiakoff, Anthony A. (Indian); (UC); (GeneFormatics)

    2010-11-10

    Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s), whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.

  7. Main Principles of the Organization of Decommissioning Activities for Legacy Sites

    As a result of more than 60 years development of nuclear industry in the former Soviet Union and in the Russian Federation there has accumulated a number of unresolved problems associated with contamination of facilities and environment during the early stages of research and industrial activities. Prior to the year 2000 most of the problems were solved slowly; the main decisions were postponed for the future. During that time were done the local works for the rehabilitation of contaminated sites. The Federal Target Programme ''Nuclear and Radiation Safety for 2008 and for the period to 2015'' was adopted in 2008. Analysis of accumulated experience as result of previous work on decontamination to develop new project management system for the rehabilitation of the nuclear legacy is needed. This CRP contribution is aimed at solving the tasks of the rehabilitation of the nuclear legacy. (author)

  8. Following [FeFe] Hydrogenase Active Site Intermediates by Time-Resolved Mid-IR Spectroscopy.

    Mirmohades, Mohammad; Adamska-Venkatesh, Agnieszka; Sommer, Constanze; Reijerse, Edward; Lomoth, Reiner; Lubitz, Wolfgang; Hammarström, Leif

    2016-08-18

    Time-resolved nanosecond mid-infrared spectroscopy is for the first time employed to study the [FeFe] hydrogenase from Chlamydomonas reinhardtii and to investigate relevant intermediates of the enzyme active site. An actinic 355 nm, 10 ns laser flash triggered photodissociation of a carbonyl group from the CO-inhibited state Hox-CO to form the state Hox, which is an intermediate of the catalytic proton reduction cycle. Time-resolved infrared spectroscopy allowed us to directly follow the subsequent rebinding of the carbonyl, re-forming Hox-CO, and determine the reaction half-life to be t1/2 ≈ 13 ± 5 ms at room temperature. This gives direct information on the dynamics of CO inhibition of the enzyme. PMID:27494400

  9. Design and performance of the Savannah River Site Billet Active Well Coincidence Counter

    The Savannah River Site (SRS) has acquired, installed, and tested a custom-built Billet Active Well (neutron) Coincidence Counter (BAWCC). The BAWCC is used to make accountability measurements of the 235U content of U-Al coextrusion billets in the SRS fuel fabrication facility. The instrument design incorporates a unique center-source configuration, with two moderated americium-lithium (AmLi) neutron sources located in a central spindle that inserts through the center hole of the U-Al billets. This configuration, a result of earlier experimental studies at SRS, yields improved response and precision for billet assay when compared to the standard AWCC source arrangement. Initial tests of the BAWCC at SRS have yielded one-sigma uncertainties of 0.8--1.0% for a fifteen-minute assay. This paper will describe the design, testing program and performance characteristics of the BAWCC

  10. Neutron activation analysis in an industrial laboratory using an off-site nuclear reactor

    A multifunctional research laboratory, such as Procter and Gamble's Miami Valley Laboratories, requires elemental analyses on many materials. A general survey technique is important even if the information it provides is incomplete or is less precise than single element analyses. Procter and Gamble has developed neutron activation analysis (NAA) capabilities using a nuclear reactor several hundred miles away. The concentration of 40 to 50 elements can be determined in a variety of matrices. We have found NAA to be a powerful supplement to some of the more classical analytical techniques even without having an on-site neutron source. We have also found an automated data acquisition system to be essential for the successful application of NAA in an industrial laboratory

  11. Alpha 4 integrin directs virus-activated CD8+ T cells to sites of infection

    Christensen, Jan Pravsgaard; Andersson, E C; Scheynius, A; Marker, O; Thomsen, Allan Randrup

    1995-01-01

    response is induced, which is associated with marked CD8+ cell-mediated inflammation. Two expressions of LCMV-induced inflammation were studied: meningitis induced by intracerebral infection and adoptive transfer of virus-specific delayed-type hypersensitivity. Our previous studies have shown that LCMV...... infection results in the appearance of activated CD8+ cells with an increased expression of VLA-4. In this study we have compared various T cell high and low responder situations, and these experiments revealed that acute inflammation correlates directly with VLA-4 expression on splenic CD8+ cells. This...... ability to transfer virus-specific, delayed-type hypersensitivity when the donor cells were given i.v., but not when the cells were injected directly into the test site. Co-transfer of CD8-depleted cells with anti-VLA-4-blocked cells did not reveal any cooperation. Taken together, these results indicate...

  12. Chemical Characterization of Ceramics from Malaysian Archeological Sites by Neutron Activation Analysis

    Neutron activation analysis technique has been applied in analysis of about 80 Chinese ceramic shards of blue and white porcelain and stoneware collected from two shipwrecks discovered in Malaysian waters as well as samples from kiln site in Jingdezhen, China. The elements determined were Ba, Ce, Co, Cr, Cs, Eu, Fe, Hf, La, Mn, Rb, Sb, Sc, Sm, Ta, Tb, Th, U, Yb, Zn and Zr. Statistical analysis including principal component analysis and cluster analysis have been used in data interpretation. The results indicated that the majority of blue and white porcelain found in the shipwrecks were from Jingdezhen. A few samples of blue and white shards were so different in elemental profile compared to those from Jingdezhen. There were also three groups of stoneware but their origin has yet to be identified. (author)

  13. Use of Temperature and Surface Gas Flux as Novel Measures of Microbial Activity at a Crude Oil Spill Site

    Bekins, B. A.; Warren, E.; Sihota, N. J.; Hostettler, F. D.

    2012-12-01

    Degradation of crude oil in the subsurface has been studied for over 30 years at a spill site located near Bemidji, Minnesota, USA. The well-characterized site is being used to experiment with the use of surface gas flux and temperature measurements as novel methods for quantifying microbial activity. In the largest subsurface oil body, a 2-m-thick smear zone spans the water table 6-8 m below the surface. Methane produced from degradation of the oil diffuses upward and mixes with oxygen from the surface supporting aerobic methanotrophy at 2-4 m depth. The methane oxidation produces CO2 and heat at rates which are hypothetically proportional to other measures of subsurface microbial activity. To test this hypothesis, vertical profiles of temperature and microbial populations, surface CO2 flux, and oil degradation state were measured at three sites in the oil body and one background site. Temperature increases in the oil zone near the water table were 1-4°C above the background site. The site with the highest temperature increase at the water table also had the highest concentrations of gene copy numbers for methanogens (mcrA) and methanotrophs (pmoA) along with the most degraded oil. Surface CO2 flux over the oil sites averaged more than twice that at the background site but was not consistently highest over the site with the highest activity by other measures. One possible explanation for this discrepancy is variation in the effective diffusion coefficient of the vadose zone between the methanotrophic zone and the surface. At the level of the methanotrophic zone, temperatures were elevated 2-6°C over the background values but again the site with greatest average annual temperature increase was not at the most active site. This may be due to enhanced recharge at the most active site, which lies at the center of a local topographic depression where focused recharge occurs. Overall, the temperature and flux data showed significant increases at the oil sites compared

  14. An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase.

    Murphy, Jesse R; Donini, Stefano; Kappock, T Joseph

    2015-10-01

    Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS. PMID:26457521

  15. Characterization of Metal Binding in the Active Sites of acireductone dioxygenase Isoforms from Klebsiella ATCC 8724

    S Chai; T Ju; M Dang; R Goldsmith; M Maroney; T Pochapsky

    2011-12-31

    The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities toward their common substrates (1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M{sup 2+} metal ion bound in the active site. The Ni{sup 2+}-bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate, and carbon monoxide, while the Fe{sup 2+}-bound FeARD catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS), and isothermal calorimetry measurements, it is concluded that the same four residues, His96, His98, Glu102 and His140, provide the protein-based ligands for the metal in both the Ni- and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a histidine ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved nonligand acidic residues, Glu95 and Glu100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu100 mutant reconstitutes readily but has low activity. Mutation of Asp101 results in an active enzyme that incorporates

  16. Irreversible loss of ice nucleation active sites in mineral dust particles caused by sulphuric acid condensation

    R. C. Sullivan

    2010-07-01

    Full Text Available During the FROST-2 (FReezing Of duST measurement campaign conducted at the Leipzig Aerosol Cloud Interaction Simulator (LACIS, we investigated changes in the ice nucleation properties of 300 nm Arizona test dust mineral particles following thermochemical processing by varying amounts and combinations of exposure to sulphuric acid vapour, ammonia gas, water vapour, and heat. The processed aerosol's heterogeneous ice nucleation properties were determined in both the water subsaturated and supersaturated humidity regimes at −30 °C and −25 °C using Colorado State University's continuous flow diffusion chamber. The amount of sulphuric acid coating material was estimated by an aerosol mass spectrometer and from CCN-derived hygroscopicity measurements. The condensation of sulphuric acid decreased the dust particles' ice nucleation ability in proportion to the amount of sulphuric acid added. Heating the coated particles in a thermodenuder at 250 °C – intended to evaporate the sulphuric acid coating – reduced their freezing ability even further. We attribute this behaviour to accelerated acid digestion of ice active surface sites by heat. Exposing sulphuric acid coated dust to ammonia gas produced particles with similarly poor freezing potential; however a portion of their ice nucleation ability could be restored after heating in the thermodenuder. In no case did any combination of thermochemical treatments increase the ice nucleation ability of the coated mineral dust particles compared to unprocessed dust. These first measurements of the effect of identical chemical processing of dust particles on their ice nucleation ability in both water subsaturated and mixed-phase supersaturated cloud conditions revealed that ice nucleation was more sensitive to all coating treatments in the water subsaturated regime. The results clearly indicate irreversible impairment of ice nucleation activity in both regimes after condensation of concentrated

  17. Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation

    Boudreaux, David A.; Maiti, Tushar K.; Davies, Christopher W.; Das, Chittaranjan (Purdue)

    2010-07-06

    Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 {angstrom} from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal {beta}-hairpin at the distal site - a surface-exposed hydrophobic crevice 17 {angstrom} away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 {angstrom} of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.

  18. Scheduling of resource-constrained projects

    Klein, Robert

    2000-01-01

    Project management has become a widespread instrument enabling organizations to efficiently master the challenges of steadily shortening product life cycles, global markets and decreasing profit margins. With projects increasing in size and complexity, their planning and control represents one of the most crucial management tasks. This is especially true for scheduling, which is concerned with establishing execution dates for the sub-activities to be performed in order to complete the project. The ability to manage projects where resources must be allocated between concurrent projects or even sub-activities of a single project requires the use of commercial project management software packages. However, the results yielded by the solution procedures included are often rather unsatisfactory. Scheduling of Resource-Constrained Projects develops more efficient procedures, which can easily be integrated into software packages by incorporated programming languages, and thus should be of great interest for practiti...

  19. Days of dismantling activities of installations and rehabilitation of contaminated sites in France; Demantelement des installations et rehabilitation de sites contamines

    NONE

    2008-07-01

    The objective of these days, organized by the section environment of the French society of radiation protection, is to present a panorama of the activities of nuclear installations dismantling and contaminated sites rehabilitation in France, by leaning in the same time on practical cases and by stating the French rule and the national and international recommendations on the subject. These days have also for object to approach the stakes associated with the sectors of waste management and the materials generated by these activities and in a more general way, the stakes to come for the different actors of the dismantling and the rehabilitation. (N.C.)

  20. A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.

    Agata Jacewicz

    Full Text Available Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A, that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the Pol(D714A mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced k pol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.

  1. Image compression using constrained relaxation

    He, Zhihai

    2007-01-01

    In this work, we develop a new data representation framework, called constrained relaxation for image compression. Our basic observation is that an image is not a random 2-D array of pixels. They have to satisfy a set of imaging constraints so as to form a natural image. Therefore, one of the major tasks in image representation and coding is to efficiently encode these imaging constraints. The proposed data representation and image compression method not only achieves more efficient data compression than the state-of-the-art H.264 Intra frame coding, but also provides much more resilience to wireless transmission errors with an internal error-correction capability.

  2. Constraining Lorentz violation with cosmology.

    Zuntz, J A; Ferreira, P G; Zlosnik, T G

    2008-12-31

    The Einstein-aether theory provides a simple, dynamical mechanism for breaking Lorentz invariance. It does so within a generally covariant context and may emerge from quantum effects in more fundamental theories. The theory leads to a preferred frame and can have distinct experimental signatures. In this Letter, we perform a comprehensive study of the cosmological effects of the Einstein-aether theory and use observational data to constrain it. Allied to previously determined consistency and experimental constraints, we find that an Einstein-aether universe can fit experimental data over a wide range of its parameter space, but requires a specific rescaling of the other cosmological densities. PMID:19113765

  3. Identification of residues involved in nucleotidyltransferase activity of JHP933 from helicobacter pyloriby site-directed mutagenesis

    Ye Xianren

    2016-01-01

    Full Text Available Helicobacter pylori is a well-known bacterial pathogen involved in the development of peptic ulcer, gastric adenocarcinoma and other forms of gastric cancer. Evidence has suggested that certain strain-specific genes in the plasticity region may play key roles in the pathogenesis of H. pylori-associated gastroduodenal diseases. Therefore there is considerable interest in the strain-specific genes located in the plasticity regions of H. pylori. JHP933 is encoded by the gene in the plasticity region of H. pylori strain J99. Recently, the crystal structure of JHP933 has confirmed it as a nucleotidyltransferase (NTase superfamily protein and a putative active site has been proposed. However, no evidence from direct functional assay has been presented to confirm the active site and little is known about the functional mechanism of JHP933. Here, through superimposition with Cid1/NTP complex structures, we modelled the complex structures of JHP933 with different NTPs. Based on the models and using rational site-directed mutagenesis combined with enzymatic activity assays, we confirm the active site and identify several residues important for the nucleotidyl transferring function of JHP933. Furthermore, mutations of these active site residues result in the abolishment of the nucleotidyltransferase activity of JHP933. This work provides preliminary insight into the molecular mechanism underlying the pathophysiological role in H. pylori infection of JHP933 as a novel NTase superfamily protein.

  4. Structural Basis for the Inhibition of RNase H Activity of HIV-1 Reverse Transcriptase by RNase H Active Site-Directed Inhibitors

    Su, Hua-Poo; Yan, Youwei; Prasad, G. Sridhar; Smith, Robert F.; Daniels, Christopher L.; Abeywickrema, Pravien D.; Reid, John C.; Loughran, H. Marie; Kornienko, Maria; Sharma, Sujata; Grobler, Jay A.; Xu, Bei; Sardana, Vinod; Allison, Timothy J.; Williams, Peter D.; Darke, Paul L.; Hazuda, Daria J.; Munshi, Sanjeev (Merck)

    2010-09-02

    HIV/AIDS continues to be a menace to public health. Several drugs currently on the market have successfully improved the ability to manage the viral burden in infected patients. However, new drugs are needed to combat the rapid emergence of mutated forms of the virus that are resistant to existing therapies. Currently, approved drugs target three of the four major enzyme activities encoded by the virus that are critical to the HIV life cycle. Although a number of inhibitors of HIV RNase H activity have been reported, few inhibit by directly engaging the RNase H active site. Here, we describe structures of naphthyridinone-containing inhibitors bound to the RNase H active site. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain. In addition, one of the naphthyridinone-based compounds was found to bind at a second site close to the polymerase active site and non-nucleoside/nucleotide inhibitor sites in a metal-independent manner. Further characterization, using fluorescence-based thermal denaturation and a crystal structure of the isolated RNase H domain reveals that this compound can also bind the RNase H site and retains the metal-dependent binding mode of this class of molecules. These structures provide a means for structurally guided design of novel RNase H inhibitors.

  5. Prediction of P53 mutants (multiple sites transcriptional activity based on structural (2D&3D properties.

    R Geetha Ramani

    Full Text Available Prediction of secondary site mutations that reinstate mutated p53 to normalcy has been the focus of intense research in the recent past owing to the fact that p53 mutants have been implicated in more than half of all human cancers and restoration of p53 causes tumor regression. However laboratory investigations are more often laborious and resource intensive but computational techniques could well surmount these drawbacks. In view of this, we formulated a novel approach utilizing computational techniques to predict the transcriptional activity of multiple site (one-site to five-site p53 mutants. The optimal MCC obtained by the proposed approach on prediction of one-site, two-site, three-site, four-site and five-site mutants were 0.775,0.341,0.784,0.916 and 0.655 respectively, the highest reported thus far in literature. We have also demonstrated that 2D and 3D features generate higher prediction accuracy of p53 activity and our findings revealed the optimal results for prediction of p53 status, reported till date. We believe detection of the secondary site mutations that suppress tumor growth may facilitate better understanding of the relationship between p53 structure and function and further knowledge on the molecular mechanisms and biological activity of p53, a targeted source for cancer therapy. We expect that our prediction methods and reported results may provide useful insights on p53 functional mechanisms and generate more avenues for utilizing computational techniques in biological data analysis.

  6. Site-directed mutation of a laccase from Thermus thermophilus: Effect on the activity profile

    Liu Xin

    2012-01-01

    Full Text Available A site-directed mutant R453T of a laccase from Thermus thermophilus HB27 (Tth-laccase was constructed in order to investigate the effect on laccase catalytic properties. The mutated gene was cloned and overexpressed in Escherichia coli. Nickel-affinity purification was achieved and followed by copper ion incorporation. The mature mutated enzyme was quantitatively equal to the wild type. A photometric assay based on the oxidation of the substrate 2,2-azino-bis-(3- ethylbenzthiazoline-6-sulfonate (ABTS was employed in comparison with the wild-type Tth-laccase on catalytic properties. The R453T mutant exhibited improvement in substrate affinity and specific activity at room temperature, whereas those parameters were not significantly influenced when the temperature increased up to 65°C or higher. The mutant had better catalytic activity than that of the wild type at acidic pH. Investigated by circular dichroism spectroscopy, the mutant Tth-laccase displayed similar profiles at low and high temperatures.

  7. Active site histidine in spinach ribulosebisphosphate carboxylase/oxygenase modified by diethyl pyrocarbonate

    [3H] Diethyl pyrocarbonate was synthesized from [3H] ethanol prepared by the reduction of acetaldehyde by NaB3H4. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from spinach was inactivated with this reagent at pH 7.0 the presence of 20 mM Mg2+, and tryptic peptides that contained modified histidine residues were isolated by reverse-phase high-performance liquid chromatography. Labeling of the enzyme was conducted in the presence and absence of the competitive inhibitor sedoheptulose 1,7-bisphosphate. The amount of one peptide that was heavily labeled in the absence of this compound was reduced 10-fold in its presence. The labeled residue was histidine-298. This result, in combination with earlier experiments, suggests that His-298 in spinach RuBisCO is located in the active site domain and is essential to enzyme activity. This region of the primary structure is strongly conserved in seven other ribulosebisphosphate carboxylases from divergent sources

  8. Divergent Contributions of Conserved Active Site Residues to Transcription by Eukaryotic RNA Polymerases I and II

    Olga V. Viktorovskaya

    2013-09-01

    Full Text Available Multisubunit RNA polymerases (msRNAPs exhibit high sequence and structural homology, especially within their active sites, which is generally thought to result in msRNAP functional conservation. However, we show that mutations in the trigger loop (TL in the largest subunit of RNA polymerase I (Pol I yield phenotypes unexpected from studies of Pol II. For example, a well-characterized gain-of-function mutation in Pol II results in loss of function in Pol I (Pol II: rpb1- E1103G; Pol I: rpa190-E1224G. Studies of chimeric Pol II enzymes hosting Pol I or Pol III TLs suggest that consequences of mutations that alter TL dynamics are dictated by the greater enzymatic context and not solely the TL sequence. Although the rpa190-E1224G mutation diminishes polymerase activity, when combined with mutations that perturb Pol I catalysis, it enhances polymerase function, similar to the analogous Pol II mutation. These results suggest that Pol I and Pol II have different rate-limiting steps.

  9. Trace cobalt speciation in bacteria and at enzymic active sites using emission Moessbauer spectroscopy

    Kamnev, A.A.; Antonyuk, L.P.; Smirnova, V.E.; Serebrennikova, O.B. [Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov (Russian Federation); Kulikov, L.A.; Perfiliev, Yu.D. [Laboratory of Nuclear Chemistry Techniques, Department of Radiochemistry, Faculty of Chemistry, Moscow State University (Russian Federation)

    2002-02-01

    {sup 57}Co emission Moessbauer spectroscopy (EMS) allows the chemical state of cobalt, as influenced by its coordination environment, to be monitored in biological samples at its physiological (trace) concentrations. To draw attention to EMS as a valuable tool for speciation of cobalt in biocomplexes, the process of cobalt(II) metabolism in cells of the plant growth-promoting rhizobacterium Azospirillum brasilense Sp245 was investigated using EMS of {sup 57}Co{sup II}-doped bacterial cells. EMS measurements also showed {sup 57}Co{sup II}-activated glutamine synthetase (GS, a key enzyme of nitrogen metabolism, isolated from this bacterium) to have two different cobalt(II) forms at its active sites, in agreement with data available on other bacterial GSs. Chemical after-effects following electron capture by the nucleus of the parent {sup 57}Co{sup II} during the {sup 57}Co{yields}{sup 57}Fe transition, which contribute to the formation of a stabilised daughter {sup 57}Fe{sup III} component along with the nucleogenic {sup 57}Fe{sup II} forms, are also briefly considered. (orig.)

  10. Effects of the cofactor binding sites on the activities of secondary alcohol dehydrogenase (SADH).

    Wang, Tao; Chen, Xiangjun; Han, Jun; Ma, Sichun; Wang, Jianmei; Li, Xufeng; Zhang, Hui; Liu, Zhibin; Yang, Yi

    2016-07-01

    SADHs from Thermoanaerobacter ethanolicus are enzymes that, together with various cofactors, catalyze the reversible reduction of carbonyl compounds to their corresponding alcohols. To explore how cofactors bind to SADH, TeSADH was cloned in this study, and Ser(199) and Arg(200) were replaced by Tyr and Asp, respectively. Both sites were expected to be inside or adjacent to the cofactor-binding domain according to computational a prediction. Analysis of TeSADH activities revealed that the enzymatic efficiency (kcat/Km) of the S199Y mutant was noticeably enhanced using by NADH, NADPH as cofactors, and similar with that of wild-type using by NADP(+), NAD(+). Conversely, the activity of the R200D mutant significantly decreased with all cofactors. Furthermore, in yeast, the S199Y mutant substantially elevated the ethanol concentration compared with the wild type. Molecular dynamics simulation results indicated the H-bonding network between TeSADH and the cofactors was stronger for the S199Y mutant and the binding energy was simultaneously increased. Moreover, the fluorescence results indicated the S199Y mutant exhibited an increased preference for NAD(P)H, binding with NAD(P)H more compactly compared with wild type. PMID:27016086

  11. Tank 241-C-103 organic vapor and liquid characterization and supporting activities, Hanford Site, Richland, Washington

    The action proposed is to sample the vapor space and liquid waste and perform other supporting activities in Tank 241-C-103 located in the 241-C Tank Farm on the Hanford Site. Operations at Tank 241-C-103 are curtailed because of an unreviewed safety question (USQ) concerning flammability issues of the organic waste in the tank. This USQ must be resolved before normal operation and surveillance of the tank can resume. In addition to the USQ, Tank 241-C-103 is thought to be involved in several cases of exposure of individuals to noxious vapors. This safety issue requires the use of supplied air for workers in the vicinity of the tank. Because of the USQ, the US Department of Energy proposes to characterize the waste in the vapor space and the organic and aqueous layers, to determine the volume of the organic layer. This action is needed to: (1) assess potential risks to workers, the public, and the environment from continued routine tank operations and (2) provide information on the waste material in the tank to facilitate a comprehensive safety analysis of this USQ. The information would be used to determine if a flammable condition within the tank is credible. This information would be used to prevent or mitigate an accident during continued waste storage and future waste characterization. Alternatives to the proposed activities have been considered in this analysis

  12. Structure analysis reveals the flexibility of the ADAMTS-5 active site

    Shieh, Huey-Sheng; Tomasselli, Alfredo G.; Mathis, Karl J.; Schnute, Mark E.; Woodard, Scott S.; Caspers, Nicole; Williams, Jennifer M.; Kiefer, James R.; Munie, Grace; Wittwer, Arthur; Malfait, Anne-Marie; Tortorella, Micky D. (Pfizer)

    2012-03-02

    A ((1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl) succinamide derivative (here referred to as Compound 12) shows significant activity toward many matrix metalloproteinases (MMPs), including MMP-2, MMP-8, MMP-9, and MMP-13. Modeling studies had predicted that this compound would not bind to ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs-5) due to its shallow S1' pocket. However, inhibition analysis revealed it to be a nanomolar inhibitor of both ADAMTS-4 and -5. The observed inconsistency was explained by analysis of crystallographic structures, which showed that Compound 12 in complex with the catalytic domain of ADAMTS-5 (cataTS5) exhibits an unusual conformation in the S1' pocket of the protein. This first demonstration that cataTS5 can undergo an induced conformational change in its active site pocket by a molecule like Compound 12 should enable the design of new aggrecanase inhibitors with better potency and selectivity profiles.

  13. Subway construction activity influence on polycyclic aromatic hydrocarbons in fine particles: Comparison with a background mountainous site

    Kong, Shaofei; Li, Xuxu; Li, Qi; Yin, Yan; Li, Li; Chen, Kui; Liu, Dantong; Yuan, Liang; Pang, Xiaobing

    2015-07-01

    Intensive construction activities worsened the surrounding atmospheric environment in China. Eighteen polycyclic aromatic hydrocarbons (PAHs) in fine particles (PM2.5) were collected at a subway construction site (SC) of Nanjing and compared with a regional background mountainous site (BM) to examine the influence of anthropogenic activities on concentrations, sources and health risks of PAHs. Average PAH concentrations at SC were higher than BM at a factor of about 5.9. All PAH species at SC were higher than BM, with the SC/BM ratios ranging from 1.3 (NaP) to 10.3 (BaP). PAH profiles differed for the two sites. The SC site had higher mass fractions of PAHs from coal combustion and vehicle emission, while the BM site held higher mass percentages of PAHs from long-range transported wood combustion and industrial activities. Lower temperature at BM may lead to the higher mass percentages of low ring PAHs. Coal combustion, traffic emissions and biomass burning were the common sources for PAHs at both SC and BM. Construction workers were exposed to higher BaPeq concentrations, nearly ten times of the background site and their lifetime cancer risk reached to 0.6 per 1,000,000 exposed worker, owing to the influence of coal combustion, vehicle emission and industrial activities at the surroundings of SC.

  14. Compositions constrained by graph Laplacian minors

    Braun, Benjamin; Harrison, Ashley; McKim, Jessica; Noll, Jenna; Taylor, Clifford

    2012-01-01

    Motivated by examples of symmetrically constrained compositions, super convex partitions, and super convex compositions, we initiate the study of partitions and compositions constrained by graph Laplacian minors. We provide a complete description of the multivariate generating functions for such compositions in the case of trees. We answer a question due to Corteel, Savage, and Wilf regarding super convex compositions, which we describe as compositions constrained by Laplacian minors for cycles; we extend this solution to the study of compositions constrained by Laplacian minors of leafed cycles. Connections are established and conjectured between compositions constrained by Laplacian minors of leafed cycles of prime length and algebraic/combinatorial properties of reflexive simplices.

  15. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

    Savic, Daniel; Roberts, Brian S.; Carleton, Julia B.; Partridge, E. Christopher; White, Michael A.; Cohen, Barak A.; Cooper, Gregory M.; Gertz, Jason; Myers, Richard M.

    2015-01-01

    Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression. It is unclear why only a subset of TF bound sites are actively involved in transcriptional regulation. Moreover, the key genomic features that accurately discriminate between active and inactive TF binding events remain ambiguous. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a marker for active regulatory sequences. Despite these correlative analyses, a thorough functional validation of these genomic co-occupancies is still lacking. To characterize the gene regulatory activity of DNA sequences underlying promoter-distal TF binding events that co-occur with RNAP2 and TF sites devoid of RNAP2 occupancy using a functional reporter assay, we performed cis-regulatory element sequencing (CRE-seq). We tested more than 1000 promoter-distal CCAAT/enhancer-binding protein beta (CEBPB)-bound sites in HepG2 and K562 cells, and found that CEBPB-bound sites co-occurring with RNAP2 were more likely to exhibit enhancer activity. CEBPB-bound sites further maintained substantial cell-type specificity, indicating that local DNA sequence can accurately convey cell-type–specific regulatory information. By comparing our CRE-seq results to a comprehensive set of genome annotations, we identified a variety of genomic features that are strong predictors of regulatory element activity and cell-type–specific activity. Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can distinguish active from inactive TF bound sites. PMID:26486725

  16. Quantum Annealing for Constrained Optimization

    Hen, Itay; Spedalieri, Federico M.

    2016-03-01

    Recent advances in quantum technology have led to the development and manufacturing of experimental programmable quantum annealers that promise to solve certain combinatorial optimization problems of practical relevance faster than their classical analogues. The applicability of such devices for many theoretical and real-world optimization problems, which are often constrained, is severely limited by the sparse, rigid layout of the devices' quantum bits. Traditionally, constraints are addressed by the addition of penalty terms to the Hamiltonian of the problem, which, in turn, requires prohibitively increasing physical resources while also restricting the dynamical range of the interactions. Here, we propose a method for encoding constrained optimization problems on quantum annealers that eliminates the need for penalty terms and thereby reduces the number of required couplers and removes the need for minor embedding, greatly reducing the number of required physical qubits. We argue the advantages of the proposed technique and illustrate its effectiveness. We conclude by discussing the experimental feasibility of the suggested method as well as its potential to appreciably reduce the resource requirements for implementing optimization problems on quantum annealers and its significance in the field of quantum computing.

  17. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid

    Shaya, D.; Hahn, Bum-Soo; Bjerkan, Tonje Marita; Kim, Wan Seok; Park, Nam Young; Sim, Joon-Soo; Kim, Yeong-Shik; Cygler, M. (Catholic Univ of Korea); (NUST); (McGill); (Nat); (Natural Products Res Inst, Korea)

    2008-03-19

    Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a {beta}-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: ({alpha}/{alpha}){sub 5} for CS (chondroitin lyases AC) and {beta}-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located {approx}12 {angstrom} from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.

  18. ENVIRONMENTAL ASSESSMENT OF OKLAHOMA ABANDONED DRILLING AND PRODUCTION SITES AND ASSOCIATED PUBLIC EDUCATION/OUTREACH ACTIVITIES

    Mike Terry

    2002-03-01

    The U.S. Department of Energy has participated with the Oklahoma Energy Resource Board (OERB) since 1995 by providing grant funding for on-going work in both environmental assessment of abandoned oilfield exploration and production sites and associated public education/outreach activities. The OERB, a state agency created in 1993 by the Oklahoma legislature, administers programs funded by an assessment of one tenth of one percent on all oil and natural gas produced and sold in the state of Oklahoma. Approximately one half of the funds are used to assess and remediate abandoned oilfield sites and the other half are being used to educate about the importance of the oil and natural gas industry and OERB's environmental efforts. Financial participation through grant funding by the U.S. D.O.E. has been $200,000 annually which represents approximately 3 percent of OERB's private funding. Most of OERB's revenues come from an assessment of 1/10th of 1% on the sale of crude and natural gas in Oklahoma. The assessment is considered voluntary in that any interest owner may ask for a refund annually of their contributions to the fund. On average, 95% of the assessment dollars have remained with OERB, which shows tremendous support by the industry. This Final Report summarizes the progress of the three year grant. The purpose of this three-year project was to continue the progress of the OERB to accomplish its environmental and educational objectives and transfer information learned to other organizations and producing states in the industry.

  19. Activated Fraction Of Black Carbon By Cloud Droplets And Ice Crystals At The High Alpine Site Jungfraujoch (3580 m asl)

    Cozic, J.; Mertes, S. [IFT Leipzig (Georgia); Verheggen, B.; Petzold, A. [DLR, Oberpfaffenhofen (Georgia); Weingartner, E.; Baltensperger, U.

    2005-03-01

    Measurements of black carbon (BC) were made in winter and summer 2004 at the high Alpine site Jungfraujoch in order to study the activation of BC into cloud droplets and ice crystals. Main results showed that the activated fraction represents 61% in summer and that for a large temperature range between -25 C and 5 C, the activated BC fraction increases with increasing temperature and increasing liquid water content. (author)

  20. EFFECTS OF SP1 SITE TO hTERT PROMOTER ACTIVITY AND ITS RESPONSE TO RETINOID ACID

    应磊; 戴冰冰; 王楚; 卢健; 钱关祥

    2005-01-01

    Objective To investigate the function of Sp1 consensus sites to human telomerase reverse transcriptase (hTERT) promoter in different cell lines and in TRA-treated Held cell. Methods Different length of hTERT promoter was cloned and inserted into pGL3/basic reporter plasmid. The last four Sp1 sites were deleted by PCR and pGL3 B/TRTP413 A reporter plasmid was constructed. All reporter plasmids were transiently transfected into 293, A549, Hela and HepG2 cell lines. 48 h after transfection, luciferase activity was analyzed. hTERT promoter activity of Held cell which was treated with trans-retinoid acid (TRA) was tested too. Total RNA of these cells were extracted and reverse transcript. hTERT mRNA level was analyzed in all tested cells. c-Myc and Sp1 expression were examined in Hela cell before and after TRA treatment. U937 was used as a positive control in TRA treatment.Results hTERT was expressed at different level in all tested cell lines. 207bp promoter upstream of transcription start site maintained complete activity. Deletion of last 4 Sp1 sites greatly decreased activity of hTERT promoter, and almost eliminated its activity in HepG2. TRA increased the activity of different length hTERT promoters in Hela cell,but the activity of Sp1 site-deleted promoter decreased by 3 times. Unlike U937 cell, hTERT expression of Held cell increased after TRA treatment, and c-Myc and Sp1 mRNA level were relatively stable. Conclusion Sp1 site was required for transactivation of hTERT promoter and played an important role during TRA treatment.

  1. A roundup of SMOS validation activities at the HOBE site in the Skjern River Catchment, Denmark

    Bircher, Simone; Richaume, Philippe; Mialon, Arnaud; Berthon, Lucie; Kerr, Yann H.; Jensen, Karsten H.

    2013-04-01

    The Soil Moisture and Ocean Salinity Mission (SMOS) delivers global surface soil moisture data at high temporal resolution which is of high relevance for water management, weather and climate predictions as well as hazard analysis. In order to estimate the quality and caveats of the SMOS data at different processing levels (e.g. L1C geolocated brightness temperatures TB, L2 soil moisture SM and optical thickness TAU, L3 spatio-temporal synthesis of TB, SM and TAU), product validation in various climatic regions is a crucial issue. In the framework of the Danish Hydrological Observatory (HOBE) one such validation site has been established in the Skjern River Catchment, Denmark. The catchment is one of Europe's northernmost intensely cultivated region with environmental features related to this latitude such as very sandy soils with large organic deposits under natural vegetation and region-specific land cover such as heathland. The area is of pronounced flatness and located at a short distance to the coast line in two directions. During fall 2009, a soil moisture and soil temperature network with 30 stations has been installed to provide continuous in-situ soil moisture data feasible for upscaling and comparison with SMOS data at large scale. One SMOS pixel (44x44 km2) to be validated was chosen by maximizing its coverage of the Skjern River Catchment and minimizing the open water fraction. Prevailing environmental conditions and their respective fractions were considered for the selection of suitable network locations. To further support validation activities an airborne campaign with the passive L-band microwave radiometer EMIRAD-2, was carried out within the chosen SMOS pixel in spring 2010 to directly acquire soil moisture data at intermediate scale (few kilometers spatial resolution). Concurrent with ascending SMOS overpasses, four flights were conducted with simultaneous ground sampling of surface soil moisture and auxiliary parameters within three 2x2 km

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

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

    2015-01-01

    Albumin fusion/conjugation (albumination) has been an effective method to prolong in vivo half-life of therapeutic proteins. However, its broader application to proteins with complex folding pathway or multi-subunit is restricted by incorrect folding, poor expression, heterogeneity, and loss of native activity of the proteins linked to albumin. We hypothesized that the site-specific conjugation of albumin to a permissive site of a target protein will expand the utilities of albumin as a thera...

  3. Three novel acetylation sites in the Foxp3 transcription factor regulate the suppressive activity of regulatory T cells

    Kwon, Hye-Sook; Lim, Hyung W; Wu, Jessica; Schnoelzer, Martina; Verdin, Eric; Ott, Melanie

    2012-01-01

    The Foxp3 transcription factor is the master regulator of regulatory T cell (Treg) differentiation and function. Its activity is regulated by reversible acetylation. Using mass spectrometry of immunoprecipitated proteins, we identify three novel acetylation sites in murine Foxp3 (K31, K262, and K267) and the corresponding sites in human FoxP3 proteins. Newly raised modification-specific antibodies against acetylated K31 and K267 confirm acetylation of these residues in murine Tregs. Mutant Fo...

  4. The effect of the distance between acidic site and basic site immobilized on mesoporous solid on the activity in catalyzing aldol condensation

    Yu, Xiaofang; Yu, Xiaobo; Wu, Shujie; Liu, Bo; Liu, Heng; Guan, Jingqi; Kan, Qiubin

    2011-02-01

    Acid-base bifunctional heterogeneous catalysts containing carboxylic and amine groups, which were immobilized at defined distance from one another on the mesoporous solid were synthesized by immobilizing lysine onto carboxyl-SBA-15. The obtained materials were characterized by X-ray diffraction (XRD), N 2 adsorption, Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning electron micrographs (SEM), transmission electron micrographs (TEM), elemental analysis, and back titration. Proximal-C-A-SBA-15 with a proximal acid-base distance was more active than maximum-C-A-SBA-15 with a maximum acid-base distance in aldol condensation reaction between acetone and various aldehydes. It appears that the distance between acidic site and basic site immobilized on mesoporous solid should be an essential factor for catalysis optimization.

  5. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

    Poongavanam, Vasanthanathan; Madala, Praveen K; Højland, Torben; Veedu, Rakesh N

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  6. Purification and sequencing of the active site tryptic peptide from penicillin-binding protein 1b of Escherichia coli

    This paper reports the sequence of the active site peptide of penicillin-binding protein 1b from Escherichia coli. Purified penicillin-binding protein 1b was labeled with [14C]penicillin G, digested with trypsin, and partially purified by gel filtration. Upon further purification by high-pressure liquid chromatography, two radioactive peaks were observed, and the major peak, representing over 75% of the applied radioactivity, was submitted to amino acid analysis and sequencing. The sequence Ser-Ile-Gly-Ser-Leu-Ala-Lys was obtained. The active site nucleophile was identified by digesting the purified peptide with aminopeptidase M and separating the radioactive products on high-pressure liquid chromatography. Amino acid analysis confirmed that the serine residue in the middle of the sequence was covalently bonded to the [14C]penicilloyl moiety. A comparison of this sequence to active site sequences of other penicillin-binding proteins and beta-lactamases is presented

  7. Discovery of fragment molecules that bind the human peroxiredoxin 5 active site.

    Sarah Barelier

    Full Text Available The search for protein ligands is a crucial step in the inhibitor design process. Fragment screening represents an interesting method to rapidly find lead molecules, as it enables the exploration of a larger portion of the chemical space with a smaller number of compounds as compared to screening based on drug-sized molecules. Moreover, fragment screening usually leads to hit molecules that form few but optimal interactions with the target, thus displaying high ligand efficiencies. Here we report the screening of a homemade library composed of 200 highly diverse fragments against the human Peroxiredoxin 5 protein. Peroxiredoxins compose a family of peroxidases that share the ability to reduce peroxides through a conserved cysteine. The three-dimensional structures of these enzymes ubiquitously found throughout evolution have been extensively studied, however, their biological functions are still not well understood and to date few inhibitors have been discovered against these enzymes. Six fragments from the library were shown to bind to the Peroxiredoxin 5 active site and ligand-induced chemical shift changes were used to drive the docking of these small molecules into the protein structure. The orientation of the fragments in the binding pocket was confirmed by the study of fragment homologues, highlighting the role of hydroxyl functions that hang the ligands to the Peroxiredoxin 5 protein. Among the hit fragments, the small catechol molecule was shown to significantly inhibit Peroxiredoxin 5 activity in a thioredoxin peroxidase assay. This study reports novel data about the ligand-Peroxiredoxin interactions that will help considerably the development of potential Peroxiredoxin inhibitors.

  8. Constrained correlation dynamics of QCD

    The complete version of constrained correlation dynamics of SU(N) gauge theories in temporal gauge and canonical form has been formulated in three steps. (1) With the aid of generating-functional technique and in the framework of correlation dynamics, a closed set of equations of motion for correlation Green's functions have been established. (2) Gauge constraint conditions are analysed by means of Dirac theory. The algebraic representations of Gauss law and Ward identities are given. In accordance with the truncation approximations of correlation dynamics, the conserved Gauss law and Ward identities due to residual gauge invariance are shifted to initial value problems. (3) The equations of motion for multi-time correlation Green's functions have been transformed into those for equal-time correlation Green's functions. In two-body truncation approximation, a tractable set of equations of motion, Gauss law, and Ward identities are given explicitly

  9. Constrained Allocation Flux Balance Analysis

    Mori, Matteo; Martin, Olivier C; De Martino, Andrea; Marinari, Enzo

    2016-01-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferr...

  10. Screening breeding sites of the common toad (Bufo bufo) in England and Wales for evidence of endocrine disrupting activity.

    Pickford, Daniel B; Jones, Alexandra; Velez-Pelez, Alejandra; Orton, Frances; Iguchi, Taisen; Mitsui, Naoko; Tooi, Osamu

    2015-07-01

    Anuran amphibians are often present in agricultural landscapes and may therefore be exposed to chemicals in surface waters used for breeding. We used passive accumulation devices (SPMD and POCIS) to sample contaminants from nine breeding sites of the Common toad (Bufo bufo) across England and Wales, measuring endocrine activity of the extracts in a recombinant yeast androgen screen (YAS) and yeast estrogen screen (YES) and an in vitro vitellogenin induction screen in primary culture of Xenopus laevis hepatocytes. We also assessed hatching, growth, survival, and development in caged larvae in situ, and sampled metamorphs for gonadal histopathology. None of the SPMD extracts exhibited estrogen receptor or androgen receptor agonist activity, while POCIS extracts from two sites in west-central England exhibited concentration-dependent androgenic activity in the YAS. Three sites exhibited significant estrogenic activity in both the YES and the Xenopus hepatocyte. Hatching rates varied widely among sites, but there was no consistent correlation between hatching rate and intensity of agricultural activity, predicted concentrations of agrochemicals, or endocrine activity measured in YES/YAS assays. While a small number of intersex individuals were observed, their incidence could not be associated with predicted pesticide exposure or endocrine activitity measured in the in vitro screens. There were no significant differences in sex ratio, as determined by gonadal histomorphology among the study sites, and no significant correlation was observed between proportion of males and predicted exposure to agrochemicals. However, a negative correlation did become apparent in later sampling periods between proportion of males and estrogenic activity of the POCIS sample, as measured in the YES. Our results suggest that larval and adult amphibians may be exposed to endocrine disrupting chemicals in breeding ponds, albeit at low concentrations, and that chemical contaminants other than

  11. Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites.

    Simon, Bertrand; Huart, Anne-Sophie; Temmerman, Koen; Vahokoski, Juha; Mertens, Haydyn D T; Komadina, Dana; Hoffmann, Jan-Erik; Yumerefendi, Hayretin; Svergun, Dmitri I; Kursula, Petri; Schultz, Carsten; McCarthy, Andrew A; Hart, Darren J; Wilmanns, Matthias

    2016-06-01

    The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation. PMID:27133022

  12. Formal language constrained path problems

    Barrett, C.; Jacob, R.; Marathe, M.

    1997-07-08

    In many path finding problems arising in practice, certain patterns of edge/vertex labels in the labeled graph being traversed are allowed/preferred, while others are disallowed. Motivated by such applications as intermodal transportation planning, the authors investigate the complexity of finding feasible paths in a labeled network, where the mode choice for each traveler is specified by a formal language. The main contributions of this paper include the following: (1) the authors show that the problem of finding a shortest path between a source and destination for a traveler whose mode choice is specified as a context free language is solvable efficiently in polynomial time, when the mode choice is specified as a regular language they provide algorithms with improved space and time bounds; (2) in contrast, they show that the problem of finding simple paths between a source and a given destination is NP-hard, even when restricted to very simple regular expressions and/or very simple graphs; (3) for the class of treewidth bounded graphs, they show that (i) the problem of finding a regular language constrained simple path between source and a destination is solvable in polynomial time and (ii) the extension to finding context free language constrained simple paths is NP-complete. Several extensions of these results are presented in the context of finding shortest paths with additional constraints. These results significantly extend the results in [MW95]. As a corollary of the results, they obtain a polynomial time algorithm for the BEST k-SIMILAR PATH problem studied in [SJB97]. The previous best algorithm was given by [SJB97] and takes exponential time in the worst case.

  13. Kinetic evidence for an anion binding pocket in the active site of nitronate monooxygenase.

    Francis, Kevin; Gadda, Giovanni

    2009-10-01

    A series of monovalent, inorganic anions and aliphatic aldehydes were tested as inhibitors for Hansenula mrakii and Neurospora crassa nitronate monooxygenase, formerly known as 2-nitropropane dioxygenase, to investigate the structural features that contribute to the binding of the anionic nitronate substrates to the enzymes. A linear correlation between the volumes of the inorganic anions and their effectiveness as competitive inhibitors of the enzymes was observed in a plot of pK(is)versus the ionic volume of the anion with slopes of 0.041+/-0.001 mM/A(3) and 0.027+/-0.001 mM/A(3) for the H. mrakii and N. crassa enzymes, respectively. Aliphatic aldehydes were weak competitive inhibitors of the enzymes, with inhibition constants that are independent of their alkyl chain lengths. The reductive half reactions of H. mrakii nitronate monooxygenase with primary nitronates containing two to four carbon atoms all showed apparent K(d) values of approximately 5 mM. These results are consistent with the presence of an anion binding pocket in the active site of nitronate monooxygenase that interacts with the nitro group of the substrate, and suggest a minimal contribution of the hydrocarbon chain of the nitronates to the binding of the ligands to the enzyme. PMID:19683782

  14. Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.

    Du, Juan; Say, Rafael F; Lü, Wei; Fuchs, Georg; Einsle, Oliver

    2011-10-27

    Fructose-1,6-bisphosphate (FBP) aldolase/phosphatase is a bifunctional, thermostable enzyme that catalyses two subsequent steps in gluconeogenesis in most archaea and in deeply branching bacterial lineages. It mediates the aldol condensation of heat-labile dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) to FBP, as well as the subsequent, irreversible hydrolysis of the product to yield the stable fructose-6-phosphate (F6P) and inorganic phosphate; no reaction intermediates are released. Here we present a series of structural snapshots of the reaction that reveal a substantial remodelling of the active site through the movement of loop regions that create different catalytic functionalities at the same location. We have solved the three-dimensional structures of FBP aldolase/phosphatase from thermophilic Thermoproteus neutrophilus in a ligand-free state as well as in complex with the substrates DHAP and FBP and the product F6P to resolutions up to 1.3 Å. In conjunction with mutagenesis data, this pinpoints the residues required for the two reaction steps and shows that the sequential binding of additional Mg(2+) cations reversibly facilitates the reaction. FBP aldolase/phosphatase is an ancestral gluconeogenic enzyme optimized for high ambient temperatures, and our work resolves how consecutive structural rearrangements reorganize the catalytic centre of the protein to carry out two canonical reactions in a very non-canonical type of bifunctionality. PMID:21983965

  15. Underground Test Area Activity Quality Assurance Plan Nevada National Security Site, Nevada. Revision 1

    Farnham, Irene [Navarro-Intera, LLC (N-I), Las Vegas, NV (United States); Krenzien, Susan [Navarro-Intera, LLC (N-I), Las Vegas, NV (United States)

    2012-10-01

    This Quality Assurance Plan (QAP) provides the overall quality assurance (QA) requirements and general quality practices to be applied to the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) Underground Test Area (UGTA) activities. The requirements in this QAP are consistent with DOE Order 414.1C, Quality Assurance (DOE, 2005); U.S. Environmental Protection Agency (EPA) Guidance for Quality Assurance Project Plans for Modeling (EPA, 2002); and EPA Guidance on the Development, Evaluation, and Application of Environmental Models (EPA, 2009). NNSA/NSO, or designee, must review this QAP every two years. Changes that do not affect the overall scope or requirements will not require an immediate QAP revision but will be incorporated into the next revision cycle after identification. Section 1.0 describes UGTA objectives, participant responsibilities, and administrative and management quality requirements (i.e., training, records, procurement). Section 1.0 also details data management and computer software requirements. Section 2.0 establishes the requirements to ensure newly collected data are valid, existing data uses are appropriate, and environmental-modeling methods are reliable. Section 3.0 provides feedback loops through assessments and reports to management. Section 4.0 provides the framework for corrective actions. Section 5.0 provides references for this document.

  16. The influence of small mammal burrowing activity on water storage at the Hanford Site

    The amount and rate at which water may penetrate a protective barrier and come into contact with buried radioactive waste is a major concern. Because burrowing animals eventually will reside on the surface of any protective barrier, the effect these burrow systems may have on the loss or retention of water needs to be determined. The first section of this document summarizes the known literature relative to small mammals and the effects that burrowing activities have on water distribution, infiltration, and the overall impact of burrows on the ecosystem. Topics that are summarized include burrow air pressures, airflow, burrow humidity, microtopography, mounding, infiltration, climate, soil evaporation, and discussions of large pores relative to water distribution. The second section of this document provides the results of the study that was conducted at the Hanford Site to determine what effect small mammal burrows have on water storage. This Biointrusion task is identified in the Permanent Isolation Surface Barrier Development Plan in support of protective barriers. This particular animal intrusion task is one part of the overall animal intrusion task identified in Animal Intrusion Test Plan

  17. Active Site Sharing and Subterminal Hairpin Recognition in a New Class of DNA Transposases

    Ronning, Donald R.; Guynet, Catherine; Ton-Hoang, Bao; Perez, Zhanita N.; Ghirlando, Rodolfo; Chandler, Michael; Dyda, Fred (Centre Nat); (NIH)

    2010-07-20

    Many bacteria harbor simple transposable elements termed insertion sequences (IS). In Helicobacter pylori, the chimeric IS605 family elements are particularly interesting due to their proximity to genes encoding gastric epithelial invasion factors. Protein sequences of IS605 transposases do not bear the hallmarks of other well-characterized transposases. We have solved the crystal structure of full-length transposase (TnpA) of a representative member, ISHp608. Structurally, TnpA does not resemble any characterized transposase; rather, it is related to rolling circle replication (RCR) proteins. Consistent with RCR, Mg{sup 2+} and a conserved tyrosine, Tyr127, are essential for DNA nicking and the formation of a covalent intermediate between TnpA and DNA. TnpA is dimeric, contains two shared active sites, and binds two DNA stem loops representing the conserved inverted repeats near each end of ISHp608. The cocrystal structure with stem-loop DNA illustrates how this family of transposases specifically recognizes and pairs ends, necessary steps during transposition.

  18. The ClpP N-Terminus Coordinates Substrate Access with Protease Active Site Reactivity

    Energy-dependent protein degradation machines, such as the Escherichia coli protease ClpAP, require regulated interactions between the ATPase component (ClpA) and the protease component (ClpP) for function. Recent studies indicate that the ClpP N-terminus is essential in these interactions, yet the dynamics of this region remain unclear. Here, we use synchrotron hydroxyl radical footprinting and kinetic studies to characterize functionally important conformational changes of the ClpP N-terminus. Footprinting experiments show that the ClpP N-terminus becomes more solvent-exposed upon interaction with ClpA. In the absence of ClpA, deletion of the ClpP N-terminus increases the initial degradation rate of large peptide substrates 5-15-fold. Unlike ClpAP, ClpP?N exhibits a distinct slow phase of product formation that is eliminated by the addition of hydroxylamine, suggesting that truncation of the N-terminus leads to stabilization of the acyl-enzyme intermediate. These results indicate that (1) the ClpP N-terminus acts as a 'gate' controlling substrate access to the active sites, (2) binding of ClpA opens this 'gate', allowing substrate entry and formation of the acyl-enzyme intermediate, and (3) closing of the N-terminal 'gate' stimulates acyl-enzyme hydrolysis.

  19. A systematic approach for future solid waste cleanup activities at the Hanford Site

    This paper describes the systematic approach to the treatment, storage, and disposal system (TSD) planning and management that has been developed and implemented by Hanford's Solid Waste Program. The systematic approach includes: collecting the forecast and waste inventory data; defining Hanford's TSD system; studying and refining the TSD system by using analysis tools; and documenting analysis results. The customers responsible for planning, funding, and managing future solid waste activities have driven the evolution of the solid waste system. Currently, all treatment facilities are several years from operating. As these facilities become closer to reality, more detailed systems analysis and modeling will be necessary to successfully remediate solid waste at the Site. The tools will continue to be developed in detail to address the complexities of the system as they become better defined. The tools will help determine which facility lay-outs are most optimal, will help determine what types of equipment should be used to optimize the transport of materials to and from each TSD facility, and will be used for performing life-cycle analysis. It is envisioned that in addition to developing the tools to be adapted to the more specific facility design issues, this approach will also be used as an example for other waste installations across the DOE complex

  20. Catalytic combustion of methane on Co/MgO. Characterisation of active cobalt sites

    Ulla, M.A.; Spretz, R.; Lombardo, E. [Instituto de Investigaciones en Catalisis y Petroquimica, INCAPE (FIQ, UNL-CONICET), Santiago del Estero 2829, C.P. 3000, Santa Fe (Argentina); Daniell, W.; Knoezinger, H. [Department Chemie, Physikalische Chemie, Ludwig Maximilians Universitaet, Butenandtstr. 5-13, Haus E, D-81377 Muenchen (Germany)

    2001-02-01

    A series of Co/MgO catalysts with 3-12wt.% Co were prepared by impregnation and calcined at 1073K for 10h. The catalytic behaviour of these samples toward CH{sub 4} combustion was found to increase with cobalt loading, though a plateau was reached at ca. 9wt.% Co content. Bulk characterisation was carried out using XRD, TPR and Raman spectroscopy, and showed that the solids were made up of a CoO-MgO solid solution and a MgO phase. A detailed examination of their surfaces was achieved through FTIR spectroscopy of adsorbed CO probe molecules, which indicated that at low cobalt loadings only a small proportion of the Co going into the solid solution was present on exposed faces as either Co{sup 2+} oxo-species or pentacoordinated Co{sup 2+}. However, as the cobalt content of the samples increased, a larger amount was exposed on the surface. This effect levelled off at 9wt.% Co, after which the increase in exposed Co{sup 2+} sites was countered by the masking effect of islands of MgO. In addition, at high cobalt loadings (9 and 12wt.%) Co formed small clusters which showed bulk CoO-like behaviour. Consequently, the benefit of having surface Co{sup 2+} species was balanced by the clustering effect of these species and the presence of MgO islands, negating their contribution to the overall catalytic activity of the samples.

  1. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: role of *OH ligands.

    Holby, Edward F; Taylor, Christopher D

    2015-01-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date. PMID:25788358

  2. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

  3. Environmental assessment of ground-water compliance activities at the Uranium Mill Tailings Site, Spook, Wyoming

    This report assesses the environmental impacts of the Uranium Mill Tailings Site at Spook, Wyoming on ground water. DOE previously characterized the site and monitoring data were collected during the surface remediation. The ground water compliance strategy is to perform no further remediation at the site since the ground water in the aquifer is neither a current nor potential source of drinking water. Under the no-action alternative, certain regulatory requirements would not be met

  4. Dynamics of microbial biomass and respiratory activity during late summer in a site of Arctic Kongsfjorden

    Rosabruna La Ferla

    2014-06-01

    The Kongsfjorden was affected by inflow of Atlantic water as well as glacier melt water runoff (Cottier et al., 2005. The experiment comprised 5 samplings performed during a 7 day period in MDI station. For each sampling, photosynthetically active radiation (PAR, temperature and conductivity (salinity were recorded along the water column with a PNF-300 profiler and a SeaBird Electronics SBE-911 plus profiler, respectively . Water samples were taken at five different depths (surface, 5, 25, 50 and 100 m to determine nutrients, particulate organic carbon, prokaryotes and phytoplankton biomass, and community respiration. In addition, prokaryotes sunk with the particulate matter were studied into the sediment trap positioned in the MDI during the period between June and September 2013. The latter assessment allowed us to determine the flow of prokaryotes, conveyed from organic matter sinking, throughout the summer. Due to melting of the glaciers in the surface water of the study site, there were sediment loads which strongly limited light penetration and low irradiance (~0.7% E0+ at 5 meters below the surface. Along the water column the intrusion of the salty and warm Atlantic water was visible in the study site and the warm core was at about 25 m depth. PO4 concentrations ranged between 0.43 (surface and 1 µM (100 m and in general the values increased from surface to bottom. NH4, NO2 and NO3 significantly changed along the vertical and with time and varied between 0.39 and 5.05µM, 0.01 and 0.67µM, 0.001 and 4.18µM, respectively. Prokaryotic abundances and cell volumes ranged between 5.6 and 15.9 E+05 cells ml-1 and 0.033 and 0.093 µm3, respectively. These latter parameters showed a peak at 25 m depth in the core of incoming Atlantic water. This evidence was not determined in chlorophyll a (range 0.034-1.102 mg m-3, where the highest values were determined at the surface and 5 m depth. Speculations will be made on the variability of the fluxes of carbon

  5. Endocrine disrupting activities of surface water associated with a West Virginia oil and gas industry wastewater disposal site

    Kassotis, Christopher D.; Iwanowicz, Luke; Akob, Denise M.; Cozzarelli, Isabelle M.; Mumford, Adam; Orem, William H.; Nagel, Susan C.

    2016-01-01

    Currently, >95% of end disposal of hydraulic fracturing wastewater from unconventional oil and gas operations in the US occurs via injection wells. Key data gaps exist in understanding the potential impact of underground injection on surface water quality and environmental health. The goal of this study was to assess endocrine disrupting activity in surface water at a West Virginia injection well disposal site. Water samples were collected from a background site in the area and upstream, on, and downstream of the disposal facility. Samples were solid-phase extracted, and extracts assessed for agonist and antagonist hormonal activities for five hormone receptors in mammalian and yeast reporter gene assays. Compared to reference water extracts upstream and distal to the disposal well, samples collected adjacent and downstream exhibited considerably higher antagonist activity for the estrogen, androgen, progesterone, glucocorticoid and thyroid hormone receptors. In contrast, low levels of agonist activity were measured in upstream/distal sites, and were inhibited or absent at downstream sites with significant antagonism. Concurrent analyses by partner laboratories (published separately) describe the analytical and geochemical profiling of the water; elevated conductivity as well as high sodium, chloride, strontium, and barium concentrations indicate impacts due to handling of unconventional oil and gas wastewater. Notably, antagonist activities in downstream samples were at equivalent authentic standard concentrations known to disrupt reproduction and/or development in aquatic animals. Given the widespread use of injection wells for end-disposal of hydraulic fracturing wastewater, these data raise concerns for human and animal health nearby.

  6. Widely available active sites on Ni2P for electrochemical hydrogen evolution--insights from first principles calculations.

    Hansen, Martin H; Stern, Lucas-Alexandre; Feng, Ligang; Rossmeisl, Jan; Hu, Xile

    2015-04-28

    We present insights into the mechanism and the active site for hydrogen evolution on nickel phosphide (Ni2P). Ni2P was recently discovered to be a very active non-precious hydrogen evolution catalyst. Current literature attributes the activity of Ni2P to a particular site on the (0001) facet. In the present study, using Density Functional Theory (DFT) calculations, we show that several widely available low index crystal facets on Ni2P have better properties for a high catalytic activity. DFT calculations were used to identify moderately bonding nickel bridge sites and nickel hollow sites for hydrogen adsorption and to calculate barriers for the Tafel pathway. The investigated surfaces in this study were the (101̅0), (1̅1̅20), (112̅0), (112̅1) and (0001) facets of the hexagonal Ni2P crystal. In addition to the DFT results, we present experiments on Ni2P nanowires growing along the 〈0001〉 direction, which are shown as efficient hydrogen evolution catalysts. The experimental results add these nanowires to a variety of different morphologies of Ni2P, which are all active for HER. PMID:25812670

  7. Endocrine disrupting activities of surface water associated with a West Virginia oil and gas industry wastewater disposal site.

    Kassotis, Christopher D; Iwanowicz, Luke R; Akob, Denise M; Cozzarelli, Isabelle M; Mumford, Adam C; Orem, William H; Nagel, Susan C

    2016-07-01

    Currently, >95% of end disposal of hydraulic fracturing wastewater from unconventional oil and gas operations in the US occurs via injection wells. Key data gaps exist in understanding the potential impact of underground injection on surface water quality and environmental health. The goal of this study was to assess endocrine disrupting activity in surface water at a West Virginia injection well disposal site. Water samples were collected from a background site in the area and upstream, on, and downstream of the disposal facility. Samples were solid-phase extracted, and extracts assessed for agonist and antagonist hormonal activities for five hormone receptors in mammalian and yeast reporter gene assays. Compared to reference water extracts upstream and distal to the disposal well, samples collected adjacent and downstream exhibited considerably higher antagonist activity for the estrogen, androgen, progesterone, glucocorticoid and thyroid hormone receptors. In contrast, low levels of agonist activity were measured in upstream/distal sites, and were inhibited or absent at downstream sites with significant antagonism. Concurrent analyses by partner laboratories (published separately) describe the analytical and geochemical profiling of the water; elevated conductivity as well as high sodium, chloride, strontium, and barium concentrations indicate impacts due to handling of unconventional oil and gas wastewater. Notably, antagonist activities in downstream samples were at equivalent authentic standard concentrations known to disrupt reproduction and/or development in aquatic animals. Given the widespread use of injection wells for end-disposal of hydraulic fracturing wastewater, these data raise concerns for human and animal health nearby. PMID:27073166

  8. Identification of sumoylation sites in CCDC6, the first identified RET partner gene in papillary thyroid carcinoma, uncovers a mode of regulating CCDC6 function on CREB1 transcriptional activity.

    Chiara Luise

    Full Text Available CCDC6 was originally identified in chimeric genes as caused by chromosomal translocation involving the RET protooncogene in some thyroid tumors. Recognised as a 65 kDa pro-apoptotic phosphoprotein, CCDC6 has been enrolled as an ATM substrate that contribute to protect genome integrity by modulating PP4c activity in response to genotoxic stress. Recently, CCDC6 has been identified as a repressor of CREB1-dependent transcription. Sumoylation has emerged as an important mechanism in transcriptional control. Here, we report the identification and characterization of three sites of sumoylation in CCDC6 (K74, K266 and K424 which are highly conserved in vertebrates. We demonstrate that the post-translational modifications by SUMO2 constrain most of the CCDC6 protein in the cytosol and affect its functional interaction with CREB1 with a decrease of CCDC6 repressive function on CREB1 transcriptional activity. Indeed, the impairment of functional outcome of sumoylated CCDC6 is obtained knocking down all three the sumoylation sites. Interestingly, in thyroid cells the SUMO2-mediated CCDC6 post-translational modifications are induced by Forskolin, a cAMP analog. Signal transduction via the cAMP pathway is known to be ubiquitous and represents a major line of communication between many organisms and their environment. We believe that CCDC6 could be an important player in the dynamics of cAMP signaling by fine regulating CREB1 transcriptional activity in normal and transformed thyroid cells.

  9. SUPPLEMENTAL COLUMBIA RIVER PROTECTION ACTIVITIES AT THE DEPARTMENT OF ENERGY HANFORD SITE 2008 TECHNICAL REVIEW

    Looney, B; Dawn S. Kaback, D; Eugene L. LeBoeuf, E; Joe Rossabi, J; Karen L. Skubal, K; David L. Cocke, D; Paul C. Deutsch, P

    2008-09-30

    Beginning in 2006, the US Department of Energy (DOE) supported nine applied research projects to improve the protection of the Columbia River and mitigate the impacts of Hanford Site groundwater. These projects were funded through a supplemental Congressional budget allocation, and are now in various stages of completion in accordance with the research plans. The DOE Office of Environmental Management Groundwater and Soil Cleanup Technologies (EM-22) sponsored a technical peer review meeting for these projects in Richland WA, July 28-31, 2008. The overall objective of the peer review is to provide information to support DOE decisions about the status and potential future application of the various technologies. The charge for the peer review panel was to develop recommendations for each of the nine 'technologies'. Team members for the July 2008 review were Brian Looney, Gene LeBoeuf, Dawn Kaback, Karen Skubal, Joe Rossabi, Paul Deutsch, and David Cocke. Previous project reviews were held in May 2007 and March-May of 2006. The team used the following four rating categories for projects: (a) Incorporate the technology/strategy in ongoing and future EM activities; (b) Finish existing scope of applied research and determine potential for EM activities when research program is finished; (c) Discontinue current development activities and do not incorporate technology/strategy into ongoing and future EM activities unless a significant and compelling change in potential viability is documented; and (d) Supplement original funded work to obtain the data needed to support a DOE decision to incorporate the technology into ongoing and future EM activities. The supplemental funding portfolio included two projects that addressed strontium, five projects that addressed chromium, one project that addressed uranium and one project that addressed carbon tetrachloride. The projects ranged from in situ treatment methods for immobilizing contaminants using chemical

  10. Constraining Modified Gravity Theories With Cosmology

    Martinelli, Matteo

    2012-01-01

    We study and constrain the Hu and Sawicki f(R) model using CMB and weak lensing forecasted data. We also use the same data to constrain extended theories of gravity and the subclass of f(R) theories using a general parameterization describing departures from General Relativity. Moreover we study and constrain also a Dark Coupling model where Dark Energy and Dark Matter are coupled toghether.

  11. Permafrost and active layer monitoring in the maritime Antarctic: Preliminary results from CALM sites on Livingston and Deception Islands

    Ramos, M.; Vieira, G.; Blanco, J.J.; Hauck, C.; Hidalgo, M.A.; Tome, D.; Nevers, M.; Trindade, A.

    2007-01-01

    This paper describes results obtained from scientific work and experiments performed on Livingston and Deception Islands. Located in the South Shetland Archipelago, these islands have been some of the most sensitive regions over the last 50 years with respect to climate change with a Mean Annual Air Temperature (MAAT) close to -2 ºC. Three Circumpolar Active Layer Monitoring (CALM) sites were installed to record the thermal regime and the behaviour of the active layer in different places with similar climate, but with different soil composition, porosity, and water content. The study’s ultimate aim is to document the influence of climate change on permafrost degradation. Preliminary results, obtained in 2006, on maximum active-layer thickness (around 40 cm in the CALM of Deception Island), active layer temperature evolution, snow thickness, and air temperatures permit early characterization of energy exchange mechanisms between the ground and the atmosphere in the CALM-S sites.

  12. Intermetallic Alloys as CO Electroreduction Catalysts-Role of Isolated Active Sites

    Karamad, Mohammadreza; Tripkovic, Vladimir; Rossmeisl, Jan

    2014-01-01

    potentially selective intermetallic surfaces on which CO can be reduced to methanol at potentials comparable to or even slightly positive than those for CO/CO2 reduction to methane on Cu. Common features shared by most of the selective alloys are single TM sites. The role of single sites is to block parasitic...

  13. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

    Mignon A Keaton

    Full Text Available The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.

  14. Pitch angle distributions of electrons at dipolarization sites during geomagnetic activity: THEMIS observations

    Wang, Kaiti; Lin, Ching-Huei; Wang, Lu-Yin; Hada, Tohru; Nishimura, Yukitoshi; Turner, Drew L.; Angelopoulos, Vassilis

    2014-12-01

    Changes in pitch angle distributions of electrons with energies from a few eV to 1 MeV at dipolarization sites in Earth's magnetotail are investigated statistically to determine the extent to which adiabatic acceleration may contribute to these changes. Forty-two dipolarization events from 2008 and 2009 observed by Time History of Events and Macroscale Interactions during Substorms probes covering the inner plasma sheet from 8 RE to 12 RE during geomagnetic activity identified by the AL index are analyzed. The number of observed events with cigar-type distributions (peaks at 0° and 180°) decreases sharply below 1 keV after dipolarization because in many of these events, electron distributions became more isotropized. From above 1 keV to a few tens of keV, however, the observed number of cigar-type events increases after dipolarization and the number of isotropic events decreases. These changes can be related to the ineffectiveness of Fermi acceleration below 1 keV (at those energies, dipolarization time becomes comparable to electron bounce time). Model-calculated pitch angle distributions after dipolarization with the effect of betatron and Fermi acceleration tested indicate that these adiabatic acceleration mechanisms can explain the observed patterns of event number changes over a large range of energies for cigar events and isotropic events. Other factors still need to be considered to assess the observed increase in cigar events around 2 keV. Indeed, preferential directional increase/loss of electron fluxes, which may contribute to the formation of cigar events, was observed. Nonadiabatic processes to accelerate electrons in a parallel direction may also be important for future study.

  15. Site-specific characterization of Castromil Brownfield area related to gold mining activities.

    Ferreira da Silva, Eduardo; Serrano Pinto, Luís; Patinha, Carla; Cardoso Fonseca, Edmundo

    2004-03-01

    Castromil is one of the gold mining areas in Portugal that has been abandoned since 1940. This area, which was first mined in Roman times, is located within a Hercynian granite body near the contact with Silurian metasediments. Gold is essentially disseminated along veins in the silicified granite, running NW-SE, related with a shear zone and frequently associated with sulphides (arsenopyrite and basically pyrite). In paragenetic terms, three stages of mineralization are considered: ferro-arseniferous (quartz + arsenopyrite I + pyrite I + pyrrhotite + bismuth), zinciferous (sphalerite + chalcopyrite), and remobilization (arsenopyrite II + galena + gold). Due to the lack of laws and environmental education, Castromil is today a gold mining heritage site where we can detect the consequences of an incautious exploration (tailings, wells and adits located in the old explored zone) and where a residential area is located. In order to characterize the actual state of the old mining area the trace metal contamination of soils and waters by mining activities was investigated. In the studied area 106 soil samples, 15 waters and 20 plants were sampled and analysed. The soil samples were analysed for 32 elements by ICP-AES. Waters were analysed by ionic chromatography and ICP-MS for major and trace elements. Plants were analysed for As, Fe and Pb by AAS. The results are discussed taking into account the risk-based standards for soils and groundwater's (target and intervention values) proposed by Swartjes (1999). The results show elevated concentration of As and Pb which were found in soils collected from agricultural areas. Foodstuff plants species collected in the Castromil agricultural area show high concentrations of As in the leaves (cabbage and lettuce) and in the tubers (potatoes). Groundwaters in the mining area contain high concentrations of As that exceeds the intervention values. The area must to be subject to a remediation process, considering the actual risks to

  16. Mean transit times and the sites of synthesis and catabolism of tissue plasminogen activator and plasminogen activator inhibitor type 1 in young subjects

    Jørgensen, M; Petersen, K R; Vinberg, N; Jespersen, J; Gram, J; Tønnesen, K H

    2001-01-01

    .8 min. No net extraction of PAI-1 antigen took place in the splanchnic circulation. In conclusion, we demonstrated that active t-PA and t-PA antigen are catabolized and active PAI-1 produced in the splanchnic circulation in young healthy subjects during steady state. Furthermore, our data show that......Using an invasive technique, we studied the mean transit time, the net quantitative turnover rate, and the sites of synthesis and catabolism of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor type 1 (PAI-1) in healthy young volunteers in the fasting, steady state. Blood was...

  17. Low temperature syntheses and reactivity of Cu2O2 active-site models.

    Citek, Cooper; Herres-Pawlis, Sonja; Stack, T Daniel P

    2015-08-18

    Nature's facility with dioxygen outmatches modern chemistry in the oxidation and oxygenation of materials and substrates for biosynthesis and cellular metabolism. The Earth's most abundant naturally occurring oxidant is-frankly-poorly understood and controlled, and thus underused. Copper-based enzyme metallocofactors are ubiquitous to the efficient consumption of dioxygen by all domains of life. Over the last several decades, we have joined many research groups in the study of copper- and dioxygen-dependent enzymes through close investigation of synthetically derived, small-molecule active-site analogs. Simple copper-dioxygen clusters bearing structural and spectroscopic similarity to dioxygen-activating enzymes can be probed for their fundamental geometrical, electronic, and reactive properties using the tools available to inorganic and synthetic chemistry. Our exploration of the copper-dioxygen arena has sustained product evaluation of the key dynamics and reactivity of binuclear Cu2O2 compounds. Almost exclusively operating at low temperatures, from -78 °C to solution characterization even at -125 °C, we have identified numerous compounds supported by simple and easily accessed, low molecular weight ligands-chiefly families of bidentate diamine chelates. We have found that by stripping away complexity in comparison to extended protein tertiary structures or sophisticated, multinucleating architectures, we can experimentally manipulate activated compounds and open pathways of reactivity toward exogenous substrates that both inform on and extend fundamental mechanisms of oxygenase enzymes. Our recent successes have advanced understanding of the tyrosinase enzyme, and related hemocyanin and NspF, and the copper membrane monooxygenases, specifically particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO). Tyrosinase, ubiquitously distributed throughout life, is fundamental to the copper-based oxidation of phenols and the production of chromophores

  18. Mutational analysis of divalent metal ion binding in the active site of class II α-mannosidase from sulfolobus solfataricus

    Hansen, Dennis K.; Webb, Helen; Nielsen, Jonas Willum; Winther, Jakob R.; Willemoes, Martin; Harris, Pernille

    2015-01-01

    Mutational analysis of Sulfolobus solfataricus class II α-mannosidase was focused on side chains that interact with the hydroxyls of the-1 mannosyl of the substrate (Asp-534) or form ligands to the active site divalent metal ion (His-228 and His-533) judged from crystal structures of homologous...

  19. Neutron activation analysis and numerical taxonomy of thin orange ceramics from the manufacturing site of Rio Carnero, Puebla, Mexico

    Rattray, E. (Universidad Nacional Autonoma de Mexico, Mexico City (Mexico). Inst. de Investigaciones Antropologicas); Harbottle, G. (Brookhaven National Lab., Upton, NY (USA))

    1991-04-01

    Examples of different types of Thin Orange ceramics found at the recently-discovered manufacturing sites in the state of Puebla have been analyzed by neutron activation. A full multivariate numerical analysis indicates that this material is chemically identical with the well-known Thin Orange of Teotihuacan.'' 33 refs., 2 figs., 2 tabs.

  20. A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior

    Kromann-Hansen, Tobias; Oldenburg, Emil; Yung, Kristen Wing Yu;

    2016-01-01

    -ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its CDR-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to...

  1. Elucidating the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts: A density functional theory study

    Wang, Ziyun; Liu, Xinyi; Rooney, D. W.; Hu, P.

    2015-10-01

    The dehydrogenation of cyclohexanol to cyclohexanone is very important in the manufacture of nylon. Copper-based catalysts are the most popular catalysts for this reaction, and on these catalysts the reaction mechanism and active site are in debate. In order to elucidate the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts, density functional theory with dispersion corrections were performed on up to six facets of copper in two different oxidation states: monovalent copper and metallic copper. By calculating the surface energies of these facets, Cu(111) and Cu2O(111) were found to be the most stable facets for metallic copper and for monovalent copper, respectively. On these two facets, all the possible elementary steps in the dehydrogenation pathway of cyclohexanol were calculated, including the adsorption, dehydrogenation, hydrogen coupling and desorption. Two different reaction pathways for dehydrogenation were considered on both surfaces. It was revealed that the dehydrogenation mechanisms are different on these two surfaces: on Cu(111) the hydrogen belonging to the hydroxyl is removed first, then the hydrogen belonging to the carbon is subtracted, while on Cu2O(111) the hydrogen belonging to the carbon is removed followed by the subtraction of the hydrogen in the hydroxyl group. Furthermore, by comparing the energy profiles of these two surfaces, Cu2O(111) was found to be more active for cyclohexanol dehydrogenation than Cu(111). In addition, we found that the coordinatively unsaturated copper sites on Cu2O(111) are the reaction sites for all the steps. Therefore, the coordinatively unsaturated copper site on Cu2O(111) is likely to be the active site for cyclohexanol dehydrogenation on the copper-based catalysts.

  2. LRRK2 Kinase Activity and Biology are Not Uniformly Predicted by its Autophosphorylation and Cellular Phosphorylation Site Status

    April Reynolds

    2014-06-01

    Full Text Available Missense mutations in the Leucine Rich Repeat protein Kinase 2 (LRRK2 gene are the most common genetic predisposition to develop Parkinson’s disease (PD LRRK2 is a large multi-domain phosphoprotein with a GTPase domain and a serine/threonine protein kinase domain whose activity is implicated in neuronal toxicity; however the precise mechanism is unknown. LRRK2 autophosphorylates on several serine/threonine residues across the enzyme and is found constitutively phosphorylated on Ser910, Ser935, Ser955 and Ser973, which are proposed to be regulated by upstream kinases. Here we investigate the phosphoregulation at these sites by analyzing the effects of disease-associated mutations Arg1441Cys, Arg1441Gly, Ala1442Pro, Tyr1699Cys, Ile2012Thr, Gly2019Ser, and Ile2020Thr. We also studied alanine substitutions of phosphosite serines 910, 935, 955 and 973 and specific LRRK2 inhibition on autophosphorylation of LRRK2 Ser1292, Thr1491, Thr2483 and phosphorylation at the cellular sites. We found that mutants in the Roc-COR domains, including Arg1441Cys, Arg1441His, Ala1442Pro and Tyr1699Cys, can positively enhance LRRK2 kinase activity while concomitantly inducing the dephosphorylation of the cellular sites. Mutation of the cellular sites individually did not affect LRRK2 intrinsic kinase activity; however, Ser910/935/955/973Ala mutations trended toward increased kinase activity of LRRK2. Increased cAMP levels did not lead to increased LRRK2 cellular site phosphorylation, 14-3-3 binding or kinase activity. In cells, inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser1292 by Calyculin A and okadaic acid sensitive phosphatases, while the cellular sites are dephosphorylated by Calyculin A sensitive phosphatases. These findings indicate that comparative analysis of both Ser1292 and Ser910/935/955/973 phosphorylation sites will provide important and distinct measures of LRRK2 kinase and biological activity in vitro and in vivo.

  3. Constrained Allocation Flux Balance Analysis

    Mori, Matteo; Hwa, Terence; Martin, Olivier C.

    2016-01-01

    New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an “ensemble averaging” procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws. PMID:27355325

  4. Gyrification from constrained cortical expansion

    Tallinen, Tuomas; Biggins, John S; Mahadevan, L

    2015-01-01

    The exterior of the mammalian brain - the cerebral cortex - has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highl...

  5. Deep-Sea Magnetics on Active and Fossil Hydrothermal Sites: a Tool to Detect and Characterize Submarine Ore Deposits

    Dyment, J.; Szitkar, F.; Fouquet, Y.; Choi, Y.

    2011-12-01

    Since the first discoveries of hydrothermal sites at mid-ocean ridges in the 70s, international efforts in the deep seafloor exploration have unravelled a wide variety of hydrothermal sites in terms of geological settings, physical parameters, and biological communities as well. Such efforts, coordinated in the InterRidge program since 1992, are becoming even more important when the increasing need in metals for developing economies makes the exploitation of metal sulfides accumulated at deep-sea hydrothermal sites a realistic target. The usual method to find hydrothermal sites is to detect the associated chemical plumes enriched in manganese, methane, hydrogen, helium 3, in the water column. How efficient it has been proven, such a method is limited to the search for active hydrothermal vents. Active vents, however, are not the best places for mining the seafloor, because (1) they host massive sulfides deposits in the making and may not represent the largest accumulation; (2) they are still very hot and would rapidly damage the mining tools; and, last but not the least, (3) they host fragile and precious ecosystem that could be dramatically affected by mining operations. Methods to find fossil hydrothermal sites (i.e. colder and devoid of specific ecosystems) include systematic rock sampling - a very tedious endeavour - and high resolution, near seafloor geophysical surveys. Existing magnetic surveys on basalt-hosted, peridotite-hosted and sediment-hosted sites revealed different types of signatures, which reflect the magnetizations of the host rock and the ore deposit, among others. Basalt-hosted sites exhibit negative magnetic anomalies, i.e. a deficit of magnetization, due to thermal demagnetization and hydrothermal alteration of the highly magnetic basalt, whereas both peridotite-hosted and sediment-hosted sites show positive anomalies, i.e. an excess of magnetization, clearly associated with the ore deposit. Results from recent cruises Serpentine (R

  6. Public communication and participation activities in siting controversial facilities in the United States and Western Europe

    This paper reviews literature discussing the siting of controversial facilities in the United States and Western Europe in order to identify lessons regarding the role of public communication and participation. Sources found that effective public communication and participation are extremely important to successful facility siting, although they do not guarantee it. Lessons fell into four categories: recognizing and addressing public concern; meeting the communication and participation needs of key publics; creating an effective siting process; and recognizing the limitations of public communication and participation. The authors discusses specific lessons, with examples from the literature, in each category

  7. Test program for closure activities at a mixed waste disposal site at the Savannah River Plant

    A 58-acre site at the Savannah River Plant which was used for disposal of low-level radioactive waste and quantities of the hazardous materials lead, cadmium, scintillation fluid, and oil will be the first large waste site at the Savannah River Plant to be permanently closed. The actions leading to closure of the facility will include surface stabilization and capping of the site. Test programs have been conducted to evaluate the effectiveness of dynamic compaction as a stabilization technique and the feasibility of using locally derived clay as a capping material

  8. Extra-Large-Pore Zeolites with UTL Topology: Control of the Catalytic Activity by Variation in the Nature of the Active Sites

    Shamzhy, Mariya; Shvets, O. V.; Opanasenko, Maksym; Kurfiřtová, Lenka; Kubička, D.; Čejka, Jiří

    2013-01-01

    Roč. 5, č. 7 (2013), s. 1891-1898. ISSN 1867-3880 R&D Projects: GA ČR GBP106/12/G015 Institutional support: RVO:61388955 Keywords : acidity * active sites * Beckmann rearrangement Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.044, year: 2013

  9. Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue.

    Arriarán, Sofía; Agnelli, Silvia; Remesar, Xavier; Fernández-López, José Antonio; Alemany, Marià

    2015-01-01

    Background and Objectives. White adipose tissue (WAT) shows marked sex- and diet-dependent differences. However, our metabolic knowledge of WAT, especially on amino acid metabolism, is considerably limited. In the present study, we compared the influence of sex on the amino acid metabolism profile of the four main WAT sites, focused on the paths related to ammonium handling and the urea cycle, as a way to estimate the extent of WAT implication on body amino-nitrogen metabolism. Experimental Design. Adult female and male rats were maintained, undisturbed, under standard conditions for one month. After killing them under isoflurane anesthesia. WAT sites were dissected and weighed. Subcutaneous, perigonadal, retroperitoneal and mesenteric WAT were analyzed for amino acid metabolism gene expression and enzyme activities. Results. There was a considerable stability of the urea cycle activities and expressions, irrespective of sex, and with only limited influence of site. Urea cycle was more resilient to change than other site-specialized metabolic pathways. The control of WAT urea cycle was probably related to the provision of arginine/citrulline, as deduced from the enzyme activity profiles. These data support a generalized role of WAT in overall amino-N handling. In contrast, sex markedly affected WAT ammonium-centered amino acid metabolism in a site-related way, with relatively higher emphasis in males' subcutaneous WAT. Conclusions. We found that WAT has an active amino acid metabolism. Its gene expressions were lower than those of glucose-lipid interactions, but the differences were quantitatively less important than usually reported. The effects of sex on urea cycle enzymes expression and activity were limited, in contrast with the wider variations observed in other metabolic pathways. The results agree with a centralized control of urea cycle operation affecting the adipose organ as a whole. PMID:26587356

  10. The complexities of measuring access to parks and physical activity sites in New York City: a quantitative and qualitative approach

    Sohler Nancy L

    2009-06-01

    Full Text Available Abstract Background Proximity to parks and physical activity sites has been linked to an increase in active behaviors, and positive impacts on health outcomes such as lower rates of cardiovascular disease, diabetes, and obesity. Since populations with a low socio-economic status as well as racial and ethnic minorities tend to experience worse health outcomes in the USA, access to parks and physical activity sites may be an environmental justice issue. Geographic Information systems were used to conduct quantitative and qualitative analyses of park accessibility in New York City, which included kernel density estimation, ordinary least squares (global regression, geographically weighted (local regression, and longitudinal case studies, consisting of field work and archival research. Accessibility was measured by both density of park acreage and density of physical activity sites. Independent variables included percent non-Hispanic black, percent Hispanic, percent below poverty, percent of adults without high school diploma, percent with limited English-speaking ability, and population density. Results The ordinary least squares linear regression found weak relationships in both the park acreage density and the physical activity site density models (Ra2 = .11 and .23, respectively; AIC = 7162 and 3529, respectively. Geographically weighted regression, however, suggested spatial non-stationarity in both models, indicating disparities in accessibility that vary over space with respect to magnitude and directionality of the relationships (AIC = 2014 and -1241, respectively. The qualitative analysis supported the findings of the local regression, confirming that although there is a geographically inequitable distribution of park space and physical activity sites, it is not globally predicted by race, ethnicity, or socio-economic status. Conclusion The combination of quantitative and qualitative analyses demonstrated the complexity of the issues around

  11. Lessons learned through tank closure activities from selected sites within the DOE complex

    The more than 230 lessons learned in this document were researched and identified from other U.S. Department of Energy (DOE) sites, with attention to the technical, regulatory, and management strategies focus of the IMAP

  12. Quality assurance requirements for an institution with diverse technical activities at the Nevada test site (NTS)

    The author describes the Nevada test site's restructuring of its approach to quality assurance. Basic requirements are being expanded and augmented. The nature of the quality assurance program is discussed

  13. Bear feeding activity at alpine insect aggregation sites in the Yellowstone ecosystem

    Mattson, David J.; Gillin, Colin M.; Benson, Scott A.; Knight, Richard R.

    1991-01-01

    Bears (Ursidae) were observed from fixed-wing aircraft on or near alpine talus in the Shoshone National Forest between 15 June and 15 September in 1981–1989. Bears fed on insect aggregations at 6 known and 12 suspected alpine talus sites, disproportionately more at elevations > 3350 m, on slopes > 30°, and on south- and west-facing aspects. While at these sites, bears almost exclusively ate invertebrates, typically army cutworm moths (Euxoa auxiliaris). Subadult grizzly bears (Ursus arctos horribilis) appeared to be underrepresented at the sites, and proportionate representation of adult females with young appeared to decrease between 15 June and 15 September. Overall, observations of bears at these sites increased between 1981 and 1989. We suggest that alpine insect aggregations are an important food source for bears in the Shoshone National Forest, especially in the absence of high-quality foraging alternatives in July and August of most years.

  14. Irreversible photolabeling of active site of neutral endopeptidase-24.11 enkephalinase by azidothiorphan and [14C]-azidothiorphan

    Azidothiorphan and its [14C]-labeled analogue have been developed as photoaffinity ligands for the active site of the neutral endopeptidase 24.11. In in vitro assays azidothiorphan inhibits the endopeptidase activity with a Ki of 0.75 nM. After ultraviolet irradiation the inhibitor binds irreversibly to the enzyme, and many factors suggest that the photolabeling occurs at the active site. The binding is accompanied by a loss of enzymatic activity, and the inclusion of the competitive inhibitor thiorphan protects the endopeptidase from this inactivation. In addition the binding of another competitive inhibitor [3H]N-[(R,S)-3-hydroxyaminocarbonyl-2-benzyl-1-oxopropyl]-glycine to the active site of endopeptidase-24.11 is inhibited after irradiation with azidothiorphan. Experiments with [14C]-azidothiorphan have shown that very little nonspecific binding of inhibitor to enzyme occurs and the the labeled probe remains bound under denaturing conditions. Azidothiorphan has also been found to produce a long-lasting naloxone-reversible analgesia after intracerebroventricular administration. The results show that azidothiorphan should prove useful both for structural studies and for investigations on the synthesis and turnover of the neutral endopeptidase-24.11

  15. Irreversible photolabeling of active site of neutral endopeptidase-24. 11 enkephalinase by azidothiorphan and (/sup 14/C)-azidothiorphan

    Beaumont, A.; Hernandez, J.F.; Chaillet, P.; Crine, P.; Roques, B.P.

    1987-11-01

    Azidothiorphan and its (/sup 14/C)-labeled analogue have been developed as photoaffinity ligands for the active site of the neutral endopeptidase 24.11. In in vitro assays azidothiorphan inhibits the endopeptidase activity with a Ki of 0.75 nM. After ultraviolet irradiation the inhibitor binds irreversibly to the enzyme, and many factors suggest that the photolabeling occurs at the active site. The binding is accompanied by a loss of enzymatic activity, and the inclusion of the competitive inhibitor thiorphan protects the endopeptidase from this inactivation. In addition the binding of another competitive inhibitor (/sup 3/H)N-((R,S)-3-hydroxyaminocarbonyl-2-benzyl-1-oxopropyl)-glycine to the active site of endopeptidase-24.11 is inhibited after irradiation with azidothiorphan. Experiments with (/sup 14/C)-azidothiorphan have shown that very little nonspecific binding of inhibitor to enzyme occurs and the the labeled probe remains bound under denaturing conditions. Azidothiorphan has also been found to produce a long-lasting naloxone-reversible analgesia after intracerebroventricular administration. The results show that azidothiorphan should prove useful both for structural studies and for investigations on the synthesis and turnover of the neutral endopeptidase-24.11.

  16. Social Networking Sites and Graduate Recruitment: Sharing Online Activities?(SoMWP1002)

    Teng, Yue; Córdoba-Pachón, José-Rodrigo

    2010-01-01

    The increasing impact of social networking sites in communication and socializing worldwide brings attention to how they affect recruitment processes of graduates in organizations. Many employers are now searching for graduates’ data to complement their assessment of job candidates and hiring decisions. While this still is not developed as a common practice by (HR) practitioners and recruiters, existing research remains underdeveloped from the perspective of graduates’ use of such sites. ...

  17. Structure of HIV-1 Reverse Transcriptase with the Inhibitor -thujaplicinol Bound at the RNase H Active Site

    Himmel, D.; Maegley, K; Pauly, T; Bauman, J; Das, K; Dharia, C; Clark, Jr., A; Ryan, K; Hickey, M; et al.

    2009-01-01

    Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, such as RNH, should be effective against all of the current drug-resistant variants. Here, we present 2.80 {angstrom} and 2.04 {angstrom} resolution crystal structures of an RNH inhibitor, {beta}-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. {beta}-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that {beta}-thujaplicinol is a slow-binding RNH inhibitor with noncompetitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.

  18. Arbuscular mycorrhizal fungal symbiosis with Sorbus torminalis does not vary with soil nutrients and enzyme activities across different sites

    Moradi M

    2015-06-01

    Full Text Available Effects of soil chemical properties on arbuscular mycorrhizal fungal (AMF symbiosis with wild service tree (Sorbus torminalis L. Crantz were examined for study the rates of root colonization at three forest sites: Kheiroud, Lalis, and Takrin in northern Iran. Soil characteristics including pH, available phosphorus (P, potassium (K, organic matter, total nitrogen, acid and alkaline phosphatase activities, CaCO3, spore density (SD and AMF colonization of soil and root samples were analyzed. The study sites were investigated in spring and autumn to highlight the effects of soil chemical properties on AMF statues for better nurseries and reforestation management of this rare tree species in forests. Changes in soil pH, P, K, organic matter, total nitrogen, acid and alkaline phosphatase, CaCO3, SD, and AMF colonization of soil and root samples were analyzed at the study sites. K, pH, root colonization, SD and acid phosphatase activity showed no significant differences among sites in spring and autumn, while total nitrogen, P, organic matter and alkaline phosphatase activities showed significant differences among sites and seasons. AMF colonization rates were more than 51% and 32% of roots in spring and autumn, respectively. No correlation between root colonization and soil chemical parameters in spring and autumn were detected. There was no correlation between percentage of AM root colonization and SD nor other soil parameters in spring and autumn. SD and CaCO3 were significantly negatively correlated in spring and autumn. Despite differences in soil characteristics, the results showed that SD and root colonization were not significantly different among the sites. They also showed that wild service trees had strong symbiosis with AMF, while soil properties might not have a significant effect on this symbiosis. Therefore, colonized seedlings can be considered as an appropriated method for reforestation and conservation of this rare tree species.

  19. Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

    Li DU; Ya-xue ZHAO; Liu-meng YANG; Yong-tang ZHENG; Yun TANG; Xu SHEN; Hua-liang JIANG

    2008-01-01

    Aim:To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide,as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) binding to viral DNA.Methods:A surface plasma resonance (SPR)-based competitive assay was employed to determine the compound's inhibitory activity,and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell assay was used to qualify the antiviral activity.The potential binding sites were predicted by molecular modeling and determined by site-directed mutagenesis and a SPR binding assay.Results:l-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide could competitively inhibit IN binding to viral DNA with a 50% inhibitory concentration (IC50) value of 7.29±0.68 μmol/L as investigated by SPR-based investigation.Another antiretroviral activity assay showed that this compound exhibited inhibition against HⅣ-Ⅰ(ⅢB) replication with a 50% effective concentration (EC50) value of 40.54 μmol/L in C8166 cells,and cytotoxicity with a cytotoxic concentration value of 173.84 μmol/L in mock-infected C8166 cells.Molecular docking predicted 3 potential residues as 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene)bis-1-pyrrolidineacetamide binding sites.The importance of 3 key amino acid residues (Lys103,Lys173,and Thr174) involved in the binding was further identified by site-directed mutagenesis and a SPR binding assay.Conclusion:This present work identified a new anti-HIV compound through a new IN-binding site which is expected to supply new potential drug-binding site information for HIV-1 integrase inhibitor discovery and development.

  20. An EXAFS study of the interaction of substrate with the ferric active site of protocatechuate 3,4-dioxygenase

    True, A.E.; Orville, A.M.; Pearce, L.L.; Lipscomb, J.D.; Que, L. Jr. (Univ. of Minnesota, Minneapolis (USA))

    1990-12-01

    X-ray crystallographic studies of the intradiol cleaving protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa have shown that the enzyme has a trigonal bipyramidal ferric active site with two histidines, two tyrosines, and a solvent molecule as ligands. Fe K-edge EXAFS studies of the spectroscopically similar protocatechuate 3,4-dioxygenase from Brevibacterium fuscum are consistent with a pentacoordinate geometry of the iron active site with 3 O/N ligands at 1.90 {angstrom} and 2 O/N ligands at 2.08 {angstrom}. The 2.08-{angstrom} bonds are assigned to the two histidines, while the 1.90-{angstrom} bonds are associated with the two tyrosines and the coordinated solvent. The short Fe-O distance for the solvent suggests that it coordinates as hydroxide rather than water. When the inhibitor terephthalate is bound to the enzyme, the XANES data indicate that the ferric site becomes 6-coordinate and the EXAFS data show a beat pattern which can only be simulated with an additional Fe-O/N interaction at 2.46 {angstrom}. Together, the data suggest that the oxygens of the carboxylate group in terephthalate displace the hydroxide and chelate to the ferric site but in an asymmetric fashion. In contrast, protocatechuate 3,4-dioxygenase remains 5-coordinate upon the addition of the slow substrate homoprotocatechuic acid (HPCA). Previous EPR data have indicated that HPCA forms an iron chelate via the two hydroxyl functions. For the iron site to remain 5-coordinate and the HPCA to be chelated to the iron, the substrate must displace not only the hydroxide but also a ligand from the protein backbone, probably a histidine. The mechanistic implications of the displacement of hydroxide and a protein ligand in the active site are discussed.