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Sample records for active site gorge

  1. Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase has been a topic of great interest. Flexibility of these residues has been suspected to be a key player in controlling ligand traversal in the gorge. This raises the question of whether the over representation of aromatic residues in the gorge implies higher than normal flexibility of those residues. The current study suggests that it does not. Large changes in the hydrophobic cross sectional area due to dihedral oscillations are probably the reason behind their presence in the gorge.

  2. Energetics of Ortho-7 (oxime drug) translocation through the active-site gorge of tabun conjugated acetylcholinesterase.

    PubMed

    Sinha, Vivek; Ganguly, Bishwajit; Bandyopadhyay, Tusar

    2012-01-01

    Oxime drugs translocate through the 20 Å active-site gorge of acetylcholinesterase in order to liberate the enzyme from organophosphorus compounds' (such as tabun) conjugation. Here we report bidirectional steered molecular dynamics simulations of oxime drug (Ortho-7) translocation through the gorge of tabun intoxicated enzyme, in which time dependent external forces accelerate the translocation event. The simulations reveal the participation of drug-enzyme hydrogen bonding, hydrophobic interactions and water bridges between them. Employing nonequilibrium theorems that recovers the free energy from irreversible work done, we reconstruct potential of mean force along the translocation pathway such that the desired quantity represents an unperturbed system. The potential locates the binding sites and barriers for the drug to translocate inside the gorge. Configurational entropic contribution of the protein-drug binding entity and the role of solvent translational mobility in the binding energetics is further assessed.

  3. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

    PubMed

    Pathak, Arup Kumar; Bandyopadhyay, Tusar

    2016-01-01

    Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.

  4. A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge, Tanzania

    PubMed Central

    Brochu, Christopher A.; Njau, Jackson; Blumenschine, Robert J.; Densmore, Llewellyn D.

    2010-01-01

    Background The fossil record reveals surprising crocodile diversity in the Neogene of Africa, but relationships with their living relatives and the biogeographic origins of the modern African crocodylian fauna are poorly understood. A Plio-Pleistocene crocodile from Olduvai Gorge, Tanzania, represents a new extinct species and shows that high crocodylian diversity in Africa persisted after the Miocene. It had prominent triangular “horns” over the ears and a relatively deep snout, these resemble those of the recently extinct Malagasy crocodile Voay robustus, but the new species lacks features found among osteolaemines and shares derived similarities with living species of Crocodylus. Methodology/Principal Findings The holotype consists of a partial skull and skeleton and was collected on the surface between two tuffs dated to approximately 1.84 million years (Ma), in the same interval near the type localities for the hominids Homo habilis and Australopithecus boisei. It was compared with previously-collected material from Olduvai Gorge referable to the same species. Phylogenetic analysis places the new form within or adjacent to crown Crocodylus. Conclusions/Significance The new crocodile species was the largest predator encountered by our ancestors at Olduvai Gorge, as indicated by hominid specimens preserving crocodile bite marks from these sites. The new species also reinforces the emerging view of high crocodylian diversity throughout the Neogene, and it represents one of the few extinct species referable to crown genus Crocodylus. PMID:20195356

  5. Taphonomic perspectives on hominid site use and foraging strategies during Bed II times at Olduvai Gorge, Tanzania.

    PubMed

    Egeland, Charles P; Domínguez-Rodrigo, Manuel

    2008-12-01

    The faunal assemblages excavated by Mary Leakey in Bed II of Olduvai Gorge, Tanzania, have, like the more well-known Bed I assemblages, traditionally been interpreted as the result of hominid butchering activities in the lake margin and riverine settings of the paleo-Olduvai Basin. A reexamination of all of Leakey's Bed I sites has shown that hominids played little or no role in the formation of all but one of those faunal assemblages, a finding that prompted the reanalysis of the Bed II sites presented here. We expand upon a previous taphonomic study that provided systematic data for HWK East Levels 1-2, MNK Main, and BK. In addition to these assemblages, we provide data on HWK East Levels 3-5, FC West, TK, and SHK. Our data contradict previous interpretations of MNK Main as a hominid accumulation but uphold the contention that BK represents a primarily hominid accumulation reflecting early access to carcasses. The small and poorly preserved assemblages from FC West and TK are difficult to link unambiguously to either hominids or carnivores. Site MNK Main and HWK East Levels 3-5 appear to be death arenas where carcasses accumulated via natural deaths and/or serial predation. Site SHK is severely biased by selective retention and therefore little can be said of its formational history. Nevertheless, no hominid modifications were documented in this assemblage. Comparisons with other Olduvai sites indicate a more conspicuous hyena taphonomic signal during Bed II times than Bed I times, which appears to mirror the changing configuration of the large carnivore guild. These findings also beg the question of what activities were being carried out by hominids with the stone tools discarded at these sites. Although it seems clear that hominids were utilizing stone tools to carry out subsistence activities unrelated to carcass butchery, more excavation and techniques such as phytolith analysis should be employed to explore alternative explanations.

  6. Disentangling hominin and carnivore activities near a spring at FLK North (Olduvai Gorge, Tanzania)

    NASA Astrophysics Data System (ADS)

    Domínguez-Rodrigo, M.; Mabulla, A. Z. P.; Bunn, H. T.; Diez-Martin, F.; Baquedano, E.; Barboni, D.; Barba, R.; Domínguez-Solera, S.; Sánchez, P.; Ashley, G. M.; Yravedra, J.

    2010-11-01

    FLK North is one of the densest concentrations of fossils found in Olduvai Gorge. A recent taphonomic re-evaluation of the collection excavated by Leakey at the site suggests that it was a palimpsest in which most of the animals were accumulated and modified by carnivores. The lithic tools therefore seem to have an independent depositional history from most of the fauna. The present study, based on new excavations, expands the evidence supporting this interpretation and demonstrates a thicker deposit than was reported by Leakey, including new archaeological levels. It also shows that in the few instances where hominins butchered carcasses, meat, not marrow, was their main target. This argues against passive scavenging hypotheses, which emphasize the dietary role of marrow, and instead underscores the importance of meat in the diet of early Pleistocene hominins.

  7. A Survey of Landslide Activity in the Columbia River Gorge from InSAR

    NASA Astrophysics Data System (ADS)

    Tong, X.; Schmidt, D. A.

    2015-12-01

    The Columbia River Gorge contains several large landslide complexes that have exhibited historical movement, both catastrophic and slow moving. Monitoring the kinematics of active movement helps to characterize the ongoing natural hazard. In this study, we document the status of several large landslide complexes along the Columbia River Gorge. We use synthetic aperture radar (SAR) data from multiple satellites (ERS, ENVISAT and ALOS) to reveal the spatial-temporal movement of slow-moving landslides over two decades, 1992-2011. To increase the spatial extent of the signal we developed a new InSAR time-series method based on pixel coherence and derived the time series of the landslides. We also investigate the ability of Persistent Scatterer InSAR to better illuminate active movement. While many historical landslide complexes show minimal or non-existent movement, we measure significant creep on the Redbluff landslide, which is part of the Cascade Landslide Complex near the Bonneville Dam. The InSAR time-series data reveal approximately 25 cm of line-of-sight movement from 5 years of ALOS observations, which translates into greater than 60 cm of downslope movement. The Redbluff landslide is seasonally activated, with accelerated movement observed during the early winter of each year. However, the amplitude of the seasonal signal is variable from year-to-year. To assess the triggering mechanisms, we compared the deformation time series data with local precipitation data. The deformation correlates well with precipitation, implying the slow movement is controlled by rainfall that infiltrates to the base of the slide. A preliminary comparison with the bare earth 2m-resolution digital elevation model from LiDAR reveals that the overall deformation pattern and the active perimeter is highly correlated with the morphology of the landslide.

  8. Study of Active Faults in the Three Gorges Dam region by Detecting and Relocating Aftershocks

    NASA Astrophysics Data System (ADS)

    Huang, R.; Zhu, L.; Xu, Y.

    2014-12-01

    Seismicity in the Three Gorges Dam (TGD) region and its adjacent areas increased dramatically as the water- level of the TGD reservoir rises since its completion in 2003. Accordingly, many efforts have been put forward to quantify the seismicity and geological hazards in the region. However, the precise detective of earthquakes, especially for the minor ones, remains difficulty because of sparse distribution of permanent seismic stations. From December 2013 to June 2014, we deployed 30 three-component broadband seismic stations in the TGD region. During the deployment, we recorded two earthquakes of magnitudes lager than 5.0, one occurred on December 16th 2013 in Badong and another on March 30th 2014 in Zigui. We firstly used a sliding-window cross-correlation (SCC) detection technique to supplement the events catalog from the China Earthquake Networks Center. Over 500 new events with ML lager than 0.5 were detected. We then relocated 502 events out of the total 987 events using the double-difference (DD) relocation algorithm. We also determined moment tensors of some large earthquakes using gCAP. The results clearly show two active faults along Yangtze River with dips of 50 degrees and 90 degrees to a maximum depth of 10 km, respectively. And they also reveal that water might have permeated to a depth of 6 km corresponds to the interface of sediments and metamorphic basement beneath Zigui Basin. We thus preliminarily judge that the quakes are triggered by local stress adjustment resulting of fluctuation of Three Gorges reservoir's loading.

  9. The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania).

    PubMed

    Diez-Martín, F; Sánchez Yustos, P; Uribelarrea, D; Baquedano, E; Mark, D F; Mabulla, A; Fraile, C; Duque, J; Díaz, I; Pérez-González, A; Yravedra, J; Egeland, C P; Organista, E; Domínguez-Rodrigo, M

    2015-12-07

    The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato.

  10. The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania)

    PubMed Central

    Diez-Martín, F.; Sánchez Yustos, P.; Uribelarrea, D.; Baquedano, E.; Mark, D. F.; Mabulla, A.; Fraile, C.; Duque, J.; Díaz, I.; Pérez-González, A.; Yravedra, J.; Egeland, C. P.; Organista, E.; Domínguez-Rodrigo, M.

    2015-01-01

    The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato. PMID:26639785

  11. Three Gorges Dam, China

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This ASTER image shows a 60 km stretch of the Yangtze River in China, including the Xiling Gorge, the eastern of the three gorges. In the left part of the image is the construction site of the Three Gorges Dam, the world's largest.

    This image was acquired on July 20, 2000 by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER will image Earth for the next 6 years to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products. Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, California, is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long-term research and technology program designed to examine Earth's land, oceans, atmosphere, ice and life as a total integrated system.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    Size: 60 x 24 km (36 x 15 miles) Location: 30.6 deg. North lat., 111.2 deg. East long. Orientation: North at top Image Data: ASTER

  12. The Effect on the Flow Conditions of Chinese Sturgeons’ Spawning Sites in the Process of Peak Regulation between the Three Gorges Dam and Gezhou Dam

    NASA Astrophysics Data System (ADS)

    Hui, Guo; Minghai, Huang; Feng, Jin

    Chinese sturgeon (Acipenser sinensis Gray) is a kind of key protected fish in ChangJiang river. Recently the Three Gorges dam has run, the peak regulation process between the two dams has serious effect on the formed spawning sites. Based on the previous research results of suitable flow conditions about the spawning sites, this article builds a 2-D shallow water numerical model, calculates the flow conditions of the spawning sites in the process of peak regulation. The results show that the water depth and velocity are various and affect the spawning sites in one 24-hours process of peak regulation, as a whole, when the discharge is below 9000 m3/s and 7500 m3/s respectively, the two spawning sites will be affected seriously.

  13. Causes of haze in the Columbia River Gorge

    SciTech Connect

    Mark Green; Jin Xu

    2007-08-15

    Visibility impairment in the Columbia River Gorge National Scenic Area is an area of concern. A field study conducted from July 2003 to February 2005 was followed by data analysis and receptor modeling to better understand the temporal and spatial patterns of haze and the sources contributing to the haze in the Columbia River Gorge in the states of Washington and Oregon. The nephelometer light scattering and surface meteorological data at eight sites along the gorge showed five distinct wind patterns, each with its characteristic diurnal and spatial patterns in light scattering by particles (b{sub sp}). In summer, winds were nearly always from west to east (upgorge) and showed decreasing b{sub sp} with distance into the gorge and a pronounced effect of the Portland, OR, metropolitan area on haze, especially in the western portions of the gorge. Winter often had winds from the east with very high levels of b{sub sp}, especially at the eastern gorge sites, with sources east of the gorge responsible for much of the haze. The major chemical components responsible for haze were organic carbon, sulfate, and nitrate. Positive matrix factorization (PMF) using chemically speciated Interagency Monitoring of Protected Visual Environments data indicated seven source factors in the western gorge and five factors in the eastern gorge. Organic mass is a large contributor to haze in the gorge in all seasons, with a peak in fall. Approximately half of the organic mass is biomass smoke, with mobile sources as the second largest contributor. PMF analysis showed nitrates mainly attributed to a generic secondary nitrate factor. Sulfate is a significant contributor in all seasons, with peak sulfate concentrations in summer. Sources east of the gorge, likely a coal-fired power plant, nearby dairy farm, and upriver cities, appear to be major contributors to wintertime haze in the gorge. 22 refs., 11 figs., 6 tabs.

  14. When felids and hominins ruled at Olduvai Gorge: A machine learning analysis of the skeletal profiles of the non-anthropogenic Bed I sites

    NASA Astrophysics Data System (ADS)

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel

    2016-05-01

    In the past twenty years, skeletal part profiles, which are prone to equifinality, have not occupied a prominent role in the interpretation of early Pleistocene sites on Africa. Alternatively, taphonomic studies on bone surface modifications and bone breakage patterns, have provided heuristic interpretations of some of the best preserved archaeological record of this period; namely, the Olduvai Bed I sites. The most recent and comprehensive taphonomic study of these sites (Domínguez-Rodrigo et al., 2007a) showed that FLK Zinj was an anthropogenic assemblage in which hominins acquired carcasses via primary access. That study also showed that the other sites were palimpsests with minimal or no intervention by hominins. The FLK N, FLK NN and DK sequence seemed to be dominated by single-agent (mostly, felid) or multiple-agent (mostly, felid-hyenid) processes. The present study re-analyzes the Bed I sites focusing on skeletal part profiles. Machine learning methods, which incorporate complex algorithms, are powerful predictive and classification methods and have the potential to better extract information from skeletal part representation than past approaches. Here, multiple algorithms (via decision trees, neural networks, random forests and support vector machines) are combined to produce a solid interpretation of bone accumulation agency at the Olduvai Bed I sites. This new approach virtually coincides with previous taphonomic interpretations on a site by site basis and shows that felids were dominant accumulating agents over hyenas during Bed I times. The recent discovery of possibly a modern lion-accumulated assemblage at Olduvai Gorge (Arriaza et al., submitted) provides a very timely analog for this interpretation.

  15. List 9 - Active CERCLIS Sites:

    EPA Pesticide Factsheets

    The List 9 displays the sequence of activities undertaken at active CERCLIS sites. An active site is one at which site assessment, removal, remedial, enforcement, cost recovery, or oversight activities are being planned or conducted.

  16. [Effects of biological regulated measures on active organic carbon and erosion-resistance in the Three Gorges Reservoir region soil].

    PubMed

    Huang, Ru; Huang, Lin; He, Bing-Hui; Zhou, Li-Jiang; Yu, Chuan; Wang, Feng

    2013-07-01

    To gain a better knowledge of characteristics of soils and provide a scientific basis for soil erosion control in the Three Gorges Reservoir Area, contents of aggregates and total soil organic carbon (SOC), as well as soil active organic carbon fractions including particulate organic carbon (POC), readily oxidized organic carbon (ROC), dissolved organic carbon (DOC), microbial biomass carbon (MBC) in the 0-30 cm soil layer under seven different biological regulated measures were studied by the field investigation combined with the laboratory analysis. Results showed that the content of the SOC and active organic carbon fractions decreased with the increasing soil depth; the content of the SOC and active organic carbon fractions in 0-10 cm was significantly higher than that in 20-30 cm. The stability of soil aggregates were also significantly influenced by biological regulated measures, the content of > 0.25 mm water-stable aggregates in seven types of biological regulated measures was in the order of Koelreuteria bipinnata + Cassia suffruticasa > hedgerows > closed forest > natural restoration > economic forest > traditional planting > control plot, moreover, the content of 0.25 mm water-stable aggregates correlated positively with the content of SOC. Soils under different biological regulated measures all demonstrated fractal features, and soil under the measure of Koelreuteria bipinnata + Cassia suffruticasa was found to have the lowest value of fractal dimension and soil erodiable K, indicating a relatively strong structure stability and erosion-resistant capacity. Negative correlation was observed when compared the content of active organic carbon fractions with the soil erodiable K. It can be concluded that properties of soil can be managed through biological regulated measures; thence had an influence on the soil erosion-resistant capacity.

  17. Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

    PubMed

    Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

    2003-05-13

    Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

  18. 2. GORGE HIGH DAM. UNUSUALLY HIGH WATER IN GORGE LAKE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. GORGE HIGH DAM. UNUSUALLY HIGH WATER IN GORGE LAKE DUE TO THE COMBINATION OF UNIT 24 BEING DOWN FOR REWINDING AND TWO UNITS COMING ON LINE UNEXPECTEDLY AT ROSS POWERHOUSE LED TO WATER FLOWING OVER THE SPILLGATES. EACH GATE IF 47 FEET WIDE AND 50 FEET HIGH, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  19. [Relationships between soil nutrient contents and soil enzyme activities in Pinus massoniana stands with different ages in Three Gorges Reservoir Area].

    PubMed

    Ge, Xiao-Gai; Xiao, Wen-Fa; Zeng, Li-Xiong; Huang, Zhi-Lin; Huang, Ling-Ling; Tan, Ben-Wang

    2012-02-01

    Based on the measurements of soil nutrient contents and enzyme activities and the canonical correspondence analysis (CCA), this paper studied the relationships between soil nutrient contents and soil enzyme activities in different age Pinus massoniana stands in Three Gorges Reservoir Area. Among the test stands, mature stand had the highest contents of organic matter, total nitrogen, ammonium nitrogen, and available phosphorus in 0-20 cm soil layer, followed by middle-aged stand, and nearly-mature stand. With the increase of the stand age, soil invertase activity increased after an initial decrease, cellulase and polyphenoloxidase activities decreased gradually, while urease and peroxidase activities decreased after an initial increase. CCA analysis showed that the effects of the main soil parameters on the soil enzyme activities in the stands ranked in the sequence of total nitrogen > organic matter > pH > bulk density > ammonium nitrogen > available phosphorus. Soil invertase activity had significant positive correlations with soil organic matter, total nitrogen, and total phosphorus, while soil peroxidase activity significantly negatively correlated with soil organic matter, total nitrogen, total phosphorus, and bulk density. The soil was rich in main nutrients, invertase activity was relatively high, while peroxidase activity was relatively low. The activities of soil invertase, cellulase and peroxidase could be used as the good biological indicators in evaluating soil quality and fertility.

  20. Probing Gorge Dimensions of Cholinesterases by Freeze-Frame Click Chemistry

    PubMed Central

    Radić, Zoran; Manetsch, Roman; Fournier, Didier; Sharpless, K. Barry; Taylor, Palmer

    2008-01-01

    Freeze-frame click chemistry is a proven approach for design in situ of high affinity ligands from bioorthogonal, reactive building blocks and macromolecular template targets. We recently described in situ design of femtomolar reversible inhibitors of fish and mammalian acetylcholinesterases (EC 3.1.1.7; AChEs) using several different libraries of acetylene and azide building blocks. Active center gorge geometries of those AChEs are rather similar and identical triazole inhibitors were detected in situ when incubating the same building block libraries in different AChEs. Drosophila melanogaster AChE crystal structure and other insect AChE homology models differ more in their overall 3D structure than other members of the cholinesterase family. The portion of the gorge proximal to the catalytic triad and choline binding site has a ~50% reduction in volume, and the gorge entrance at the peripheral anionic site (PAS) is more constricted than in the fish and mammalian AChE’s. In this communication we describe rationale for using purified recombinant Drosophila AChE as a template for in situ reaction of tacrine and propidium based libraries of acetylene and azide building blocks. The structures of resulting triazole inhibitors synthesized in situ are expected to differ appreciably from the fish and mammalian AChEs. While the latter AChEs exclusively promote synthesis of syn-substituted triazoles, the best Drosophila AChE triazole inhibitors were always anti-substituted. The anti- regioisomer triazoles were by about one order of magnitude better inhibitors of Drosophila than mammalian and fish AChEs. Moreover, the preferred site of acetylene + azide reaction in insect AChE and the resulting triazole ring formation shifts from near the base of the gorge to closer to its rim due to substantial differences of the gorge geometry in Drosophila AChE. Thus, in addition to synthesizing high affinity, lead inhibitors in situ, freeze-frame, click chemistry has capacity to

  1. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  2. Environments and hominin activities across the FLK Peninsula during Zinjanthropus times (1.84 Ma), Olduvai Gorge, Tanzania.

    PubMed

    Blumenschine, Robert J; Stanistreet, Ian G; Njau, Jackson K; Bamford, Marion K; Masao, Fidelis T; Albert, Rosa M; Stollhofen, Harald; Andrews, Peter; Prassack, Kari A; McHenry, Lindsay J; Fernández-Jalvo, Yolanda; Camilli, Eileen L; Ebert, James I

    2012-08-01

    We establish through 13 excavations the landscape context and nature of hominin activities across the Zinjanthropus land surface from which the Leakeys recovered the FLK 22 and FLK NN 1 paleoanthropological assemblages. The land surface was created by fluvial incision of the eastern margin of paleo-Lake Olduvai following a major lake withdrawal. Erosion was uneven, leaving a peninsula bounded by a river channel, the FLK Fault, and a freshwater wetland. This FLK Peninsula supported groves of trees that attracted hominins and carnivores, and that preserved the dense concentrations of carcass remains and stone tools they left behind, including those at FLK 22. Some carcasses appear to have been acquired at the ecotone of the Peninsula and Wetland, where another dense artifact and bone assemblage accumulated. A lesser topographic high at the edge of a Typha marsh in the Wetland was the site of FLK NN 1 and a scatter of large stone tools used possibly for rootstock processing. Our landscape reconstruction delimits the vegetation mosaic indicated by previous work and provides a topographical explanation for the existence of FLK 22 and FLK NN 1. Both are unexpected if the FLK area was the flat, featureless lake margin terrain typical of lake basins similar to paleo-Olduvai. The results show that the Leakeys' sites were not isolated occupation floors but rather parts of a land surface utilized intensively by hominins. Although commonly considered to have been home bases, their likely high predation risk, evidenced by large carnivore feeding traces and the remains of four hominin individuals, suggests visits to them were brief and limited to feeding. Finally, stratigraphic observations confirm that FLK NN 3 accumulated on an older land surface, refuting the hypothesis that the OH 8 foot found there is the same individual as the OH 35 leg from FLK 22.

  3. NDVI indicated long-term interannual changes in vegetation activities and their responses to climatic and anthropogenic factors in the Three Gorges Reservoir Region, China.

    PubMed

    Wen, Zhaofei; Wu, Shengjun; Chen, Jilong; Lü, Mingquan

    2017-01-01

    Natural and social environmental changes in the China's Three Gorges Reservoir Region (TGRR) have received worldwide attention. Identifying interannual changes in vegetation activities in the TGRR is an important task for assessing the impact these changes have on the local ecosystem. We used long-term (1982-2011) satellite-derived Normalized Difference Vegetation Index (NDVI) datasets and climatic and anthropogenic factors to analyze the spatiotemporal patterns of vegetation activities in the TGRR, as well as their links to changes in temperature (TEM), precipitation (PRE), downward radiation (RAD), and anthropogenic activities. At the whole TGRR regional scale, a statistically significant overall uptrend in NDVI variations was observed in 1982-2011. More specifically, there were two distinct periods with different trends split by a breakpoint in 1991: NDVI first sharply increased prior to 1991, and then showed a relatively weak rate of increase after 1991. At the pixel scale, most parts of the TGRR experienced increasing NDVI before the 1990s but different trend change types after the 1990s: trends were positive in forests in the northeastern parts, but negative in farmland in southwest parts of the TGRR. The TEM warming trend was the main climate-related driver of uptrending NDVI variations pre-1990s, and decreasing PRE was the main climate factor (42%) influencing the mid-western farmland areas' NDVI variations post-1990s. We also found that anthropogenic factors such as population density, man-made ecological restoration, and urbanization have notable impacts on the TGRR's NDVI variations. For example, large overall trend slopes in NDVI were more likely to appear in TGRR regions with large fractions of ecological restoration within the last two decades. The findings of this study may help to build a better understanding of the mechanics of NDVI variations in the periods before and during TGDP construction for ongoing ecosystem monitoring and assessment in the

  4. How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations.

    PubMed

    Xu, Yechun; Shen, Jianhua; Luo, Xiaomin; Silman, Israel; Sussman, Joel L; Chen, Kaixian; Jiang, Hualiang

    2003-09-17

    The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.

  5. Wetland plant waxes from Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Tamalavage, A.; Magill, C. R.; Barboni, D.; Ashley, G. M.; Freeman, K. H.

    2013-12-01

    Olduvai Gorge, northern Tanzania, exposes a Plio-Pleistocene sedimentary record that includes lake and lake-margin sediments and fossil remains of ancient plants and early humans. There are rich paleontological and cultural records at Olduvai Gorge that include thousands of vertebrate fossils and stone tools. Previous studies of plant biomarkers in lake sediments from Olduvai Gorge reveal repeated, abrupt changes in landscape dominance by woodland or grassland vegetation during the early Pleistocene, about 1.8 million years ago. However, the reconstruction of wetland vegetation in the past is limited by a dearth of published lipid signatures for modern wetland species. Here, we present lipid and isotopic data for leaf tissues from eight modern plants (i.e., sedge and Typha species) living in wetlands near Olduvai Gorge. Trends in values for molecular and leaf δ13C and average chain length (ACL) of n-alkanes in plant tissues are similar to values for underlying soils. Compound-specific δ13C values for n-alkanes C25 to C33 range between -36.4 to -23.1‰ for C3 plants and -22.3 to -19.5‰ for C4 plants. Fractionation factors between leaf and lipids, ɛ29 and ɛ33, fall within the range reported in the literature, but they differ more widely within a single plant. For C3 plants, the average difference between ɛ29 and ɛ33 is 6.5 ‰, and the difference between ɛ29 and ɛ33 for C4 plants is less than 2‰. Both plant types show a parabolic relationship between chain length and δ13C values, in which C29 typically has the most depleted value, and typically shift by 3-5‰ between alkane homologs. This pattern has not been previously reported, and could be unique for sedge lipids. If so, these data help constrain the application of plant wax biomarkers from sedges for paleo-vegetation reconstruction in paleoclimate studies and at archaeological sites.

  6. Do we need big flood to cut spectacular river gorges?

    NASA Astrophysics Data System (ADS)

    Antón, Loreto; Muñoz-Martín, Alfonso; Mather, Anne; Stokes, Martin

    2016-04-01

    The study of a historical erosional process occurred in a dam spillway in NW Spain evidences extremely rapid gorge formation in granite. Historic documents, photographs and surveys preserved at the Historical Archives allowed the reconstruction of the whole erosion process. A ~270 m long, ~100 m deep and ~100 to 160 m wide amphitheater headed canyon was carved over 6 years. The study approaches the reconstruction of the scour site topography prior to the gorge formation and during the erosion events, and analyses the erosion mechanisms involved in the canyon cutting. Data reveal extremely high (>100 m/year) erosion rates, the highest reported so far on earth, associated to small-moderate floods (~100-1500m3/s). Results come to nuance the established models of erosion and gorge formation which are used to analyze the landscape evolution. The example demonstrates that moderate water discharges are capable of radical erosion suggesting that adjustments to changes such as drainage diversion and capture, or glacier outburst, may be initially much more rapid than has hereto been assumed. Structural preconditioning of the bedrock through jointing and faulting was the primary control on landscape change, conditioning gorge morphology and the rate at which erosion progress.

  7. Occurrence, fate and ecotoxicological assessment of pharmaceutically active compounds in wastewater and sludge from wastewater treatment plants in Chongqing, the Three Gorges Reservoir Area.

    PubMed

    Yan, Qing; Gao, Xu; Chen, You-Peng; Peng, Xu-Ya; Zhang, Yi-Xin; Gan, Xiu-Mei; Zi, Cheng-Fang; Guo, Jin-Song

    2014-02-01

    The occurrence, removal and ecotoxicological assessment of 21 pharmaceutically active compounds (PhACs) including antibiotics, analgesics, antiepileptics, antilipidemics and antihypersensitives, were studied at four municipal wastewater treatment plants (WWTP) in Chongqing, the Three Gorges Reservoir Area. Individual treatment unit effluents, as well as primary and secondary sludge, were sampled and analyzed for the selected PhACs to evaluate their biodegradation, persistence and partitioning behaviors. PhACs were identified and quantified using high performance liquid chromatography/tandem mass spectrometry after solid-phase extraction. All the 21 analyzed PhACs were detected in wastewater and the target PhACs except acetaminophen, ibuprofen and gemfibrozil, were also found in sludge. The concentrations of the antibiotics and SVT were comparable to or even higher than those reported in developed countries, while the case of other target PhACs was opposite. The elimination of PhACs except acetaminophen was incomplete and a wide range of elimination efficiencies during the treatment were observed, i.e. from "negative removal" to 99.5%. The removal of PhACs was insignificant in primary and disinfection processes, and was mainly achieved during the biological treatment. Based on the mass balance analysis, biodegradation is believed to be the primary removal mechanism, whereas only about 1.5% of the total mass load of the target PhACs was removed by sorption. Experimentally estimated distribution coefficients (<500 L/kg, with a few exceptions) also indicate that biodegradation/transformation was responsible for the removal of the target PhACs. Ecotoxicological assessment indicated that the environment concentrations of single compounds (including sulfadiazine, sulfamethoxazole, ofloxacin, azithromycin and erythromycin-H2O) in effluent and sludge, as well as the mixture of the 21 detected PhACs in effluent, sludge and receiving water had a significant ecotoxicological

  8. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  9. Landslide Monitoring in Three Gorges Area Using Multi-Frequency Insar Techniques

    NASA Astrophysics Data System (ADS)

    Liao, M.; Balz, T.; Tantianuparp, P.; Shi, X.; Zhang, L.; Wang, T.

    2012-12-01

    Landslide is a term describing the downslope movement of soil, rock, and organic materials under the effects of gravity. Landslides are very destructive forces. In order to decrease landslide occurrences and its impacts, landslide monitoring is applied to analyze, forecast, and control landslides. The Three Gorges Project, the largest hydroelectric project of the world, began to function in 2003. The dam site is situated at Sandouping in China's Hubei Province. The reservoir has a length of approximately 600 km along the Yangtze River. In 2001, in a statistical survey, carried out by the Ministry of Land and Resources of China, landslides were observed in all counties surrounding the Three Gorges reservoir and nearly 2500 landslide bodies were observed. There are many landslide triggering factors in this area, for example the dam was built on a geologically unstable zone, the large surface-water level change, the construction of new buildings and roads, deforestation, etc. The potential landslide hazards are threatening the lives of millions of residents in the area. The Three Gorges area has a rough topography and is heavily vegetated. In an effort to reduce the landslide risks, advanced monitoring techniques and methods, such as a GPS network and other terrestrial surveillance technologies, are used in the area. Although these techniques can acquire highly accurate results, their results are only available over sparse measurement points and it they requires high costs for manpower and rather high costs for the instrument manipulation. Synthetic Aperture Radar (SAR), an active microwave imaging system, suffers from temporal decorrelation when monitoring heavily vegetated area as the Three Gorges. In order to analysis long-term and continuous displacement trend in this area, Differential Interferometric SAR (D-InSAR) and Persistent Scatterer Interferometry (PSI) are applied. Both techniques are able to detect surface motions. We use high resolution TerraSAR-X X

  10. Impacts of the Three Gorges Dam on microbial structure and potential function

    PubMed Central

    Yan, Qingyun; Bi, Yonghong; Deng, Ye; He, Zhili; Wu, Liyou; Van Nostrand, Joy D.; Shi, Zhou; Li, Jinjin; Wang, Xi; Hu, Zhengyu; Yu, Yuhe; Zhou, Jizhong

    2015-01-01

    The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function. PMID:25721383

  11. Patterns in atmospheric circulation affect emission sources contributing to nitrogen deposition in the Columbia River Gorge, Pacific Northwest USA

    NASA Astrophysics Data System (ADS)

    Anderson, S. M.; Chung, S. H.; Welker, J. M.; Harlow, B.; Evans, R. D.

    2014-12-01

    The Columbia River Gorge separating Oregon and Washington provides an ideal setting to investigate how atmospheric circulation patterns determine types of emission sources contributing to atmospheric deposition. Up-gorge and down-gorge atmospheric circulation patterns each provide a different suite of emission sources. Up-gorge airflow originates in the Portland-Vancouver metro area dominated by urban and industrial sources. Down-gorge patterns originate in the Columbia River basin, which is dominated by agricultural production. We tested the dependence of emission sources contributing to atmospheric deposition on circulation patterns by measuring the isotopic composition of nitrate (NO3-) in 2003-2004 precipitation samples from the WA98-Columbia River Gorge NADP & USNIP site. Circulation patterns were determined using back-trajectory analysis with the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model using the archived EDAS meteorological dataset. We observed a significant difference (P=0.01) between up-gorge and down-gorge patterns with mean δ15N-NO3- of +1.8 and -2.1‰ for up- and down-gorge, respectively. The differences observed between these two patterns is likely tied to the different emission sources of N found in these different geographic areas. The lower δ15N of down-gorge sources is due to the large amount of agricultural production in the Columbia River basin. Observed values for the up-gorge patterns likely result from industrial and fossil fuel emissions of NOx, the precursor of deposited NO3-, in the Portland-Vancouver area. The significantly greater amount of NO3- in precipitation from up-gorge patterns (0.72 mg/L) compared to down-gorge patterns (0.36 mg/L, P=0.01) supports the influence of urban sources rather than relatively clean marine air which characteristically has low amounts of NO3-. No significant differences are found in δ18Onitrate or Δ17Onitrate between the two patterns, suggesting that atmospheric chemistry

  12. Meat-eating by early hominids at the FLK 22 Zinjanthropus site, Olduvai Gorge (Tanzania): an experimental approach using cut-mark data.

    PubMed

    Domínguez-Rodrigo, M

    1997-12-01

    The meat-eating behavior of Plio-Pleistocene hominids, responsible for the bone accumulations at the earliest archaeological sites, is still a hotly-debated issue in paleoanthropology. In particular, meat-eating and bone marrow consumption are often presented as either complementary or opposing strategies of carcass exploitation. The presence of cut marks on fossil archeofauna is a potential source of information that has not been consistently used as evidence of carcass consumption by hominids. Some authors interpret cut marks as the result of hominids manipulating meat-bearing bones, while others argue that they can also be the result of hominids extracting marginal scraps of carcass flesh that have survived carnivores' initial consumption. In this study, a referential framework concerning the interpretation of cut marks is presented, based on a set of experiments conducted by the author. It is suggested, according to these experiments and data drawn from the FLK "Zinj" site, that hominids processed meat-bearing bones (on which flesh was abundant) rather than defleshed carcasses from felid kills.

  13. Validated ligand mapping of ACE active site

    NASA Astrophysics Data System (ADS)

    Kuster, Daniel J.; Marshall, Garland R.

    2005-08-01

    Crystal structures of angiotensin-converting enzyme (ACE) complexed with three inhibitors (lisinopril, captopril, enalapril) provided experimental data for testing the validity of a prior active site model predicting the bound conformation of the inhibitors. The ACE active site model - predicted over 18 years ago using a series of potent ACE inhibitors of diverse chemical structure - was recreated using published data and commercial software. Comparison between the predicted structures of the three inhibitors bound to the active site of ACE and those determined experimentally yielded root mean square deviation (RMSD) values of 0.43-0.81 Å, among the distances defining the active site map. The bound conformations of the chemically relevant atoms were accurately deduced from the geometry of ligands, applying the assumption that the geometry of the active site groups responsible for binding and catalysis of amide hydrolysis was constrained. The mapping of bound inhibitors at the ACE active site was validated for known experimental compounds, so that the constrained conformational search methodology may be applied with confidence when no experimentally determined structure of the enzyme yet exists, but potent, diverse inhibitors are available.

  14. Post-glacial rock avalanche causing epigenetic gorge incision (Strassberg gorge, Eastern Alps).

    NASA Astrophysics Data System (ADS)

    Sanders, Diethard

    2015-04-01

    fractured clasts up to boulder size. Comparison with areas with intense neotectonism (e. g., Central Apennines) suggests that fracturation may have been caused by seismicity. For the area, historical earthquakes with Me 3-3.9 imply the incidence of stronger quakes on longer timescales. The considered rock avalanche thus perhaps was triggered by a seismic event. The investigated RAD is the hitherto unappreciated, easternmost outlier of a cluster of rock avalanches in the area; these rock avalanches are grouped within a seismically active belt of strike-slip faults related to the Neogene to recent deformation of the Eastern Alps. This study links structural deformation with catastrophic mass-wasting which, in turn, caused incision of an epigenetic bedrock gorge. Surface exposure dating of boulders is intended to constrain the age of rock avalanching.

  15. Dating the Naisiusiu Beds, Olduvai Gorge, by electron spin resonance

    NASA Astrophysics Data System (ADS)

    Skinner, A. R.; Hay, R. L.; Masao, F.; Blackwell, B. A. B.

    2003-05-01

    The lower beds at Olduvai Gorge are well known for containing early hominid fossils and Oldowan stone tools, and their ages have been established by 40Ar/ 39Ar dating and paleomagnetic stratigraphy. Ages are generally less certain for the upper deposits at Olduvai Gorge because of the scarcity of datable tuffs. The youngest archaeologically significant site at Olduvai is microlithic LSA, which lies in the type section of the Naisiusiu Beds. The age for the site is controversial, with 14C dates of 17,000-17,550 (Hay, R.L., 1976 Geology of Olduvai Gorge, University of California Press, Berkeley) and >42,000 BP (Manega, P.C., 1993. Geochronology, geochemistry, and isotopic study of the Plio-Pleistocene Hominid sites and the Ngorongoro Volcanic Highland in Northern Tanzania. Unpublished Ph.D. Thesis, University of Colorado, Boulder, CO). The tuff bed in the zone with artifacts does not contain materials datable by 40Ar/ 39Ar, and some other dating method was needed. In the summer of 2001, five equid teeth were collected from the type Naisiusiu site. Another tooth had previously been collected. ESR ages have been determined for three teeth from the archaeological level and their ages cluster around 62±5 ka, assuming linear uranium uptake. Another tooth from a level without artifacts and believed to be significantly younger dated to 39±5 ka, again assuming LU. These dates are considerably older than previous estimates and suggest that the East African MSA/LSA transition occurred very early.

  16. GEOMORPHOLOGY. Comment on "Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet".

    PubMed

    Zeitler, Peter K; Koons, Peter O; Hallet, Bernard; Meltzer, Anne S

    2015-08-21

    Wang et al. (Reports, 21 November, 2014, p. 978) describe a buried canyon upstream of the Yarlung Tsangpo Gorge and argue that rapid erosion of the gorge was merely a passive response to rapid uplift at ~2.5 million years ago (Ma). We view these data as an expected consequence emerging from feedbacks between erosion and crustal rheology active well before 2.5 Ma.

  17. 6. VIEW FROM THE ROOF OF GORGE POWERHOUSE LOOKING EAST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. VIEW FROM THE ROOF OF GORGE POWERHOUSE LOOKING EAST TO THE FORMER GRAVITY OIL STORAGE BUILDING, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  18. Nutritional and behavioral effects of gorge and fast feeding in captive lions.

    PubMed

    Altman, Joanne D; Gross, Kathy L; Lowry, Stephen R

    2005-01-01

    Nonhuman animals in captivity manifest behaviors and physiological conditions that are not common in the wild. Lions in captivity face problems of obesity, inactivity, and stereotypy. To mediate common problems of captive lions, this study implemented a gorge and fast feeding schedule that better models naturalistic patterns: African lions (Panthera leo) gradually adapted from a conventional feeding program to a random gorge and fast feeding schedule. Digestibility increased significantly and food intake and metabolizable energy intake correspondingly decreased. Lions also showed an increase in appetitive active behaviors, no increase in agonistic behavior, and paced half as frequently on fast days as on feeding days. Thus, switching captive lions to a gorge and fast feeding schedule resulted in improved nutritional status and increased activity.

  19. Initiation age and incision rates of inner gorges: Do they record multiple glacial-interglacial cycles?

    NASA Astrophysics Data System (ADS)

    Delunel, Romain; Casagrande, Jan; Schlunegger, Fritz; Akçar, Naki; Kubik, Peter W.

    2015-04-01

    Inner gorges represent some of the most conspicuous landforms in the European Alps. They form narrow and deep active-channel incisions that link hanging tributaries with trunk valleys in glacially-conditioned environments. Despite abundant research carried out on these objects, both their origin and evolution have remained unclear. In particular, the age of initiation, the rate of incision, and the respective contribution of fluvial and subglacial processes in the evolution of inner gorges have still been a matter of scientific debate. Indeed, answering these questions has been complicated by the lack of appropriate quantitative methods and/or suitable sampling strategies for studying inner gorges. Here, we report 10Be concentrations measured in alluvial sediments that have been collected along the main stream of a ~20-km2-catchment in the Swiss foreland (Central European Alps). This catchment hosts a ca. 100-m-deep and 2-km-long inner gorge that has been cut mainly in glacial till. Catchment wide denudation rates inferred from 10Be analyses (n = 15) vary from ~120 to 650 mm/ka and show a general downstream increasing trend. Additional field observations and GIS analyses reveal that the denudation rates within the catchment increase from the headwaters, characterized by relict glacial/periglacial landscapes, to the downstream end of the basin where the inner gorge has been formed. Using a 10Be-based sediment budget approach and the delineation of topographic domains from a 2-m-resolution LIDAR, we provide an estimate of erosion rates within the gorge that are higher than 2.5 m/ka and can reach up to ~ 7 m/ka. Combining these estimated erosion rates with the reconstruction of eroded volumes within the gorge, we obtain a rough initiation age in the early Holocene, in general agreement with previous studies reporting a postglacial origin for the inner gorges. Our results therefore appear contradictory with recent findings arguing for a gradual formation of inner

  20. 1. GORGE HIGH DAM. THIS THIN ARCH DAM WITH A ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. GORGE HIGH DAM. THIS THIN ARCH DAM WITH A GRAVITY SECTION IS THE THIRD DAM BUILT BY SEATTLE CITY LIGHT TO PROVIDE WATER FOR GORGE POWERHOUSE AND WAS COMPLETED IN 1961, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  1. MIDDLE GORGE POWER PLANT, OWENS RIVER STREAM FLOWING OVER TAIL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    MIDDLE GORGE POWER PLANT, OWENS RIVER STREAM FLOWING OVER TAIL RACE OF POWER PLANT AND PENSTOCK HEADGATE TO LOWER GORGE CONTROL PLANT. A MINIMAL FLOW OF RIVER WATER IS REQUIRED TO MAINTAIN FISH LIFE - Los Angeles Aqueduct, Middle Gorge Power Plant, Los Angeles, Los Angeles County, CA

  2. Monitoring the Dynamic of a Fluvial Channel after Lahar Disturbance: Huiloac Gorge (Popocatepetl Volcano, Mexico)

    NASA Astrophysics Data System (ADS)

    Andres, N.; Palacios, D.; Zamorano, J. J.; Tanarro, L. M.; Renschler, C.; Sanjosé, J. J.; Atkinson, A.

    2009-04-01

    Volcanic eruptions generate disturbances that affect hydrological systems (Major, 2003) by depositing large volumes of sediments in watersheds that exceed amounts common to non-volcanic river systems (Montgomery, 2005). If the eruption releases abundant melt water, the river system may respond immediately by forming hazardous flows called lahars. River system recovery following eruptive and laharic impact is an important process, but it has received little attention (Gran and Montgomery, 2005) despite the fact that Major et al. (2000) and Hayes et al. (2002) have shown that these disruptions cause long term instability and their effects persist for decades. Lahar deposits resulting from interaction between volcanic activity and the glacier located above the Huiloac Gorge on the northern slope of Popocatepetl volcano (19°02´ N, 98°62´ W, 5,424 m), have infilled the gorge (Palacios, 1995; Palacios et al., 1998 and 2001; Capra et al., 2004; Muñoz, 2007). All of the major lahars that occurred on the volcano in 1995 (4 km), 1997 (21 km), and 2001 (14 km) have channelled through Huiloac Gorge, and have dramatically altered its morphology and dynamics through erosion and deposition. The present study traces these changes in the aftermath of the laharic events that occurred from 1997-2001. A sector of the channel, located at 3200m-3240m altitude, of 500 m long and 15 to 20 m wide, in the mid-section of the gorge, was chosen as the control site. Precipitation is heaviest there and is most apt to trigger secondary post-eruptive lahars. ArcGis software was used to draw 6 geomorphic maps of the site showing spatial variations in the landforms for the period February 2002 - February 2008. In addition, 29 cross-profiles were made of the gorge for the same time interval, excluding February 2004. The volume of sediment eroded and deposited was calculated for each date by comparing variations in the height of the floor and banks of the gorge depicted in the cross-profile, and

  3. Recreation impacts to cliff resources in the Potomac Gorge: Final report, June 2011

    USGS Publications Warehouse

    Marion, Jeffrey L.; Carr, C.; Davis, C.A.

    2011-01-01

    Managers of the National Park Service (NPS) are directed by law to accommodate appropriate types and amounts of visitation while ensuring that: any adverse impacts are the minimum necessary, unavoidable, cannot be further mitigated, and do not constitute impairment or derogation of park resources and values. (NPS 2006). The increasing popularity of the national park system presents substantial management challenges. High visitatation may cause unacceptable impacts to fragile natural and cultural resources, and may also cause crowding and other social impacts, which can also degrade the quality of visitor experiences. Responding to these concerns, NPS managers at Chesapeake & Ohio Canal National Historical Park (CHOH) and George Washington Memorial Parkway (GWMP) sponsored this research within the upper Potomac Gorge portions of these parks to investigate visitation-related impacts to the park?s cliff resources. The cliffs and rocky areas within the Great Falls and Mather Gorge areas provide important habitats for numerous sensitive rare plants and plant communities. A recent General Management Planning process for Great Falls Park (GFP), a portion of GWMP, highlighted the potential impacts of cliff-associated recreational activities, including hiking, climbing, and fishing, on sensitive cliff resources. The planning process identified the need for development of a Climbing Management Plan and a Trail Plan to more specifically address site and visitor management actions needed to protect rare and sensitive natural and cultural resources. Good science to assess cliff-associated rare plants and communities and to determine the existing and potential effects of cliff-related recreational activities is required for these new planning efforts. This research is designed to specifically address these informational needs and to assist park managers on both sides of the river with current and future cliff and recreation management decisions.

  4. Corrosion Research And Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2001-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  5. Corrosion Research and Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2002-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  6. Effects of hydropower operations on recreational use and nonuse values at Glen Canyon and Flaming Gorge Dams

    SciTech Connect

    Carlson, J.L.

    1995-03-01

    Increases in streamflows are generally positively related to the use values of angling and white-water boating, and constant flows tend to increase the use values more than fluctuating flows. In most instances, however, increases in streamflows beyond some threshold level cause the use values to decrease. Expenditures related to angling and white-water boating account for about $24 million of activity in the local economy around Glen Canyon Dam and $24.8 million in the local economy around flaming Gorge Dam. The range of operational scenarios being considered in the Western Area Power Administration`s Electric Power Marketing Environmental Impact Statement, when use rates are held constant, could change the combined use value of angling and white-water boating below Glen Canyon Dam, increasing it by as much as 50%, depending on prevailing hydrological conditions. Changes in the combined use value below Flaming Gorge Dam could range from a decrease of 9% to an increase of 26%. Nonuse values, such as existence and bequest values, could also make a significant contribution to the total value of each site included in this study; however, methodological and data limitations prevented estimating how each operational scenario could change nonuse values.

  7. Spatial patterns of erosion in a bedrock gorge

    NASA Astrophysics Data System (ADS)

    Beer, Alexander. R.; Turowski, Jens M.; Kirchner, James W.

    2017-01-01

    Understanding the physical processes driving bedrock channel formation is essential for interpreting and predicting the evolution of mountain landscapes. Here we analyze bedrock erosion patterns measured at unprecedented spatial resolution (mm) over 2 years in a natural bedrock gorge. These spatial patterns show that local bedrock erosion rates depend on position in the channel cross section, height above the streambed, and orientation relative to the main streamflow and sediment path. These observations are consistent with the expected spatial distribution of impacting particles (the tools effect) and shielding by sediment on the bed (the cover effect). Vertical incision by bedrock abrasion averaged 1.5 mm/a, lateral abrasion averaged 0.4 mm/a, and downstream directed abrasion of flow obstacles averaged 2.6 mm/a. However, a single plucking event locally exceeded these rates by orders of magnitude (˜100 mm/a), and accounted for one third of the eroded volume in the studied gorge section over the 2 year study period. Hence, if plucking is spatially more frequent than we observed in this study period, it may contribute substantially to long-term erosion rates, even in the relatively massive bedrock at our study site. Our observations demonstrate the importance of bedrock channel morphology and the spatial distribution of moving and static sediment in determining local erosion rates.

  8. Altered streamflow and sediment entrainment in the Gunnison Gorge

    USGS Publications Warehouse

    Elliott, J.G.; Parker, R.S.

    1997-01-01

    The Gunnison River in the Gunnison Gorge is a canyon river where upstream dams regulate mainstem discharge but do not affect debris-flow sediment supply from tributaries entering below the reservoirs. Regulation since 1966 has altered flood frequency, streambed mobility, and fluvial geomorphology creating potential resource-management issues. The duration of moderate streamflows between 32.3 and 85.0 m3/s has increased threefold since 1966. This, along with flood-peak attenuation, has facilitated fine-sediment deposition and vegetation encroachment on stream banks. The Shields equation and on-site channel geometry and bed-material measurements were used to assess changes in sediment entrainment in four alluvial reaches. Sand and fine gravel are transported through riffle/pool reaches at most discharges, but the cobbles and boulders composing the streambed in many reaches now are infrequently entrained. Periodic debris flows add coarse sediment to rapids and can increase pool elevation and the streambed area affected by backwater and fine-sediment accumulation. Debris-flow supplied boulders accumulate on fans and in rapids and constrict the channel until reworked by larger floods. The response to streamflow-regime changes in the Gunnison Gorge could serve as an analog for alluvial reaches in other regulated canyon rivers.

  9. Inner gorge-slot canyon system produced by repeated stream incision (eastern Alps): Significance for development of bedrock canyons

    NASA Astrophysics Data System (ADS)

    Sanders, Diethard; Wischounig, Lukas; Gruber, Alfred; Ostermann, Marc

    2014-06-01

    Many inner bedrock gorges of the Alps show abrupt downstream changes in gorge width, as well as channel type and gradient, as a result of epigenetic incision of slot canyons. Many slot canyons also are associated with older gorge reaches filled with Quaternary deposits. The age of slot canyons and inner bedrock gorges, however, commonly is difficult to constrain. For the inner-bedrock gorge system of the Steinberger Ache catchment (eastern Alps), active slot canyons as well as older, abandoned gorge reaches filled with upper Würmian proglacial deposits record three phases of gorge development and slot-canyon incision. A 234U/230Th age of cement of 29.7 ± 1.8 ka in fluvial conglomerates onlapping the flank of an inner gorge fits with late Würmian valley-bottom aggradation shortly before pleniglacial conditions; in addition, the age indicates that at least the corresponding canyon reach must be older. During advance of ice streams in the buildup of the Last Glacial Maximum (LGM), the catchment was blocked, and a proglacial lake formed. Bedrock gorges submerged in that lake were filled with fluviolacustrine deposits. During the LGM, the entire catchment was overridden by ice. During post-glacial reincision, streams largely found again their preexisting inner bedrock canyons. In some areas, however, the former stream course was 'missed', and a slot canyon formed. The distribution of Pleistocene deposits, the patterns of canyon incision, and the mentioned U/Th cementation age, however, together record a further discrete phase of base-level rise and stream incision well before the LGM. The present course of Steinberger Ache and its tributaries is a patchwork of (1) slot canyons incised during post-glacial incision; (2) vestiges of slot canyons cut upon an earlier (middle to late Würmian?) cycle of base-level rise and fall; (3) reactivated reaches up to ~ 200 m in width of inner bedrock gorge that are watershed at present, and more than at least ~ 30 ka in age; and (4

  10. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

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

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  11. Columbia Gorge Community College Business Survey.

    ERIC Educational Resources Information Center

    McKee, Jonathon V.

    This is a report on a business survey conducted by Columbia Gorge Community College (CGCC) (Oregon) to review the success and quality of the college's degree and certificate programs in business administration, computer application systems, and computer information systems. The community college surveyed 104 local businesses to verify the…

  12. Raptor Use of the Rio Grande Gorge

    SciTech Connect

    Ponton, David A.

    2015-03-20

    The Rio Grande Gorge is a 115 km long river canyon located in Southern Colorado (15 km) and Northern New Mexico (100 km). The majority of the canyon is under the administration of the Bureau of Land Management {BLM), and 77 km of the canyon south of the Colorado/New Mexico border are designated Wild River under the National Wild and Scenic Rivers Act of 1968. Visits I have made to the Rio Grande Gorge over the past 15 .years disclosed some raptor utilization. As the Snake River Birds of Prey Natural Area gained publicity, its similarity to the Rio Grande Gorge became obvious, and I was intrigued by the possibility of a high raptor nesting density in the Gorge. A survey in 1979 of 20 km of the northern end of the canyon revealed a moderately high density of red-tailed hawks and prairie falcons. With the encouragement of that partial survey, and a need to assess the impact of river-running on nesting birds of prey, I made a more comprehensive survey in 1980. The results of my surveys, along with those of a 1978 helicopter survey by the BLM, are presented in this report, as well as general characterization of the area, winter use by raptors, and an assessment of factors influencing the raptor population.

  13. [Structural regularities in activated cleavage sites of thrombin receptors].

    PubMed

    Mikhaĭlik, I V; Verevka, S V

    1999-01-01

    Comparison of thrombin receptors activation splitting sites sequences testifies to their similarity both in activation splitting sites of protein precursors and protein proteinase inhibitors reactive sites. In all these sites corresponded to effectory sites P2'-positions are placed by hydrophobic amino-acids only. The regularity defined conforms with previous thesis about the role of effectory S2'-site in regulation of the processes mediated by serine proteinases.

  14. PAH distribution and mass fluxes in the Three Gorges Reservoir after impoundment of the Three Gorges Dam.

    PubMed

    Deyerling, Dominik; Wang, Jingxian; Hu, Wei; Westrich, Bernhard; Peng, Chengrong; Bi, Yonghong; Henkelmann, Bernhard; Schramm, Karl-Werner

    2014-09-01

    Mass fluxes of polycyclic aromatic hydrocarbons (PAHs) were calculated for the Three Gorges Reservoir (TGR) in China, based on concentration and discharge data from the Yangtze River. Virtual Organisms (VOs) have been applied during four campaigns in 2008, 2009 (twice) and 2011 at sampling sites distributed from Chongqing to Maoping. The total PAH mass fluxes ranged from 110 to 2,160 mg s(-1). Highest loads were determined at Chongqing with a decreasing trend towards Maoping in all four sampling campaigns. PAH remediation capacity of the TGR was found to be high as the mass flux reduced by more than half from upstream to downstream. Responsible processes are thought to be adsorption of PAH to suspended particles, dilution and degradation. Furthermore, the dependence of PAH concentration upon water depth was investigated at Maoping in front of the Three Gorges Dam. Although considerable differences could be revealed, there was no trend observable. Sampling of water with self-packed filter cartridges confirmed more homogenous PAH depth distribution. Moreover, PAH content of suspended particles was estimated from water concentrations gathered by VOs based on a water-particle separation model and subsequently compared to PAH concentration measured in water and in filter cartridges. It could be shown that the modeled data predicts the concentration caused by particle-bound PAHs to be about 6 times lower than PAHs dissolved in water. Besides, the model estimates the proportions of 5- and 6-ring PAHs being higher than in water phase.

  15. The Three Gorges Project: How sustainable?

    NASA Astrophysics Data System (ADS)

    Kepa Brian Morgan, Te Kipa; Sardelic, Daniel N.; Waretini, Amaria F.

    2012-08-01

    SummaryIn 1984 the Government of China approved the decision to construct the Three Gorges Dam Project, the largest project since the Great Wall. The project had many barriers to overcome, and the decision was made at a time when sustainability was a relatively unknown concept. The decision to construct the Three Gorges Project remains contentious today, especially since Deputy Director of the Three Gorges Project Construction Committee, Wang Xiaofeng, stated that "We absolutely cannot relax our guard against ecological and environmental security problems sparked by the Three Gorges Project" (Bristow, 2007; McCabe, 2007). The question therefore was posed: how sustainable is the Three Gorges Project? Conventional approaches to sustainability assessment tend to use monetary based assessment aligned to triple bottom line thinking. That is, projects are evaluated as trade-offs between economic, environmental and social costs and benefits. The question of sustainability is considered using such a traditional Cost-Benefit Analysis approach, as undertaken in 1988 by a CIPM-Yangtze Joint Venture, and the Mauri Model Decision Making Framework (MMDMF). The Mauri Model differs from other approaches in that sustainability performance indicators are considered independently from any particular stakeholder bias. Bias is then introduced subsequently as a sensitivity analysis on the raw results obtained. The MMDMF is unique in that it is based on the Māori concept of Mauri, the binding force between the physical and the spiritual attributes of something, or the capacity to support life in the air, soil, and water. This concept of Mauri is analogous to the Chinese concept of Qi, and there are many analogous concepts in other cultures. It is the universal relevance of Mauri that allows its use to assess sustainability. This research identified that the MMDMF was a strong complement to Cost-Benefit Analysis, which is not designed as a sustainability assessment tool in itself. The

  16. Assessing internal biophysical vulnerability to landslide hazards - a nested catchment approach: Xiangxi Watershed / Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Wiegand, Matthias; Seeber, Christoph; Hartmann, Heike; Xiang, Wei; King, Lorenz

    2010-05-01

    The Three Gorges dam construction was completed in 2006. Besides the international media, also the responsible authorities and various scholarly communities pay close attention to potential and actual environmental impacts related to the impoundment and development activities. The geo-environment within the Three Gorges region is highly conducive to landslides. Consequently, a scientific monitoring and risk mitigation system was established and is still under development. Risk analysis with regard to gravity driven mass movements is highly complex and strongly site specific - several aspects hamper a universal methodology applicable for landslide risk and site assessment. The interdisciplinary Sino-German Yangtze-Project Research co-operation aims, among others, to support the sustainable cultivation of the newly developed ecosystems within the Yangtze catchments. Land use change and increasing population growth are causing severe pressure on the scarce land resources. Landslides are acknowledged as important threat, hence vulnerability of certain landscape components have to be identified, quantified and monitored. A nested quantitative approach for vulnerability analysis is developed. The applied risk and vulnerability model understands risk as the product of hazard and vulnerability. Whereas vulnerability is characterized by: mass movement intensity and susceptibility of the respective element at risk. The watershed of Xiangxi river serves as study area. In general, catchment approaches intent and proved to be a functional geographical unit for successful integrated resources management. Several limitations with regard to data accessibility, availability and accuracy have to be considered due to restrictions of feasible scales. Comprehensive large-scale site investigations are confined to training areas for model calibration and validation. Remote sensing potentials are utilised for land use/ land cover change analysis and localization of selected elements

  17. MYST protein acetyltransferase activity requires active site lysine autoacetylation.

    PubMed

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-04

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases.

  18. MYST protein acetyltransferase activity requires active site lysine autoacetylation

    PubMed Central

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-01

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases. PMID:22020126

  19. YANGTZE project: Investigation of mass movements in the Three Gorges Reservoir Area (P. R. China)

    NASA Astrophysics Data System (ADS)

    Ehret, Dominik; Rohn, Joachim; Wiedenmann, Johannes; Rudolph, René; Otte, Karel; Ernstberger, Stefanie; Eckstein, Susan; Dumperth, Christian

    2010-05-01

    Within the German YANGTZE Project, mass movement hazard is investigated for the Xiangxi Catchment which is part of the Three Gorges Reservoir (P. R. China). The objective of our sub-project is to investigate the impact of the Three Gorges Reservoir on slope stability and (re-)activation of mass movements. Within this paper first results of investigations on mass movements in the Xiangxi Catchment that were started in summer 2008 are presented. They show a significant correlation between mass movement distribution and activity on the one hand and lithology and altitude on the other hand. In Xiangxi Catchment, correlation between geology and occurrence of mass movements can be studied ideally as most of the geological formations outcropping in the reservoir area can be found there. Furthermore, the mouth of Xiangxi River is quite close to the Three Gorges Dam so that the impact of the impoundment is distinctive in the Xiangxi Catchment. In 2008 and 2009, about 70 km² were mapped geotechnically. The mapping was done for (a) the backwater area of Xiangxi River influenced by the impoundment of the Three Gorges Reservoir (from Yangtze River to Gaoyang Town), (b) Quyuan Valley as a sub-catchment of Xiangxi Catchment, and (c) along the main roads from Gaoyang Town towards Gufu City and towards Shennongjia Nature Reserve. The investigated area comprises marine and continental sedimentary layers from Cambrian to Jurassic Period. The lithology of these layers is dominated by carbonates (limestone, dolostone and marlstone) on the one hand and clastic sediments (shale, mudstone, siltstone, sandstone, and conglomerate) on the other hand. A total of 180 mass movements was found and mapped. Mainly rotational or combined rotational-translational landslides, but also some rockslides and rockfalls were found. As expected, a strong correlation between lithology on the one side and occurrence and activity of mass movements on the other side could be found. In the study area, Jurassic

  20. Unmet Expectations and Symptoms of Depression among the Three Gorges Project Resettlers

    PubMed Central

    Xi, Juan; Hwang, Sean-Shong

    2010-01-01

    To successfully resettle 1.27 million Chinese for the construction of the Three Gorges Project (TGP), the Chinese government employed a new re-resettlement policy which emphasizes infrastructural development of the resettlement sites to assure resettlers a sustainable livelihood following resettlement. Unfortunately, many benefits the policy promised have not materialized. As a result, many resettlers have suffered an increase in depressive symptoms associated with unmet expectations. Using panel data collected before and after relocation from a sample of Three Gorges resettlers, we found that a high proportion of resettlers reported unmet expectations which were significantly associated with an increase in depressive symptoms. Our findings indicate that undeliverable promises can backfire and further aggravate the harm inflicted on the displaced caused by the project-induced displacement. From the perspective of resettlers, a sound coping strategy to minimize the harm caused by the displacement on their mental wellbeing is to expect for the worst. PMID:21278844

  1. 22. TURBINE PIT AREA GORGE POWERHOUSE SHOWING RELIEF VALVE FOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. TURBINE PIT AREA GORGE POWERHOUSE SHOWING RELIEF VALVE FOR UNIT 23 IN FOREGROUND AND GOVERNOR OIL TANKS AND PUMPS IN THE LEFT REAR, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  2. 36 CFR 7.89 - New River Gorge National River.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false New River Gorge National River. 7.89 Section 7.89 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.89 New River Gorge National River....

  3. Historic interior view of gorge wall, taken shortly after battle, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic interior view of gorge wall, taken shortly after battle, looking northwest at the entrance and northwest shoeing damage to gorge wall as well as timber and earth blindage (see also HABS No. GA-2158-39). - Fort Pulaski, Cockspur Island, Savannah, Chatham County, GA

  4. 18. SHEAR PIN, UNIT 24 GORGE POWERHOUSE. THE WICKET GATES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. SHEAR PIN, UNIT 24 GORGE POWERHOUSE. THE WICKET GATES ON THE TURBINE ARE EACH EQUIPPED WITH A SHEAR PIN AND OIL PRESSURE GAUGE. IF A GATE JAMS, THE PIN SMEARS AND THE CHANGE IN OIL PRESSURE TRIGGERS AN ALARM, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  5. Rapid Gorge Formation in an Artificially Created Waterfall

    NASA Astrophysics Data System (ADS)

    Anton, L.; Mather, A. E.; Stokes, M.; Munoz Martin, A.

    2014-12-01

    A number of studies have examined rates of gorge formation, nick point retreat, and the controls on those rates via bedrock erodibility, the effectiveness of bedrock erosion mechanisms and the role of hillslope processes. Most findings are based on conceptual / empirical models or long term landscape analysis; but studies of recent quantifiable events are scarce yet highly valuable. Here we present expert eye witness account and quantitative survey of large and rapid fluvial erosion events that occurred over an artificially created waterfall at a spillway mouth. In 6 years a ~270 m long, ~100 m deep and ~100 to 160 m wide canyon was carved, and ~1.58 x106 m3 of granite bedrock was removed from the spillway site. Available flow data indicates that the erosion took place under unremarkable flood discharge conditions. The analysis of historic topographic maps enables the reconstruction of the former topography and successive erosion events, enabling the quantification of bedrock erosion amounts, and rates. Analysis of bedrock erodibility and discontinuity patterns demonstrates that the bedrock is mechanically strong, and that similar rock strength and fracture patterns are found throughout the region. It is apparent that structural pre-conditioning through fracture density and orientation in relation to flow and slope direction is of paramount importance in the gorge development. The presented example provides an exceptional opportunity for studying the evolution process of a bedrock canyon and to precisely measure the rate of bedrock channel erosion over a six year period. Results illustrate the highly episodic nature of the erosion and highlight several key observations for the adjustability of bedrock rivers. The observations have implications for the efficiency of bedrock erosion and raise important questions about incision rates, driving mechanisms and timescale assumptions' in models of landscape change.

  6. Long Valley Caldera Lake and reincision of Owens River Gorge

    USGS Publications Warehouse

    Hildreth, Wes; Fierstein, Judy

    2016-12-16

    Owens River Gorge, today rimmed exclusively in 767-ka Bishop Tuff, was first cut during the Neogene through a ridge of Triassic granodiorite to a depth as great as its present-day floor and was then filled to its rim by a small basaltic shield at 3.3 Ma. The gorge-filling basalt, 200 m thick, blocked a 5-km-long reach of the upper gorge, diverting the Owens River southward around the shield into Rock Creek where another 200-m-deep gorge was cut through the same basement ridge. Much later, during Marine Isotope Stage (MIS) 22 (~900–866 ka), a piedmont glacier buried the diversion and deposited a thick sheet of Sherwin Till atop the basalt on both sides of the original gorge, showing that the basalt-filled reach had not, by then, been reexcavated. At 767 ka, eruption of the Bishop Tuff blanketed the landscape with welded ignimbrite, deeply covering the till, basalt, and granodiorite and completely filling all additional reaches of both Rock Creek canyon and Owens River Gorge. The ignimbrite rests directly on the basalt and till along the walls of Owens Gorge, but nowhere was it inset against either, showing that the basalt-blocked reach had still not been reexcavated. Subsidence of Long Valley Caldera at 767 ka produced a steep-walled depression at least 700 m deeper than the precaldera floor of Owens Gorge, which was beheaded at the caldera’s southeast rim. Caldera collapse reoriented proximal drainages that had formerly joined east-flowing Owens River, abruptly reversing flow westward into the caldera. It took 600,000 years of sedimentation in the 26-km-long, usually shallow, caldera lake to fill the deep basin and raise lake level to its threshold for overflow. Not until then did reestablishment of Owens River Gorge begin, by incision of the gorge-filling ignimbrite.

  7. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  8. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    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.

  9. Savannah River Site prioritization of transition activities

    SciTech Connect

    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.

  10. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    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.

  11. Does erosion of Himalayan gorges drive focused uplift along transverse rivers?

    NASA Astrophysics Data System (ADS)

    Harvey, J. E.; Burbank, D. W.; Hourigan, J. K.

    2012-12-01

    Erosion of deep river gorges has long been hypothesized to be capable of driving isostatic uplift focused along valley axes. Numerical modeling suggests that such an effect may be enhanced where rivers cut gorges into rocks that are deforming plastically in response to regional compression. Some authors argue that apparent river-parallel anticlines in the Himalaya could be manifestations of this process and may even represent the youngest phase of deformation in the range. These hypotheses, however, remain largely untested with quantitative data on erosion and rock uplift. To explore this proposed river incision-anticlinal uplift hypothesis, we attempt to measure and compare exhumation rates from the core and limbs of a river anticline in the high Himalaya of northwest Nepal. We focus on the Karnali River gorge, which trends nearly transverse to the structural grain of the range and generally lacks the neotectonic complexity of other Himalayan river anticlines. We present new apatite and zircon U-Th/He cooling ages collected along relief transects entirely within the Greater Himalayan sequence. Transects span 1-2 km of relief over <4 km distance and were sited to track variations in exhumation rate from the core toward the limbs of the anticline. Reconstruction of isochronous cooling-age surfaces with respect to modern topography and both bedrock structure and stratigraphy will be used to assess the validity of the river anticline hypothesis in this region.

  12. Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

    PubMed Central

    Lim, Sung In; Yang, Byungseop; Jung, Younghan; Cha, Jaehyun; Cho, Jinhwan; Choi, Eun-Sil; Kim, Yong Hwan; Kwon, Inchan

    2016-01-01

    Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other. PMID:28004799

  13. Perspective: On the active site model in computational catalyst screening

    NASA Astrophysics Data System (ADS)

    Reuter, Karsten; Plaisance, Craig P.; Oberhofer, Harald; Andersen, Mie

    2017-01-01

    First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts.

  14. Diffusional correlations among multiple active sites in a single enzyme.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2014-04-07

    Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

  15. Robotics at Savannah River site: activity report

    SciTech Connect

    Byrd, J.S.

    1984-09-01

    The objectives of the Robotics Technology Group at the Savannah River Laboratory are to employ modern industrial robots and to develop unique automation and robotic systems to enhance process operations at the Savannah River site (SRP and SRL). The incentives are to improve safety, reduce personnel radiation exposure, improve product quality and productivity, and to reduce operating costs. During the past year robotic systems have been installed to fill chemical dilution vials in a SRP laboratory at 772-F and remove radioactive waste materials in the SRL Californium Production Facility at 773-A. A robotic system to lubricate an extrusion press has been developed and demonstrated in the SRL robotics laboratory and is scheduled for installation at the 321-M fuel fabrication area. A mobile robot was employed by SRP for a radiation monitoring task at a waste tank top in H-Area. Several other robots are installed in the SRL robotics laboratories and application development programs are underway. The status of these applications is presented in this report.

  16. Active sites of thioredoxin reductases: why selenoproteins?

    PubMed

    Gromer, Stephan; Johansson, Linda; Bauer, Holger; Arscott, L David; Rauch, Susanne; Ballou, David P; Williams, Charles H; Schirmer, R Heiner; Arnér, Elias S J

    2003-10-28

    Selenium, an essential trace element for mammals, is incorporated into a selected class of selenoproteins as selenocysteine. All known isoenzymes of mammalian thioredoxin (Trx) reductases (TrxRs) employ selenium in the C-terminal redox center -Gly-Cys-Sec-Gly-COOH for reduction of Trx and other substrates, whereas the corresponding sequence in Drosophila melanogaster TrxR is -Ser-Cys-Cys-Ser-COOH. Surprisingly, the catalytic competence of these orthologous enzymes is similar, whereas direct Sec-to-Cys substitution of mammalian TrxR, or other selenoenzymes, yields almost inactive enzyme. TrxRs are therefore ideal for studying the biology of selenocysteine by comparative enzymology. Here we show that the serine residues flanking the C-terminal Cys residues of Drosophila TrxRs are responsible for activating the cysteines to match the catalytic efficiency of a selenocysteine-cysteine pair as in mammalian TrxR, obviating the need for selenium. This finding suggests that the occurrence of selenoenzymes, which implies that the organism is selenium-dependent, is not necessarily associated with improved enzyme efficiency. Our data suggest that the selective advantage of selenoenzymes is a broader range of substrates and a broader range of microenvironmental conditions in which enzyme activity is possible.

  17. The Volcanic Story of the Columbia River Gorge.

    ERIC Educational Resources Information Center

    Allen, John Eliot

    1982-01-01

    Uses maps, diagrams, and geological accounts to describe the Columbia River Gorge which separates Oregon from Washington and exposes an unexcelled record of Cenozoic volcanic stratigraphy, sedimentation, flooding, and landsliding for the visiting tourists, geologists, or students. (Author/DC)

  18. PERSPECTIVE VIEW OF ENTRANCE INTO GORGE WALL, LOOKING TOWARD TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    PERSPECTIVE VIEW OF ENTRANCE INTO GORGE WALL, LOOKING TOWARD TO NORTHWEST BASTION, SHOWING DRAWBRIDGE AND MOAT (DUPLICATE OF HABS No. GA-2158-42) - Fort Pulaski, Cockspur Island, Savannah, Chatham County, GA

  19. View of interior facade of gorge wall looking from southeast ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of interior facade of gorge wall looking from southeast to northwest at the northern half of the wall ( see also HABS No. GA-2158-56 & 57). - Fort Pulaski, Cockspur Island, Savannah, Chatham County, GA

  20. Community Update on Site Activities, July 19, 2013

    EPA Pesticide Factsheets

    In an effort to engage and inform community members interested in the New Bedford Harbor Superfund Site cleanup, EPA will be issuing periodic topic-based fact sheets that will provide background information and updates about ongoing activities.

  1. 8. INTERIOR GORGE POWERHOUSE LOOKING SOUTH AT UNITS 23, 22, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. INTERIOR GORGE POWERHOUSE LOOKING SOUTH AT UNITS 23, 22, AND 21 FROM THE TOP OF UNIT 24. THE SHAW BRIDGE CRANE IS AT THE TOP REAR OF THE POWERHOUSE. THE UPPER SET OF WINDOWS TO THE LEFT ARE FOR THE VISITORS' GALLERY; THE LOWER SET ARE THE POWERHOUSE CONTROL ROOM, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  2. Identification of putative active site residues of ACAT enzymes.

    PubMed

    Das, Akash; Davis, Matthew A; Rudel, Lawrence L

    2008-08-01

    In this report, we sought to determine the putative active site residues of ACAT enzymes. For experimental purposes, a particular region of the C-terminal end of the ACAT protein was selected as the putative active site domain due to its high degree of sequence conservation from yeast to humans. Because ACAT enzymes have an intrinsic thioesterase activity, we hypothesized that by analogy with the thioesterase domain of fatty acid synthase, the active site of ACAT enzymes may comprise a catalytic triad of ser-his-asp (S-H-D) amino acid residues. Mutagenesis studies revealed that in ACAT1, S456, H460, and D400 were essential for activity. In ACAT2, H438 was required for enzymatic activity. However, mutation of D378 destabilized the enzyme. Surprisingly, we were unable to identify any S mutations of ACAT2 that abolished catalytic activity. Moreover, ACAT2 was insensitive to serine-modifying reagents, whereas ACAT1 was not. Further studies indicated that tyrosine residues may be important for ACAT activity. Mutational analysis showed that the tyrosine residue of the highly conserved FYXDWWN motif was important for ACAT activity. Furthermore, Y518 was necessary for ACAT1 activity, whereas the analogous residue in ACAT2, Y496, was not. The available data suggest that the amino acid requirement for ACAT activity may be different for the two ACAT isozymes.

  3. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  4. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide.

  5. Analysis and assessment of the nutrients, biochemical indexes and heavy metals in the Three Gorges Reservoir, China, from 2008 to 2013.

    PubMed

    Gao, Qiang; Li, Yi; Cheng, Qingyuan; Yu, Mingxia; Hu, Bo; Wang, Zhigang; Yu, Zhiqiang

    2016-04-01

    The Three Gorges Reservoir, the world's largest hydropower project, has operated stably for more than five years. To understand its water quality status, the nutrient and biochemical indexes, the total nitrogen (TN), the total phosphorus (TP), the potassium permanganate index (CODMn), the five-day biochemical oxygen demand (BOD5) and fecal coliform (F. coli), as well as the heavy metals (Cu, Hg, As, Cd, Zn and Pb) of samples collected from 10 sites during the time period of 2008-2013 were studied via using multiple analysis approaches. For each parameter, pictures of the spatial and temporal distributions were presented, and the reasons behind their variation trends were elaborated. Principal component analysis (PCA) was applied to identify the types of pollution. The Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) was calculated to concisely mark the water quality. In addition, a human health risk assessment of the heavy metals in a representative site was conducted. The results showed that the water quality state in the Three Gorges Reservoir was intricate but stable and acceptable from 2008 to 2013. The TN, TP and Pb were considered to be the key pollution indexes. Enforcements to alleviate industrial and urban pollution, along with ship management, have worked. The decrease in heavy metal concentrations from upstream to downstream was associated with the self-purification of the reservoir. However, rural pollution became worse in those years. Improper agricultural activity was an important reason for this trend. For local residents, drinking water was generally safe, but cancer caused by As and Pb is a potential issue.

  6. Promoter-proximal polyadenylation sites reduce transcription activity

    PubMed Central

    Andersen, Pia K.; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on 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 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels. PMID:23028143

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

    PubMed

    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.

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

    SciTech Connect

    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.

  9. Active and regulatory sites of cytosolic 5'-nucleotidase.

    PubMed

    Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

    2010-12-01

    Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation.

  10. BAX Activation is Initiated at a Novel Interaction Site

    PubMed Central

    Gavathiotis, Evripidis; Suzuki, Motoshi; Davis, Marguerite L.; Pitter, Kenneth; Bird, Gregory H.; Katz, Samuel G.; Tu, Ho-Chou; Kim, Hyungjin; Cheng, Emily H.-Y.; Tjandra, Nico; Walensky, Loren D.

    2008-01-01

    BAX is a pro-apoptotic protein of the BCL-2 family stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. Anti-apoptotic proteins such as BCL-2 counteract BAX-mediated cell death. Although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for BAX, rendering its explicit trigger mechanism unknown. We previously developed Stabilized Alpha-Helix of BCL-2 domains (SAHBs) that directly initiate BAX-mediated mitochondrial apoptosis. Here we demonstrate by NMR analysis that BIM SAHB binds BAX at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. The specificity of the BIM SAHB-BAX interaction is highlighted by point mutagenesis that abrogates functional activity, confirming that BAX activation is initiated at this novel structural location. Thus, we have now defined a BAX interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis. PMID:18948948

  11. Management of municipal solid waste in the Three Gorges region

    SciTech Connect

    Wang Liao Pei Tingquan Huang Chuan; Yuan Hui

    2009-07-15

    As the fourth phase of the Three Gorges reservoir project commenced in 2008, the rate of water flow in the Yangtze River has obviously decelerated further downstream and water clarity within the storage facility has decreased. Meanwhile, the rate of urbanization in the region is adding to the amount of municipal solid waste (MSW) being generated by every day life. The composition of the waste is becoming more diversified and complicated, thereby presenting an increasing threat to the ecological environment and water resources of the Three Gorges region. This paper is a probe into MSW in terms of its characteristics as well as methods of storage, collection, transportation, recycling, treatment and disposal, the protection of environmental ecosystems. Municipal solid waste management (MSWM) is one of the major environmental problems in the Three Gorges region, and indeed the whole of China. Based on the analysis of the present situation of MSWM and its treatment/disposal, some methods of sorting, recycling, decomposing, incineration and reuse are described, sanitary landfill as the main disposal method in Chongqing city, incineration being the second. Sanitary landfill or dump was also used for MSW treatment in the Three Gorges region, and this paper also provides some suggestions for improving MSWM in the Three Gorges region.

  12. Involvement of novel autophosphorylation sites in ATM activation.

    PubMed

    Kozlov, Sergei V; Graham, Mark E; Peng, Cheng; Chen, Philip; Robinson, Phillip J; Lavin, Martin F

    2006-08-09

    ATM kinase plays a central role in signaling DNA double-strand breaks to cell cycle checkpoints and to the DNA repair machinery. Although the exact mechanism of ATM activation remains unknown, efficient activation requires the Mre11 complex, autophosphorylation on S1981 and the involvement of protein phosphatases and acetylases. We report here the identification of several additional phosphorylation sites on ATM in response to DNA damage, including autophosphorylation on pS367 and pS1893. ATM autophosphorylates all these sites in vitro in response to DNA damage. Antibodies against phosphoserine 1893 revealed rapid and persistent phosphorylation at this site after in vivo activation of ATM kinase by ionizing radiation, paralleling that observed for S1981 phosphorylation. Phosphorylation was dependent on functional ATM and on the Mre11 complex. All three autophosphorylation sites are physiologically important parts of the DNA damage response, as phosphorylation site mutants (S367A, S1893A and S1981A) were each defective in ATM signaling in vivo and each failed to correct radiosensitivity, genome instability and cell cycle checkpoint defects in ataxia-telangiectasia cells. We conclude that there are at least three functionally important radiation-induced autophosphorylation events in ATM.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    ERIC Educational Resources Information Center

    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…

  15. Spectroscopic studies of the active site of galactose oxidase

    SciTech Connect

    Knowles, P.F.; Brown, R.D. III; Koenig, S.H.

    1995-07-19

    X-ray absorption and EPR spectroscopy have been used to probe the copper site structure in galactose oxidase at pH 4.5 and 7.0. the results suggest that there are no major differences in the structure of the tetragonal Cu(II) site at these pH values. Analysis of the extended X-ray absorption fine structure (EXAFS) indicates that four N,O scatterers are present at approximately 2 {Angstrom}; these are presumably the equatorial ligands. In addition, the EXAFS data establish that oxidative activation to produce the active-site tyrosine radical does not cause major changes in the copper coordination environment. Therefore results obtained on the one-electron reduced enzyme, containing Cu(II) but not the tyrosine radical, probably also apply to the catalytically active Cu(II)/tyrosine radical state. Solvent water exchange, inhibitor binding, and substrate binding have been probed via nuclear magnetic relaxation dispersion (NMRD) measurements. The NMRD profile of galactose oxidase is quantitatively consistent with the rapid exchange of a single, equatorial water ligand with a Cu(II)-O separation of about 2.4 {Angstrom}. Azide and cyanide displace this coordinated water. The binding of azide and the substrate dihydroxyacetone produce very similar effects on the NMRD profile of galactose oxidase, indicating that substrates also bind to the active site Cu(II) in an equatorial position.

  16. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  17. The Three Gorges Dam Affects Regional Precipitation

    NASA Technical Reports Server (NTRS)

    Wu, Liguang; Zhang, Qiang; Jiang, Zhihong

    2006-01-01

    Issues regarding building large-scale dams as a solution to power generation and flood control problems have been widely discussed by both natural and social scientists from various disciplines, as well as the policy-makers and public. Since the Chinese government officially approved the Three Gorges Dam (TGD) projects, this largest hydroelectric project in the world has drawn a lot of debates ranging from its social and economic to climatic impacts. The TGD has been partially in use since June 2003. The impact of the TGD is examined through analysis of the National Aeronautics and Space Administration (NASA) Tropical Rainfall Measuring Mission (TRMM) rainfall rate and Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature and high-resolution simulation using the Pennsylvania State University-National Center for Atmospheric Research (PSU-NCAR) fifth-generation Mesoscale Model (MM5). The independent satellite data sets and numerical simulation clearly indicate that the land use change associated with the TGD construction has increased the precipitation in the region between Daba and Qinling mountains and reduced the precipitation in the vicinity of the TGD after the TGD water level abruptly rose from 66 to 135 m in June 2003. This study suggests that the climatic effect of the TGD is on the regional scale (approx.100 km) rather than on the local scale (approx.10 km) as projected in previous studies.

  18. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  19. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-06

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions.

  20. Changes in active site histidine hydrogen bonding trigger cryptochrome activation

    PubMed Central

    Ganguly, Abir; Manahan, Craig C.; Top, Deniz; Yee, Estella F.; Lin, Changfan; Young, Michael W.; Thiel, Walter; Crane, Brian R.

    2016-01-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa. Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  1. Probing the promiscuous active site of myo-inositol dehydrogenase using synthetic substrates, homology modeling, and active site modification.

    PubMed

    Daniellou, Richard; Zheng, Hongyan; Langill, David M; Sanders, David A R; Palmer, David R J

    2007-06-26

    The active site of myo-inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis recognizes a variety of mono- and disaccharides, as well as 1l-4-O-substituted inositol derivatives. It catalyzes the NAD+-dependent oxidation of the axial alcohol of these substrates with comparable kinetic constants. We have found that 4-O-p-toluenesulfonyl-myo-inositol does not act as a substrate for IDH, in contrast to structurally similar compounds such as those bearing substituted benzyl substituents in the same position. X-ray crystallographic analysis of 4-O-p-toluenesulfonyl-myo-inositol and 4-O-(2-naphthyl)methyl-myo-inositol, which is a substrate for IDH, shows a distinct difference in the preferred conformation of the aryl substituent. Conformational analysis of known substrates of IDH suggests that this conformational difference may account for the difference in reactivity of 4-O-p-toluenesulfonyl-myo-inositol in the presence of IDH. A sequence alignment of IDH with the homologous glucose-fructose oxidoreductase allowed the construction of an homology model of inositol dehydrogenase, to which NADH and 4-O-benzyl-scyllo-inosose were docked and the active site energy minimized. The active site model is consistent with all experimental results and suggests that a conserved tyrosine-glycine-tyrosine motif forms the hydrophobic pocket adjoining the site of inositol recognition. Y233F and Y235F retain activity, while Y233R and Y235R do not. A histidine-aspartate pair, H176 and D172, are proposed to act as a dyad in which H176 is the active site acid/base. The enzyme is inactivated by diethyl pyrocarbonate, and the mutants H176A and D172N show a marked loss of activity. Kinetic isotope effect experiments with D172N indicate that chemistry is rate-determining for this mutant.

  2. The active site structure and mechanism of phosphoenolpyruvate utilizing enzymes

    SciTech Connect

    Cheng, K.C.

    1989-01-01

    Arginine specific reagents showed irreversible inhibition of avian liver mitochondrial phosphoenolpyruvate carboxykinase. Potent protection against modification was elicited by CO{sub 2} or CO{sub 2} in the presence of other substrates. Labeling of enzyme with (7-{sup 14}C) phenylglyoxal showed that 1 or 2 arginines are involved in CO{sub 2} binding and activation. Peptide map studies showed this active site arginine residues is located at position 289. Histidine specific reagents showed pseudo first order inhibition of avian mitochondrial phosphoenolpyruvate carboxykinase activity. The best protection against modification was elicited by IDP or IDP and Mn{sup +2}. One histidine residue is at or near the phosphoenolpyruvate binding site as demonstrated in the increased absorbance at 240 nm and proton relaxation rate studies. Circular dichroism studies reveal that enzyme structure was perturbed by diethylpyrocarbonate modification. Metal binding studies suggest that this enzyme has only one metal binding site. The putative binding sites from several GTP and phosphoenolpyruvate utilizing enzymes are observed in P-enolpyruvate carboxykinase from different species.

  3. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania

    PubMed Central

    Reti, Jay S.

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  4. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania.

    PubMed

    Reti, Jay S

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  5. Methane emissions from the surface of the Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Chen, Huai; Yuan, Xingzhong; Chen, Zhongli; Wu, Yuyuan; Liu, Xianshu; Zhu, Dan; Wu, Ning; Zhu, Qiu'an; Peng, Changhui; Li, Weizhong

    2011-11-01

    After our previous study about methane (CH4) emissions from littoral marshes of the Three Gorges Reservoir (TGR), Chinese dams have raised a world-wide concern. Through measurements from the surface of the TGR, a CH4 emission rate was recorded as 0.26 ± 0.38 mg CH4 m-2 h-1 (Mean ± SD), relatively low compared with those from other hydropower reservoirs. We also recorded CH4 emission rate from the surface of downstream water, which was also relatively low (0.24 ± 0.37 mg CH4 m-2 h-1). Such result may indicate that TGR is not a great CH4 emitter (not "CH4 menace"). One possible reason for such a low emission rate is that measures to maintain water quality and protect environment and ecosystem decrease the input of organic materials (for methanogenesis), which in turn limits the CH4 production in the sediment of the TGR. We also found that CH4 emission from the flooding drawdown area (0.29 ± 0.37 mg CH4 m-2 h-1) was higher than other permanently flooded sites (0.23 ± 0.38 mg CH4 m-2 h-1). Because of annual vegetation re-growth, the drawdown zone is the especially important carbon source for methanogenesis in flooding season. Interestingly, we also observed that mean CH4 emission was significantly higher in winter than in spring and summer. This was partly due to seasonal dynamics of hydrology. In order to estimate the net CH4 emissions caused by the reservoir and reservoir operation, the best approach would be Life Cycle Analysis.

  6. Canyons and gorges as potential geotourism destinations in Serbia: comparative analysis from two perspectives - general geotourists' and pure geotourists'

    NASA Astrophysics Data System (ADS)

    Božić, Sanja; Tomić, Nemanja

    2015-10-01

    Serbia represents one of those countries which have not yet differentiated themselves on the world tourism map. However, it has an immense but still unrevealed potential for geotourism development. In this paper we analyzed several remarkable canyons and gorges of great scientific importance and geotourism potential. These sites include the Djerdap Gorge and Lazar River Canyon, located in Eastern Serbia and the Ovcar-Kablar Gorge and Uvac Canyon located in Western Serbia. One of the main goals of this paper was to analyze and compare the current state and tourism potential of these geosites by using the M-GAM model for geosite assessment. However, the principal aim of the paper is to analyze how important is each subindicator in the assessment process for different market segments. In this paper, we also analyzed how giving different importance to subindicators can influence the position of the geosites in the matrix indicating different assessment done by two chosen market segments. The research showed that general geotourists appreciate considerably different values when assessing a geosite in comparison to pure geotourists. The paper can be used as framework for developing the tourism management strategy of geosites taking into consideration the needs and preferences of the target market segments.

  7. Identification of Ice Nucleation Active Sites on Silicate Dust Particles

    NASA Astrophysics Data System (ADS)

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-04-01

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts [1-3]. Nevertheless, among those structures K-feldspar showed by far the highest ice nucleation activity. In this study, the reasons for its activity and the difference in the activity of the different feldspars were investigated in closer details. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. We give a potential explanation of the increased ice nucleation activity of K-feldspar. The ice nucleating sites are very much dependent on the alkali ion present by altering the water structure and the feldspar surface. The higher activity of K-feldspar can be attributed to the presence of potassium ions on the surface and surface bilayer. The alkali-ions have different hydration shells and thus an influence on the ice nucleation activity of feldspar. Chaotropic behavior of Calcium and Sodium ions are lowering the ice nucleation potential of the other feldspars, while kosmotropic Potassium has a neutral or even positive effect. Furthermore we investigated the influence of milling onto the ice nucleation of quartz particles. The ice nucleation activity can be increased by mechanical milling, by introducing more molecular, nucleation active defects to the particle surface. This effect is larger than expected by plane surface increase. [1] Atkinson et al. The Importance of Feldspar for Ice Nucleation by Mineral Dust in Mixed-Phase Clouds. Nature 2013, 498, 355-358. [2] Yakobi-Hancock et al.. Feldspar Minerals as Efficient Deposition Ice Nuclei. Atmos. Chem. Phys. 2013, 13, 11175-11185. [3] Zolles et al. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles. J. Phys. Chem. A 2015 accepted.

  8. Face the Edges: Catalytic Active Sites of Nanomaterials

    PubMed Central

    Ni, Bing

    2015-01-01

    Edges are special sites in nanomaterials. The atoms residing on the edges have different environments compared to those in other parts of a nanomaterial and, therefore, they may have different properties. Here, recent progress in nanomaterial fields is summarized from the viewpoint of the edges. Typically, edge sites in MoS2 or metals, other than surface atoms, can perform as active centers for catalytic reactions, so the method to enhance performance lies in the optimization of the edge structures. The edges of multicomponent interfaces present even more possibilities to enhance the activities of nanomaterials. Nanoframes and ultrathin nanowires have similarities to conventional edges of nanoparticles, the application of which as catalysts can help to reduce the use of costly materials. Looking beyond this, the edge structures of graphene are also essential for their properties. In short, the edge structure can influence many properties of materials. PMID:27980960

  9. Active sites in char gasification: Final technical report

    SciTech Connect

    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.

  10. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  11. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    Martin, T E; Scott, J; Menge, C

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection. PMID:11413645

  12. Active site amino acid sequence of human factor D.

    PubMed

    Davis, A E

    1980-08-01

    Factor D was isolated from human plasma by chromatography on CM-Sephadex C50, Sephadex G-75, and hydroxylapatite. Digestion of reduced, S-carboxymethylated factor D with cyanogen bromide resulted in three peptides which were isolated by chromatography on Sephadex G-75 (superfine) equilibrated in 20% formic acid. NH2-Terminal sequences were determined by automated Edman degradation with a Beckman 890C sequencer using a 0.1 M Quadrol program. The smallest peptide (CNBr III) consisted of the NH2-terminal 14 amino acids. The other two peptides had molecular weights of 17,000 (CNBr I) and 7000 (CNBr II). Overlap of the NH2-terminal sequence of factor D with the NH2-terminal sequence of CNBr I established the order of the peptides. The NH2-terminal 53 residues of factor D are somewhat more homologous with the group-specific protease of rat intestine than with other serine proteases. The NH2-terminal sequence of CNBr II revealed the active site serine of factor D. The typical serine protease active site sequence (Gly-Asp-Ser-Gly-Gly-Pro was found at residues 12-17. The region surrounding the active site serine does not appear to be more highly homologous with any one of the other serine proteases. The structural data obtained point out the similarities between factor D and the other proteases. However, complete definition of the degree of relationship between factor D and other proteases will require determination of the remainder of the primary structure.

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

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    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.

  14. [Mechanism of arginine deiminase activity by site-directed mutagenesis].

    PubMed

    Li, Lifeng; Ni, Ye; Sun, Zhihao

    2012-04-01

    Arginine deiminase (ADI) has been studied as a potential anti-cancer agent for inhibiting arginine-auxotrophic tumors (such as melanomas and hepatocellular carcinomas) in phase III clinical trials. In this work, we studied the molecular mechanism of arginine deiminase activity by site-directed mutagenesis. Three mutation sites, A128, H404 and 1410, were introduced into wild-type ADI gene by QuikChange site-directed mutagenesis method, and four ADI mutants M1 (A128T), M2 (H404R), M3 (I410L), and M4 (A128T, H404R) were obtained. The ADI mutants were individually expressed in Escherichia coli BL21 (DE3), and the enzymatic properties of the purified mutant proteins were determined. The results show that both A128T and H404R had enhanced optimum pH, higher activity and stability of ADI under physiological condition (pH 7.4), as well as reduced K(m) value. This study provides an insight into the molecular mechanism of the ADI activity, and also the experimental evidence for the rational protein evolution in the future.

  15. Preliminary small mammal taphonomy of FLK NW level 20 (Olduvai Gorge, Tanzania)

    NASA Astrophysics Data System (ADS)

    Arcos, Saleta; Sevilla, Paloma; Fernández-Jalvo, Yolanda

    2010-11-01

    The Bed-I series of Olduvai Gorge (Tanzania) is a reference site in human evolution, having yielded the holotypes of Paranthropus boisei and Homo habilis, together with manufactured artefacts and abundant large and micro-fauna. Excavations in Olduvai Gorge have been recently resumed, with new aims and new results. This paper presents the results of the taphonomic analysis carried out on a fossil small-mammal assemblage recovered from FLK NW level 20, a layer overlying Tuff C, dated from 1.84 Ma. The analysis provides good evidence of a category 1 predator, most likely a barn owl, as the predator of the bone assemblage. Trampling and sediment compression might influence postdepositional breakage of the bones. This study is especially relevant since previous taphonomic analyses carried out at levels above and below this sample led to inconclusive results due to a low number of fossils ( Fernández-Jalvo et al., 1998). The new sample provides new information to reconstruct the paleoenvironmental context in which early hominins inhabited.

  16. Assessing Collembola biodiversity under human influence at Three Gorges Area, China.

    PubMed

    Huang, Cheng; Wang, Tianle; Luo, Yongzheng; Chen, Shi; Kim, Ke Chung

    2013-04-01

    In this study we comprehensively assessed Collembola biodiversity at Three Gorges Area, one of most diverse habitat regions in China. In total, 3,796 Collembola specimens comprising 9 families, 45 genera, and 103 species (including 14 new species and new records in China) were collected from three primary sampling areas: one nature reserve and two rural and urban areas representing different degrees of human influence. Each sampling area was further divided into nine sampling sites associated with different habitats and altitudes. Analyses of biodiversity data showed that individual abundance was highest in the nature reserve followed by mildly human influenced areas, and then highly influenced areas, and species richness was lowest in highly influenced areas. Hence, we suggest Collembola biodiversity is systematically lost after urbanization. In the nature reserve, altitude significantly influenced both the species richness and individual abundance, whereas in rural and urban areas, both altitude and the human-altered environmental gradient were influential. We also measured sampling efficiency and estimated potential species richness in these areas. This study serves as both a fundamental survey of Collembola biodiversity, as well as an assessment of human/environmental influence on the Collembola community, and can provide further insight into protecting the soil integrity of the Three Gorges Area.

  17. Potential sites of CFTR activation by tyrosine kinases

    PubMed Central

    Billet, Arnaud; Jia, Yanlin; Jensen, Timothy J.; Hou, Yue-Xian; Chang, Xiu-Bao; Riordan, John R.; Hanrahan, John W.

    2016-01-01

    ABSTRACT The CFTR chloride channel is tightly regulated by phosphorylation at multiple serine residues. Recently it has been proposed that its activity is also regulated by tyrosine kinases, however the tyrosine phosphorylation sites remain to be identified. In this study we examined 2 candidate tyrosine residues near the boundary between the first nucleotide binding domain and the R domain, a region which is important for channel function but devoid of PKA consensus sequences. Mutating tyrosines at positions 625 and 627 dramatically reduced responses to Src or Pyk2 without altering the activation by PKA, suggesting they may contribute to CFTR regulation. PMID:26645934

  18. MSK1 activity is controlled by multiple phosphorylation sites

    PubMed Central

    McCOY, Claire E.; Campbell, David G.; Deak, Maria; Bloomberg, Graham B.; Arthur, J. Simon C.

    2004-01-01

    MSK1 (mitogen- and stress-activated protein kinase) is a kinase activated in cells downstream of both the ERK1/2 (extracellular-signal-regulated kinase) and p38 MAPK (mitogen-activated protein kinase) cascades. In the present study, we show that, in addition to being phosphorylated on Thr-581 and Ser-360 by ERK1/2 or p38, MSK1 can autophosphorylate on at least six sites: Ser-212, Ser-376, Ser-381, Ser-750, Ser-752 and Ser-758. Of these sites, the N-terminal T-loop residue Ser-212 and the ‘hydrophobic motif’ Ser-376 are phosphorylated by the C-terminal kinase domain of MSK1, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain of MSK1 and therefore for the phosphorylation of MSK1 substrates in vitro. Ser-381 is also phosphorylated by the C-terminal kinase domain, and mutation of Ser-381 decreases MSK1 activity, probably through the inhibition of Ser-376 phosphorylation. Ser-750, Ser-752 and Ser-758 are phosphorylated by the N-terminal kinase domain; however, their function is not known. The activation of MSK1 in cells therefore requires the activation of the ERK1/2 or p38 MAPK cascades and does not appear to require additional signalling inputs. This is in contrast with the closely related RSK (p90 ribosomal S6 kinase) proteins, whose activity requires phosphorylation by PDK1 (3-phosphoinositide-dependent protein kinase 1) in addition to phosphorylation by ERK1/2. PMID:15568999

  19. 3. RUSTIC BENCH AT THE LADDER CREEK GARDENS NEAR GORGE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. RUSTIC BENCH AT THE LADDER CREEK GARDENS NEAR GORGE POWERHOUSE AT NEWHALEM. J.D. ROSS HAD THE GROUNDS LANDSCAPED AND PLANTED WITH EXOTIC FLOWERS AND VEGETATION DURING THE 1930S AS AN ADDITIONAL TOURIST ATTRACTION, 1989. - Skagit Power Development, Skagit River & Newhalem Creek Hydroelectric Project, On Skagit River, Newhalem, Whatcom County, WA

  20. 36 CFR 7.89 - New River Gorge National River.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... valid West Virginia State hunting license or permit, or are exempt under provisions of West Virginia law... Superintendent for reasons of public safety, resource protection, or other management considerations. (2) Do West Virginia state hunting laws apply within New River Gorge National River? Yes, non-conflicting State...

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

    SciTech Connect

    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.

  2. Vitamin K epoxide reductase: homology, active site and catalytic mechanism.

    PubMed

    Goodstadt, Leo; Ponting, Chris P

    2004-06-01

    Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1, a subunit of the VKOR complex, has recently been shown to possess this activity. Here, we show that VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases. These might reduce disulfide bonds of VKORC1-like enzymes as a prerequisite for their catalytic activities.

  3. Occurrence of organotin compounds in river sediments under the dynamic water level conditions in the Three Gorges Reservoir Area, China.

    PubMed

    Gao, Jun-Min; Zhang, Ke; Chen, You-Peng; Guo, Jin-Song; Wei, Yun-Mei; Jiang, Wen-Chao; Zhou, Bin; Qiu, Hui

    2015-06-01

    The Three Gorges Project is the largest hydro project in the world, and the water level of the Three Gorges Reservoir (TGR) is dynamic and adjustable with the aim of flood control and electrical power generation. It is necessary to investigate the pollutants and their underlying contamination processes under dynamic water levels to determine their environmental behaviors in the Three Gorges Reservoir Area (TGRA). Here, we report the assessment of organotin compounds (OTs) pollution in the river sediments of the TGRA. Surface sediment samples were collected in the TGRA at low and high water levels. Tributyltin (TBT), triphenyltin (TPhT), and their degradation products in sediments were quantified by gas chromatography-mass spectrometry. Butyltins (BTs) and phenyltins (PhTs) were detected in sediments, and BTs predominated over PhTs in the whole study area under dynamic water level conditions. The concentrations of OTs in sediments varied markedly among locations, and significant concentrations were found in river areas with high levels of boat traffic and wastewater discharge. Sediments at all stations except Cuntan were lightly contaminated with TBT, and total organic carbon (TOC) was a significant factor affecting the fate of TBT in the TGRA. The butyltin and phenyltin degradation indices showed no recent inputs of TBT or TPhT into this region, with the exception of fresh TPhT input at Xiakou Town. Shipping activity, wastewater discharge, and agriculture are the most likely sources of OTs in the TGRA.

  4. Crystal Structure of Snake Venom Acetylcholinesterase in Complex with Inhibitory Antibody Fragment Fab410 Bound at the Peripheral Site

    PubMed Central

    Bourne, Yves; Renault, Ludovic; Marchot, Pascale

    2015-01-01

    The acetylcholinesterase found in the venom of Bungarus fasciatus (BfAChE) is produced as a soluble, non-amphiphilic monomer with a canonical catalytic domain but a distinct C terminus compared with the other vertebrate enzymes. Moreover, the peripheral anionic site of BfAChE, a surface site located at the active site gorge entrance, bears two substitutions altering sensitivity to cationic inhibitors. Antibody Elec410, generated against Electrophorus electricus acetylcholinesterase (EeAChE), inhibits EeAChE and BfAChE by binding to their peripheral sites. However, both complexes retain significant residual catalytic activity, suggesting incomplete gorge occlusion by bound antibody and/or high frequency back door opening. To explore a novel acetylcholinesterase species, ascertain the molecular bases of inhibition by Elec410, and document the determinants and mechanisms for back door opening, we solved a 2.7-Å resolution crystal structure of natural BfAChE in complex with antibody fragment Fab410. Crystalline BfAChE forms the canonical dimer found in all acetylcholinesterase structures. Equally represented open and closed states of a back door channel, associated with alternate positions of a tyrosine phenol ring at the active site base, coexist in each subunit. At the BfAChE molecular surface, Fab410 is seated on the long Ω-loop between two N-glycan chains and partially occludes the gorge entrance, a position that fully reflects the available mutagenesis and biochemical data. Experimentally based flexible molecular docking supports a similar Fab410 binding mode onto the EeAChE antigen. These data document the molecular and dynamic peculiarities of BfAChE with high frequency back door opening, and the mode of action of Elec410 as one of the largest peptidic inhibitors targeting the acetylcholinesterase peripheral site. PMID:25411244

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

    PubMed Central

    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

  6. Inner gorges cut by subglacial meltwater during Fennoscandian ice sheet decay.

    PubMed

    Jansen, J D; Codilean, A T; Stroeven, A P; Fabel, D; Hättestrand, C; Kleman, J; Harbor, J M; Heyman, J; Kubik, P W; Xu, S

    2014-05-09

    The century-long debate over the origins of inner gorges that were repeatedly covered by Quaternary glaciers hinges upon whether the gorges are fluvial forms eroded by subaerial rivers, or subglacial forms cut beneath ice. Here we apply cosmogenic nuclide exposure dating to seven inner gorges along ~500 km of the former Fennoscandian ice sheet margin in combination with a new deglaciation map. We show that the timing of exposure matches the advent of ice-free conditions, strongly suggesting that gorges were cut by channelized subglacial meltwater while simultaneously being shielded from cosmic rays by overlying ice. Given the exceptional hydraulic efficiency required for meltwater channels to erode bedrock and evacuate debris, we deduce that inner gorges are the product of ice sheets undergoing intense surface melting. The lack of postglacial river erosion in our seven gorges implicates subglacial meltwater as a key driver of valley deepening on the Baltic Shield over multiple glacial cycles.

  7. Environmental impact assessments of the Three Gorges Project in China: Issues and interventions

    NASA Astrophysics Data System (ADS)

    Xu, Xibao; Tan, Yan; Yang, Guishan

    2013-09-01

    The paper takes China's authoritative Environmental Impact Statement for the Yangzi (Yangtze) Three Gorges Project (TGP) in 1992 as a benchmark against which to evaluate emerging major environmental outcomes since the initial impoundment of the Three Gorges reservoir in 2003. The paper particularly examines five crucial environmental aspects and associated causal factors. The five domains include human resettlement and the carrying capacity of local environments (especially land), water quality, reservoir sedimentation and downstream riverbed erosion, soil erosion, and seismic activity and geological hazards. Lessons from the environmental impact assessments of the TGP are: (1) hydro project planning needs to take place at a broader scale, and a strategic environmental assessment at a broader scale is necessary in advance of individual environmental impact assessments; (2) national policy and planning adjustments need to react quickly to the impact changes of large projects; (3) long-term environmental monitoring systems and joint operations with other large projects in the upstream areas of a river basin should be established, and the cross-impacts of climate change on projects and possible impacts of projects on regional or local climate considered.

  8. Target-classification approach applied to active UXO sites

    NASA Astrophysics Data System (ADS)

    Shubitidze, F.; Fernández, J. P.; Shamatava, Irma; Barrowes, B. E.; O'Neill, K.

    2013-06-01

    This study is designed to illustrate the discrimination performance at two UXO active sites (Oklahoma's Fort Sill and the Massachusetts Military Reservation) of a set of advanced electromagnetic induction (EMI) inversion/discrimination models which include the orthonormalized volume magnetic source (ONVMS), joint diagonalization (JD), and differential evolution (DE) approaches and whose power and flexibility greatly exceed those of the simple dipole model. The Fort Sill site is highly contaminated by a mix of the following types of munitions: 37-mm target practice tracers, 60-mm illumination mortars, 75-mm and 4.5'' projectiles, 3.5'', 2.36'', and LAAW rockets, antitank mine fuzes with and without hex nuts, practice MK2 and M67 grenades, 2.5'' ballistic windshields, M2A1-mines with/without bases, M19-14 time fuzes, and 40-mm practice grenades with/without cartridges. The site at the MMR site contains targets of yet different sizes. In this work we apply our models to EMI data collected using the MetalMapper (MM) and 2 × 2 TEMTADS sensors. The data for each anomaly are inverted to extract estimates of the extrinsic and intrinsic parameters associated with each buried target. (The latter include the total volume magnetic source or NVMS, which relates to size, shape, and material properties; the former includes location, depth, and orientation). The estimated intrinsic parameters are then used for classification performed via library matching and the use of statistical classification algorithms; this process yielded prioritized dig-lists that were submitted to the Institute for Defense Analyses (IDA) for independent scoring. The models' classification performance is illustrated and assessed based on these independent evaluations.

  9. Identification of Phosphorylation Sites Altering Pollen Soluble Inorganic Pyrophosphatase Activity.

    PubMed

    Eaves, Deborah J; Haque, Tamanna; Tudor, Richard L; Barron, Yoshimi; Zampronio, Cleidiane G; Cotton, Nicholas P J; de Graaf, Barend H J; White, Scott A; Cooper, Helen J; Franklin, F Christopher H; Harper, Jeffery F; Franklin-Tong, Vernonica E

    2017-03-01

    Protein phosphorylation regulates numerous cellular processes. Identifying the substrates and protein kinases involved is vital to understand how these important posttranslational modifications modulate biological function in eukaryotic cells. Pyrophosphatases catalyze the hydrolysis of inorganic phosphate (PPi) to inorganic phosphate Pi, driving biosynthetic reactions; they are essential for low cytosolic inorganic phosphate. It was suggested recently that posttranslational regulation of Family I soluble inorganic pyrophosphatases (sPPases) may affect their activity. We previously demonstrated that two pollen-expressed sPPases, Pr-p26.1a and Pr-p26.1b, from the flowering plant Papaver rhoeas were inhibited by phosphorylation. Despite the potential significance, there is a paucity of data on sPPase phosphorylation and regulation. Here, we used liquid chromatographic tandem mass spectrometry to map phosphorylation sites to the otherwise divergent amino-terminal extensions on these pollen sPPases. Despite the absence of reports in the literature on mapping phosphorylation sites on sPPases, a database survey of various proteomes identified a number of examples, suggesting that phosphorylation may be a more widely used mechanism to regulate these enzymes. Phosphomimetic mutants of Pr-p26.1a/b significantly and differentially reduced PPase activities by up to 2.5-fold at pH 6.8 and 52% in the presence of Ca(2+) and hydrogen peroxide over unmodified proteins. This indicates that phosphoregulation of key sites can inhibit the catalytic responsiveness of these proteins in concert with key intracellular events. As sPPases are essential for many metabolic pathways in eukaryotic cells, our findings identify the phosphorylation of sPPases as a potential master regulatory mechanism that could be used to attenuate metabolism.

  10. Evidence for segmental mobility in the active site of pepsin

    SciTech Connect

    Pohl, J.; Strop, P.; Senn, H.; Foundling, S.; Kostka, V.

    1986-05-01

    The low hydrolytic activity (k/sub cat/ < 0.001 s/sup -1/) of chicken pepsin (CP) towards tri- and tetrapeptides is enhanced at least 100 times by modification of its single sulfhydryl group of Cys-115, with little effect on K/sub m/-values. Modification thus simulates the effect of secondary substrate binding on pepsin catalysis. The rate of Cys-115 modification is substantially decreased in the presence of some competitive inhibitors, suggesting its active site location. Experiments with CP alkylated at Cys-115 with Acrylodan as a fluorescent probe or with N-iodoacetyl-(4-fluoro)-aniline as a /sup 19/F-nmr probe suggest conformation change around Cys-115 to occur on substrate or substrate analog binding. The difference /sup 1/H-nmr spectra (500 MHz) of unmodified free and inhibitor-complexed CP reveal chemical shifts almost exclusively in the aromatic region. The effects of Cu/sup + +/ on /sup 19/F- and /sup 1/H-nmr spectra have been studied. Examination of a computer graphics model of CP based on E. parasitica pepsin-inhibitor complex X-ray coordinates suggests that Cys-115 is located near the S/sub 3//S/sub 5/ binding site. The results are interpreted in favor of segmental mobility of this region important for pepsin substrate binding and catalysis.

  11. First Principles Computational Study of the Active Site of Arginase

    SciTech Connect

    Ivanov, Ivaylo; Klien, Micheal

    2004-01-14

    Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible -1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

  12. C-H Activation on Co,O Sites: Isolated Surface Sites versus Molecular Analogs.

    PubMed

    Estes, Deven P; Siddiqi, Georges; Allouche, Florian; Kovtunov, Kirill V; Safonova, Olga V; Trigub, Alexander L; Koptyug, Igor V; Copéret, Christophe

    2016-11-16

    The activation and conversion of hydrocarbons is one of the most important challenges in chemistry. Transition-metal ions (V, Cr, Fe, Co, etc.) isolated on silica surfaces are known to catalyze such processes. The mechanisms of these processes are currently unknown but are thought to involve C-H activation as the rate-determining step. Here, we synthesize well-defined Co(II) ions on a silica surface using a metal siloxide precursor followed by thermal treatment under vacuum at 500 °C. We show that these isolated Co(II) sites are catalysts for a number of hydrocarbon conversion reactions, such as the dehydrogenation of propane, the hydrogenation of propene, and the trimerization of terminal alkynes. We then investigate the mechanisms of these processes using kinetics, kinetic isotope effects, isotopic labeling experiments, parahydrogen induced polarization (PHIP) NMR, and comparison with a molecular analog. The data are consistent with all of these reactions occurring by a common mechanism, involving heterolytic C-H or H-H activation via a 1,2 addition across a Co-O bond.

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

    PubMed Central

    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

  14. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

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

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  15. Landscape distribution and ecology of Plio-Pleistocene avifaunal communities from Lowermost Bed II, Olduvai Gorge, Tanzania.

    PubMed

    Prassack, Kari A

    2014-05-01

    Plio-Pleistocene avifaunal communities are used to reconstruct Lowermost Bed II landscapes at the early hominin site of Olduvai Gorge, Tanzania. These deposits are laterally extensive, have strong chronostratigraphic control, and were excavated using a landscape archaeological approach. Such factors allow for horizontal spatial-correlation of avian communities across the paleolandscape over a geologically short time frame (approximately 65,000 years). Lowermost Bed II avifaunal communities point to an extensive freshwater wetland system across the extent of paleo-Lake Olduvai's eastern margin.

  16. Olduvai Gorge, Shaded Relief and Colored Height

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Three striking and important areas of Tanzania in eastern Africa are shown in this color-coded shaded relief image from the Shuttle Radar Topography Mission. The largest circular feature in the center right is the caldera, or central crater, of the extinct volcano Ngorongoro. It is surrounded by a number of smaller volcanoes, all associated with the Great Rift Valley, a geologic fault system that extends for about 4,830 kilometers (2,995 miles) from Syria to central Mozambique.

    Ngorongoro's caldera is 22.5 kilometers (14 miles) across at its widest point and is 610 meters (2,000 feet) deep. Its floor is very level, holding a lake fed by streams running down the caldera wall. It is part of the Ngorongoro Conservation Area and is home to over 75,000 animals. The lakes south of the crater are Lake Eyasi and Lake Manyara, also part of the conservation area.

    The relatively smooth region in the upper left of the image is the Serengeti National Park, the largest in Tanzania. The park encompasses the main part of the Serengeti ecosystem, supporting the greatest remaining concentration of plains game in Africa including more than 3,000,000 large mammals. The animals roam the park freely and in the spectacular migrations, huge herds of wild animals move to other areas of the park in search of greener grazing grounds (requiring over 4,000 tons of grass each day) and water.

    The faint, nearly horizontal line near the center of the image is Olduvai Gorge, made famous by the discovery of remains of the earliest humans to exist. Between 1.9 and 1.2 million years ago a salt lake occupied this area, followed by the appearance of fresh water streams and small ponds. Exposed deposits show rich fossil fauna, many hominid remains and items belonging to one of the oldest stone tool technologies, called Olduwan. The time span of the objects recovered dates from 2,100,000 to 15,000 years ago.

    Two visualization methods were combined to produce the image: shading and

  17. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

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

    2015-01-01

    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

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

    SciTech Connect

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

    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.

  19. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  20. An active site water network in the plasminogen activator pla from Yersinia pestis.

    PubMed

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-07-14

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  1. Spatial bedrock erosion distribution in a natural gorge

    NASA Astrophysics Data System (ADS)

    Beer, A. R.; Turowski, J. M.; Kirchner, J. W.

    2015-12-01

    Quantitative analysis of morphological evolution both in terrestrial and planetary landscapes is of increasing interest in the geosciences. In mountainous regions, bedrock channel formation as a consequence of the interaction of uplift and erosion processes is fundamental for the entire surface evolution. Hence, the accurate description of bedrock channel development is important for landscape modelling. To verify existing concepts developed in the lab and to analyse how in situ channel erosion rates depend on the interrelations of discharge, sediment transport and topography, there is a need of highly resolved topographic field data. We analyse bedrock erosion over two years in a bedrock gorge downstream of the Gorner glacier above the town of Zermatt, Switzerland. At the study site, the Gornera stream cuts through a roche moutonnée in serpentine rock of 25m length, 5m width and 8m depth. We surveyed bedrock erosion rates using repeat terrestrial laser scanning (TLS) with an average point spacing of 5mm. Bedrock erosion rates in direction of the individual surface normals were studied directly on the scanned point clouds applying the M3C2 algorithm (Lague et al., 2013, ISPRS). The surveyed erosion patterns were compared to a simple stream erosivity visualisation obtained from painted bedrock sections at the study location. Spatially distributed erosion rates on bedrock surfaces based on millions of scan points allow deduction of millimeter-scale mean annual values of lateral erosion, incision and downstream erosion on protruding streambed surfaces. The erosion rate on a specific surface point is shown to depend on the position of this surface point in the channel's cross section, its height above the streambed and its spatial orientation to the streamflow. Abrasion by impacting bedload was likely the spatially dominant erosion process, as confirmed by the observed patterns along the painted bedrock sections. However, a single plucking event accounted for the half

  2. Portland, Mount Hood, & Columbia River Gorge, Oregon, Perspective View

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Portland, the largest city in Oregon, is located on the Columbia River at the northern end of the Willamette Valley. On clear days, Mount Hood highlights the Cascade Mountains backdrop to the east. The Columbia is the largest river in the American Northwest and is navigable up to and well beyond Portland. It is also the only river to fully cross the Cascade Range, and has carved the Columbia River Gorge, which is seen in the left-central part of this view. A series of dams along the river, at topographically favorable sites, provide substantial hydroelectric power to the region.

    This perspective view was generated using topographic data from the Shuttle Radar Topography Mission (SRTM), a Landsat satellite image, and a false sky. Topographic expression is vertically exaggerated two times.

    Landsat has been providing visible and infrared views of the Earth since 1972. SRTM elevation data substantially help in analyzing Landsat images by revealing the third dimension of Earth's surface, topographic height. The Landsat archive is managed by the U.S. Geological Survey's Eros Data Center (USGS EDC).

    Elevation data used in this image were acquired by the Shuttle Radar Topography Mission (SRTM) aboard the Space Shuttle Endeavour, launched on February 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. SRTM was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Geospatial-Intelligence Agency (NGA) of the U.S. Department of Defense (DoD), and the German and Italian space agencies. It is managed by NASA's Jet

  3. [Seasonal variation of phosphorus in Xiaojiang backwater area, Three Gorges Reservoir].

    PubMed

    Fang, Fang; Li, Zhe; Tian, Guang; Guo, Jing-song; Zhang, Chao

    2009-12-01

    Phosphorus is regarded as the limiting factor for eutrophication in backwater areas of tributaries in Three Gorges Reservoir (TGR). However, distinct seasonal variation patterns and potential ecological impacts of phosphorus are apparent due to the ultimate hydrodynamic condition in the site. Seasonal variation of different forms of phosphorus in Xiaojiang backwater area (XBA) in Three Gorges Reservoir from Mar. 2007 to Mar. 2008 was reported. It was found that average concentration of total phosphorus (TP) was (61.7 +/- 2.7) microg x L(-1). No remarkable difference was found among sampling sites, while significant variation among seasons were detected. Generally, TP was high in summer and winter while low in autumn. Particulate phosphorus (PP) was the major forms of phosphorus in XBA. The co-analysis among phosphorus and key environmental variables, i.e., chlorophyll, inorganic/organic particles, flows and water levels in river estuary, indicate that inorganic forms of PP should dominate in PP, and might transfer into the water body by rainfall and river flows, resulting in the increase of TP in XBA. This phenomenon was more significant when TGR was set at low water level. Soluble reactive phosphorus (SRP) had a significantly negative correlation with chlorophyll a, indicating the evident assimilation process of phosphorus by algae. It was inferred that heavy rainfall and increased river flow shortened the water renewal cycle and brought in amounts of suspended sediments that increased the light attenuation underwater. With the frequent flood impulse, phytoplankton community should suffered the instable living environment that decreased the concentration level of chlorophyll a in XBA. This might be the potential reason for the negative correlation between TP and chlorophyll a.

  4. Simulation of spatial and temporal distributions of non-point source pollution load in the Three Gorges Reservoir Region.

    PubMed

    Shen, Zhenyao; Qiu, Jiali; Hong, Qian; Chen, Lei

    2014-09-15

    Non-point source (NPS) pollution has become the largest threat to water quality in recent years. Major pollutants, particularly from agricultural activities, which include nitrogen, phosphorus and sediment that have been released into aquatic environments, have caused a range of problems in the Three Gorges Reservoir Region (TGRR), China. It is necessary to identify the spatial and temporal distributions of NPS pollutants and the highly polluted areas for the purpose of watershed management. In this study, the NPS pollutant load was simulated using the Soil and Water Assessment Tool (SWAT) and the small-scale watershed extended method (SWEM). The simulation results for four typical small catchments were extended to the entire watershed leading to estimates of the NPS load from 2001 to 2009. The results demonstrated that the NPS pollution load in the western area was the highest and that agricultural land was the primary pollutant source. The similar annual variation trends of runoff and sediment loads demonstrated that the sediment load was closely related to runoff. The loads of total nitrogen (TN) and total phosphorus (TP) were relatively stable from 2001 to 2007, except for high loads in 2006. The increase in pollution source strength was an important reason for the significant upward trend of TN and TP loads from 2008 to 2009. The rainfall from April to October contributed to the largest amount of runoff, sediment and nutrient loads for the year. The NPS load intensities in each sub-basin reveal large variations in the spatial distribution of different pollutants. It was shown that the temporal and spatial distributions of pollutant loads were positively correlated with the annual rainfall amounts and with human activities. Furthermore, this finding illustrates that conservation practices and nutrient management should be implemented in specific sites during special periods for the purpose of NPS pollution control in the TGRR.

  5. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    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. PMID:25706379

  6. Characterization of the active site of ADP-ribosyl cyclase.

    PubMed

    Munshi, C; Thiel, D J; Mathews, I I; Aarhus, R; Walseth, T F; Lee, H C

    1999-10-22

    ADP-ribosyl cyclase synthesizes two Ca(2+) messengers by cyclizing NAD to produce cyclic ADP-ribose and exchanging nicotinic acid with the nicotinamide group of NADP to produce nicotinic acid adenine dinucleotide phosphate. Recombinant Aplysia cyclase was expressed in yeast and co-crystallized with a substrate, nicotinamide. x-ray crystallography showed that the nicotinamide was bound in a pocket formed in part by a conserved segment and was near the central cleft of the cyclase. Glu(98), Asn(107) and Trp(140) were within 3.5 A of the bound nicotinamide and appeared to coordinate it. Substituting Glu(98) with either Gln, Gly, Leu, or Asn reduced the cyclase activity by 16-222-fold, depending on the substitution. The mutant N107G exhibited only a 2-fold decrease in activity, while the activity of W140G was essentially eliminated. The base exchange activity of all mutants followed a similar pattern of reduction, suggesting that both reactions occur at the same active site. In addition to NAD, the wild-type cyclase also cyclizes nicotinamide guanine dinucleotide to cyclic GDP-ribose. All mutant enzymes had at least half of the GDP-ribosyl cyclase activity of the wild type, some even 2-3-fold higher, indicating that the three coordinating amino acids are responsible for positioning of the substrate but not absolutely critical for catalysis. To search for the catalytic residues, other amino acids in the binding pocket were mutagenized. E179G was totally devoid of GDP-ribosyl cyclase activity, and both its ADP-ribosyl cyclase and the base exchange activities were reduced by 10,000- and 18,000-fold, respectively. Substituting Glu(179) with either Asn, Leu, Asp, or Gln produced similar inactive enzymes, and so was the conversion of Trp(77) to Gly. However, both E179G and the double mutant E179G/W77G retained NAD-binding ability as shown by photoaffinity labeling with [(32)P]8-azido-NAD. These results indicate that both Glu(179) and Trp(77) are crucial for catalysis and

  7. Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity.

    PubMed

    Lipski, Alexandra; Watzlawick, Hildegard; Ravaud, Stéphanie; Robert, Xavier; Rhimi, Moez; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2013-02-01

    Sucrose isomerase is an enzyme that catalyzes the production of sucrose isomers of high biotechnological and pharmaceutical interest. Owing to the complexity of the chemical synthesis of these isomers, isomaltulose and trehalulose, enzymatic conversion remains the preferred method for obtaining these products. Depending on the microbial source, the ratio of the sucrose-isomer products varies significantly. In studies aimed at understanding and explaining the underlying molecular mechanisms of these reactions, mutations obtained using a random-mutagenesis approach displayed a major hydrolytic activity. Two of these variants, R284C and F164L, of sucrose isomerase from Rhizobium sp. were therefore crystallized and their crystal structures were determined. The three-dimensional structures of these mutants allowed the identification of the molecular determinants that favour hydrolytic activity compared with transferase activity. Substantial conformational changes resulting in an active-site opening were observed, as were changes in the pattern of water molecules bordering the active-site region.

  8. 4-Aryl-4-oxo-N-phenyl-2-aminylbutyramides as acetyl- and butyrylcholinesterase inhibitors. Preparation, anticholinesterase activity, docking study, and 3D structure-activity relationship based on molecular interaction fields.

    PubMed

    Vitorović-Todorović, Maja D; Juranić, Ivan O; Mandić, Ljuba M; Drakulić, Branko J

    2010-02-01

    Synthesis and anticholinesterase activity of 4-aryl-4-oxo-N-phenyl-2-aminylbutyramides, novel class of reversible, moderately potent cholinesterase inhibitors, are reported. Simple substituent variation on aroyl moiety changes anti-AChE activity for two orders of magnitude; also substitution and type of hetero(ali)cycle in position 2 of butanoic moiety govern AChE/BChE selectivity. The most potent compounds showed mixed-type inhibition, indicating their binding to free enzyme and enzyme-substrate complex. Alignment-independent 3D QSAR study on reported compounds, and compounds having similar potencies obtained from the literature, confirmed that alkyl substitution on aroyl moiety of molecules is requisite for inhibition activity. The presence of hydrophobic moiety at close distance from hydrogen bond acceptor has favorable influence on inhibition potency. Docking studies show that compounds probably bind in the middle of the AChE active site gorge, but are buried deeper inside BChE active site gorge, as a consequence of larger BChE gorge void.

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

    PubMed Central

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

    2015-01-01

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

  10. Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

    PubMed

    Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

    2016-08-01

    Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

  11. Paleoenvironmental reconstruction of a paleosol catena, the Zinj archeological level, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Driese, Steven G.; Ashley, Gail M.

    2016-01-01

    Paleosols record paleoclimatic processes in the Earth's Critical Zone and are archives of ancient landscapes associated with archeological sites. Detailed field, micromorphologic, and bulk geochemical analysis of paleosols were conducted near four sites at Olduvai Gorge, Tanzania within the same stratigraphic horizon as the Zinjanthropus (Paranthropus) boisei archeological site. Paleosols are thin (< 35 cm), smectitic, and exhibit Vertisol shrink-swell features. Traced across the paleolandscape over 1 km and just beneath Tuff IC (1.845 Ma), the paleosols record a paleocatena in which soil moisture at the four sites was supplemented by seepage additions from adjacent springs, and soil development was enhanced by this additional moisture. Field evidence revealed an abrupt lateral transition in paleosol composition at the PTK site (< 1.5 m apart) in which paleosol B, formed nearest the spring system, is highly siliceous, vs. paleosol A, formed in smectitic clay. Thin-section investigations combined with mass-balance geochemistry, using Chapati Tuff as parent material and assuming immobile Ti, show moderately intense weathering. Pedotransfer functions indicate a fertile soil system, but sodicity may have limited some plant growth. Paleosol bulk geochemical proxies used to estimate paleoprecipitation (733-944 mm/yr), are higher than published estimates of 250-700 mm/yr using δD values of lipid biomarkers.

  12. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

    PubMed Central

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

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

    PubMed Central

    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 factor of ten and promotes closure. We conclude that closure occurs during the rate-limiting catalytic step of decapping, juxtaposing the cap-binding region of each domain to form a composite active site. This work suggests a model for regulation of decapping, where coactivators trigger decapping by stabilizing a labile composite active site. PMID:20711189

  14. Rainfall-Runoff and Erosion Data from the Mancos Shale Formation in the Gunnison Gorge National Conservation Area, Southwestern Colorado, 2003-2006

    USGS Publications Warehouse

    Elliott, John G.; Herring, James R.; Ingersoll, George P.; Kosovich, John J.; Fahy, Juli

    2008-01-01

    Data were collected and experiments were conducted from 2003 to 2006 by the U.S. Geological Survey, in cooperation with the Bureau of Land Management, to support research into understanding processes that liberate, disperse, and concentrate erosion byproducts in Mancos Shale landscapes. The study area was the Gunnison Gorge National Conservation Area near Montrose and Delta, Colorado. This report includes data collected from 24, small-plot, rainfall-runoff simulations, 6 hillslope-erosion monitoring plots, 20 hillslope-creep monitoring sites, and 3 precipitation gages. Small-plot rainfall-runoff simulations were performed on paired (undisturbed and disturbed) plots to examine the effect of off-highway vehicle use on runoff and erosion. These data were collected in conjunction with several other studies done by the U.S. Geological Survey in the Gunnison Gorge National Conservation Area. Data collected in companion studies are published in separate open-file reports.

  15. Landslides in the western Columbia Gorge, Skamania County, Washington

    USGS Publications Warehouse

    Pierson, Thomas C.; Evarts, Russell C.; Bard, Joseph A.

    2016-11-04

    SummaryRecent light detection and ranging (lidar) imagery has allowed us to identify and map a large number of previously unrecognized landslides, or slides, in heavily forested terrain in the western Columbia Gorge, Skamania County, Washington, and it has revealed that the few previously recognized areas of instability are actually composites of multiple smaller landslides. The high resolution of the imagery further reveals that landslides in the map area have complex movement histories and span a wide range of relative ages. Movement histories are inferred from relative landslide locations and crosscutting relations of surface features. Estimated age ranges are based on (1) limited absolute dating; (2) relative fineness of landscape surface textures, calibrated by comparison with surfaces of currently active and dated landslides as interpreted from interferometric synthetic aperture radar (InSAR), global positioning system (GPS), and historical records; (3) sharpness and steepness of larger-scale surface morphologic features, calibrated by comparison with similar dated features in other regions; (4) degree of surface erosion; and (5) evidence of erosion or deposition by late Pleistocene (15–22 ka) Missoula floods at or below 200 m altitude. The relative age categories are recent (0 to ~1,000 years old), intermediate-age (~1,000 to ~15,000 years old), and old (>~15,000 years old). Within the 221.5 km2 map area, we identified 215 discrete landslides, covering 140.9 km2 (64 percent of the map area). At least 12 of the recent landslides are currently moving or have moved within the last two decades. Mapping for this study expanded the area of previously recognized unstable terrain by 56 percent. Landslide geometries suggest that more than half (62 percent) of these slope failures are translational landslides or composite landslides with translational elements, with failure occurring along gently sloping bedding planes in zones of deeply weathered, locally clay rich

  16. Comparison of two methods for detection of fecal indicator bacteria used in water quality monitoring of the Three Gorges Reservoir.

    PubMed

    Wang, Zhaodan; Xiao, Guosheng; Zhou, Nong; Qi, Wenhua; Han, Lin; Ruan, Yu; Guo, Dongqin; Zhou, Hong

    2015-12-01

    Scientifically sound methods to rapidly measure fecal indicator bacteria are important to ensure safe water for drinking and recreational purposes. A total of 200 water samples obtained from the Three Gorges Reservoir during three successive one-year study periods (October 2009 to September 2012) were analyzed using multiple-tube fermentation (MTF) and most probable numbers combined with polymerase chain reaction (MPN-PCR). The MPN-PCR method was found to be significantly more sensitive than the MTF method for detecting Escherichia coli and Enterococcus spp., and of equal sensitivity for detecting total coliforms when all surface water samples were grouped together. The two analytical methods had a strong, significant relationship, but MPN-PCR took only 12-18hr, compared with the 3-8days needed using the MTF method. Bacterial concentrations varied per sampling site but were significantly lower in the mainstream of the Yangtze River than those in the backwater areas of tributaries. The water quality of 85.8% of water samples from the mainstream was suitable for use as a centralized potable water source, while the water quality of 52.5% of water samples from the backwater areas was unsuitable for recreational activities. Relationships between fecal indicator bacteria showed significant correlation (r=0.636-0.909, p<0.01, n=200), while a weak but significant correlation was found between fecal indicators and water turbidity, water temperature, daily inflow, and total dissolved solids (r=0.237-0.532, p<0.05, n=200). The study indicated that MPN-PCR is a rapid and easily performed deoxyribonucleic acid (DNA)-based method for quantitative detection of viable total coliforms, E. coli, and Enterococcus spp. in surface water.

  17. Statistical evaluation of the effects of fall and winter flows on the spring condition of rainbow and brown trout in the green river downstream of Flaming Gorge Dam.

    SciTech Connect

    Magnusson, A. K.; LaGory, K. E.; Hayse, J. W.; Environmental Science Division

    2009-01-09

    Flaming Gorge Dam, a hydroelectric facility operated by the Bureau of Reclamation (Reclamation), is located on the Green River in Daggett County, northeastern Utah. In recent years, single peak releases each day or steady flows have been the operational pattern during the winter period. A double-peak pattern (two flow peaks each day) was implemented during the winter of 2006-2007 by Reclamation. Because there is no recent history of double-peaking at Flaming Gorge Dam, the potential effects of double-peaking operations on the body condition of trout in the dam's tailwater are not known. A study plan was developed that identified research activities to evaluate potential effects from double-peaking operations during winter months. Along with other tasks, the study plan identified the need to conduct a statistical analysis of existing data on trout condition and macroinvertebrate abundance to evaluate potential effects of hydropower operations. This report presents the results of this analysis. We analyzed historical data to (1) describe temporal patterns and relationships among flows, benthic macroinvertebrate abundance, and condition of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in the tailwaters of Flaming Gorge Dam and (2) to evaluate the degree to which flow characteristics (i.e., flow volumes and flow variability) and benthic macroinvertebrate abundance affect the condition of trout in this area. This information, together with further analyses of size-stratified trout data, may also serve as baseline data to which the effects of potential future double-peaking flows can be compared. The condition (length, weight and/or relative weight) of rainbow trout (Oncorhynchus mykiss) at two sites in the Green River downstream of Flaming Gorge Dam (Tailrace and Little Hole) and weight of brown trout (Salmo trutta) at the Little Hole site has been decreasing since 1990 while the abundance of brown trout has been increasing at the two sites. At the

  18. Characterization of Active Site Residues of Nitroalkane Oxidase†

    PubMed Central

    Valley, Michael P.; Fenny, Nana S.; Ali, Shah R.; Fitzpatrick, Paul F.

    2010-01-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitrolkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Serl71 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by ~5-fold and decreases in the rate constant for product release of ~2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

  19. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    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.

  20. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems.

  1. Use of aerial videography to evaluate the effects of Flaming Gorge Dam operations on natural resources of the Green River

    SciTech Connect

    Snider, M.A.; Hayse, J.W.; Hlohowskyj, I.; LaGory, K.E.; Greaney, M.M.; Kuiper, J.A.; Van Lonkhuyzen, R.A.

    1993-07-01

    Peaking hydropower operations can profoundly alter natural stream flow and thereby affect the natural resources dependent on these flows. In this paper, we describe how aerial videography was used to collect environmental data and evaluate impacts of hydropower operations at Flaming Gorge Dam on natural resources of the Green River. An airborne multispectral video/radiometer remote sensing system was used to collect resource data under four different flow conditions from seven sites (each about one mile in length) located downstream from the dam. Releases from Flaming Gorge Dam during data collection ranged from approximately 800 to 4,000 cubic feet/sec (cfs), spanning most of the normal operating range for this facility. For each site a series of contiguous, non-overlapping images was prepared from the videotapes and used to quantify surface water area, backwater habitats, and areas of riparian vegetation under varying flow conditions. From this information, relationships between flow and habitat parameters were developed and used in conjunction with hydrologic modeling and ecological information to evaluate impacts of various modes of operation.

  2. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  3. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  4. Crocodylian and mammalian carnivore feeding traces on hominid fossils from FLK 22 and FLK NN 3, Plio-Pleistocene, Olduvai Gorge, Tanzania.

    PubMed

    Njau, Jackson K; Blumenschine, Robert J

    2012-08-01

    Taphonomic analysis of the Olduvai Hominid (OH) 8 left foot from FLK NN Level 3 and the OH 35 left leg from FLK Level 22 (Zinjanthropus level) in Middle Bed I, Olduvai Gorge, indicates that both were fed upon by crocodiles. Both bear extensive tooth marking, including bisected tooth marks diagnostic of crocodylian feeding. The location of the bisected tooth marks on the distal tibia and the talus indicates disarticulation of the foot by crocodiles. The broken proximal ends of the tibia and fibula are more typical of feeding by a leopard-like carnivore, as is damage to the OH 7 mandible and parietals that are associated with and may derive from the same individual as OH 8. Previous work showing a close articulation of the foot and the leg has been used to suggest that the two specimens belong to the same individual despite deriving from sites separated by 200 m and slightly different stratigraphic levels according to previous work. The location and agent of tooth marking and the nature of gross damage do not refute this hypothesis, but the punctures on the talus and distal tibia differ in size and sharpness. Recent work shows that the stratigraphic discrepancy between OH 8 and OH 35 is greater than previously thought, refuting the single-individual hypothesis. Although seemingly unlikely, this denotes that two hominids represented by rarely found leg and foot elements both lost their left foot to crocodiles at nearby sites within a 6,000 year interval. We cannot determine if the hominids were preyed upon by crocodiles or mammalian carnivores. However, the carnivore damage to them and associated faunal remains suggests that high predation risk constrained hominid activities involving discard of the stone artifacts found at these sites. This finding is inconsistent with the interpretation of the sites as home bases or living floors.

  5. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  6. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  7. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  8. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  9. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

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

    SciTech Connect

    Teese, G.D.

    1995-09-28

    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.

  11. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  12. Advancing analysis of spatio-temporal variations of soil nutrients in the water level fluctuation zone of China's Three Gorges Reservoir using self-organizing map.

    PubMed

    Ye, Chen; Li, Siyue; Yang, Yuyi; Shu, Xiao; Zhang, Jiaquan; Zhang, Quanfa

    2015-01-01

    The ~350 km2 water level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) of China, situated at the intersection of terrestrial and aquatic ecosystems, experiences a great hydrological change with prolonged winter inundation. Soil samples were collected in 12 sites pre- (September 2008) and post submergence (June 2009) in the WLFZ and analyzed for soil nutrients. Self-organizing map (SOM) and statistical analysis including multi-way ANOVA, paired-T test, and stepwise least squares multiple regression were employed to determine the spatio-temporal variations of soil nutrients in relation to submergence, and their correlations with soil physical characteristics. Results showed significant spatial variability in nutrients along ~600 km long shoreline of the TGR before and after submergence. There were higher contents of organic matter, total nitrogen (TN), and nitrate (NO3-) in the lower reach and total phosphorus (TP) in the upper reach that were primarily due to the spatial variations in soil particle size composition and anthropogenic activities. Submergence enhanced soil available potassium (K), while significantly decreased soil N, possibly due to the alterations of soil particle size composition and increase in soil pH. In addition, SOM analysis determined important roles of soil pH value, bulk density, soil particle size (i.e., silt and sand) and nutrients (TP, TK, and AK) on the spatial and temporal variations in soil quality. Our results suggest that urban sewage and agricultural runoffs are primary pollutants that affect soil nutrients in the WLFZ of TGR.

  13. Validation of bone surface modification models for inferring fossil hominin and carnivore feeding interactions, with reapplication to FLK 22, Olduvai Gorge, Tanzania.

    PubMed

    Pante, Michael C; Blumenschine, Robert J; Capaldo, Salvatore D; Scott, Robert S

    2012-08-01

    Resolving the issue of how Early Stone Age hominins acquired large mammal carcasses requires information on their feeding interactions with large carnivores. This ecological information and its behavioral and evolutionary implications are revealed most directly from the tooth, cut, and percussion marks on bone surfaces generated by hominin and carnivore feeding activities. This paper employs a bootstrap method, a form of random resampling with replacement, to refine published neotaphonomic models that use the assemblage-wide proportions of long bones bearing feeding traces to infer the sequences in which Plio-Pleistocene hominins and carnivores accessed flesh, marrow, and/or grease from carcasses. Results validate the sensitivity of the models for inferring hominin feeding ecology, which have been questioned on grounds shown here to be unfounded. The bootstrapped feeding trace models are applied to the late Pliocene larger mammal fossil assemblage from FLK 22 (Zinjanthropus site), Olduvai Gorge, Tanzania. High frequencies of tooth and percussion marking on long bone midshaft fragments from FLK 22 are most consistent with those feeding trace models that simulate hominin scavenging from carcasses defleshed by carnivores, while cut mark data indicate that hominins more often had access to upper forelimb flesh than upper hind limb flesh. Together, the bone surface modification data indicate that hominins typically gained secondary access to partially defleshed carnivore kills, but they also allow for the possibility of some carcasses being processed only by carnivores and only by hominins.

  14. Lidar research activities and observations at NARL site, Gadanki, India

    NASA Astrophysics Data System (ADS)

    Yellapragada, Bhavani Kumar

    2016-05-01

    The National Atmospheric Research Laboratory (NARL), a unit of Department of Space (DOS), located at Gadanki village (13.5°N, 79.2°E, 370 m AMSL) in India, is involved in the development of lidar remote sensing technologies for atmospheric research. Several advanced lidar technologies employing micropulse, polarization, Raman and scanning have been developed at this site and demonstrated for atmospheric studies during the period between 2008 and 2015. The technology of micropulse lidar, operates at 532 nm wavelength, was successfully transferred to an industry and the commercial version has been identified for Indian Lidar network (I-LINK) programme. Under this lidar network activity, several lidar units were installed at different locations in India to study tropospheric aerosols and clouds. The polarization sensitive lidar technology was realized using a set of mini photomultiplier tube (PMT) units and has the capability to operate during day and night without a pause. The lidar technology uses a compact flashlamp pumped Qswitched laser and employs biaxial configuration between the transmitter and receiver units. The lidar technology has been utilized for understanding the polarization characteristics of boundary layer aerosols during the mixed layer development. The demonstrated Raman lidar technology, uses the third harmonic wavelength of Nd:YAG laser, provides the altitude profiles of aerosol backscattering, extinction and water vapor covering the boundary layer range and allows operation during nocturnal periods. The Raman lidar derived height profiles of aerosol backscattering and extinction coefficient, lidar ratio, and watervapor mixing ratio inform the tropical boundary layer aerosol characteristics. The scanning lidar technology uses a near infrared laser wavelength for probing the lower atmosphere and has been utilized for high resolution cloud profiling during convective periods. The lidar technology is also used for rain rate measurement during

  15. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  16. Active-site zinc ligands and activated H2O of zinc enzymes.

    PubMed Central

    Vallee, B L; Auld, D S

    1990-01-01

    The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing. Images PMID:2104979

  17. Fission-Track Dating of Bed I, Olduvai Gorge.

    PubMed

    Fleischer, R L; Price, P B; Walker, R M; Leakey, L S

    1965-04-02

    The discoveries of a series of hominid remains in the Olduvai Gorge, Tanganyika, has focused attention upon the age of the deposits of Bed 1, in which both Zinjanthropus and Homo habilis were found. Because the age of 1.75 million years, as determined by the radioactive decay of potassium and argon, has been questioned several times, a fission-track age was measured for the pumice from Bed 1. The result is 2.03 +/- 0.28 million years, in good agreement with the result obtained by the potassium-argon decay method.

  18. Examining time trends in the Oldowan technology at Beds I and II, Olduvai Gorge.

    PubMed

    Kimura, Yuki

    2002-09-01

    The lithic analysis of the Bed I and II assemblages from Olduvai Gorge reveals both static and dynamic time trends in early hominids' technology from 1.8 to 1.2 m.y.a. The Bed I Oldowan (1.87-1.75 m.y.a.) is characterized by the least effort strategy in terms of raw material exploitation and tool production. The inclusion of new raw material, chert, for toolmaking in the following Developed Oldowan A (DOA, 1.65-1.53 m.y.a.) facilitated more distinctive and variable flaking strategies depending on the kind of raw materials. The unique characters of DOA are explainable by this raw material factor, rather than technological development of hominids. The disappearance of chert in the subsequent Developed Oldowan B and Acheulian (1.53-1.2 m.y.a.) necessitated a shift in tool production strategy more similar to that of Bed I Oldowan than DOA. However, the evidence suggests that Bed II hominids might have been more skillful toolmakers, intensive tool-users, and engaged in more active transport of stone tools than the Bed I predecessors. Koobi Fora hominids maintained a more static tool-using behavior than their Olduvai counterparts due mainly to a stable supply of raw materials. They differed from Olduvai hominids in terms of less battering of cores, consistent transport behavior, and few productions of side-struck flakes, indicating a regional variation of toolmaking and using practice. However, they shared with Olduvai hominids a temporal trend toward the production of larger flakes from larger cores after 1.6 m.y.a. Increased intake of animal resources and the expansion of ranging area of Homo ergaster would have led to the development of technological organization. Technological changes in the Oldowan industry are attested at Olduvai Gorge, Koobi Fora, and Sterkfontein, suggesting that it was a pan-African synchronous phenomenon, beginning at 1.5 m.y.a.

  19. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  20. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge

    PubMed Central

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

  1. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge.

    PubMed

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution.

  2. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.

    PubMed

    Xiang, Kehui; Manley, James L; Tong, Liang

    2012-07-10

    The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.

  3. Mice that gorged during dietary restriction increased foraging related behaviors and differed in their macronutrient preference when released from restriction

    PubMed Central

    Speakman, John R.

    2015-01-01

    Caloric restriction (CR) can trigger gorging behavior. We examined macronutrient choice and behavior in mice that gorged during restriction compared to restricted non-gorgers and controls. Fifty MF1 male mice were restricted to 75% of ad-libitum food intake (FI), while ten controls were fed ad-lib. Body mass (BM) and FI were measured two and 24-h after food inclusion over 14-days. ‘Gorging’ mice were defined as those which ate over 25% of their daily FI in 2-h. The top 11 gorgers and the lowest 9 gorgers, along with 10 controls, had their behavior analysed during restriction, and were then provided with an unrestricted food choice, consisting of three diets that were high in fat, protein or carbohydrate. During restriction gorgers ate on average 51% of their daily FI in the 2-h following food introduction while the non-gorgers ate only 16%. Gorgers lost significantly more BM than non-gorgers possibly due to an increased physical activity linked to anticipation of daily food provision. Controls and non-gorgers spent most of their time sleeping. After restriction, both gorgers and non-gorgers were hyperphagic until their lost weight was regained. All 3 groups favoured high fat food. Gorgers and non-gorgers had a significantly greater high carbohydrate diet intake than controls, and gorgers also had a significantly greater high protein diet intake than non-gorgers and controls. On unrestricted food, they did not continue to gorge, although they still had a significantly greater 2-h FI than the other groups. Elevated protein intake may play an important role in the recovery of the lost lean tissue of gorgers after restriction. PMID:26157640

  4. Tiny bubbles challenge giant turbines: Three Gorges puzzle.

    PubMed

    Li, Shengcai

    2015-10-06

    Since the birth of the first prototype of the modern reaction turbine, cavitation as conjectured by Euler in 1754 always presents as a challenge. Following his theory, the evolution of modern reaction (Francis and Kaplan) turbines has been completed by adding the final piece of the element 'draft-tube' that enables turbines to explore water energy at efficiencies of almost 100%. However, during the last two and a half centuries, with increasing unit capacity and specific speed, the problem of cavitation has been manifested and complicated by the draft-tube surges rather than being solved. Particularly, during the last 20 years, the fierce competition in the international market for extremely large turbines with compact design has encouraged the development of giant Francis turbines of 700-1000 MW. The first group (24 units) of such giant turbines of 700 MW each was installed in the Three Gorges project. Immediately after commission, a strange erosion phenomenon appeared on the guide vane of the machines that has puzzled professionals. From a multi-disciplinary analysis, this Three Gorges puzzle could reflect an unknown type of cavitation inception presumably triggered by turbulence production from the boundary-layer streak transitional process. It thus presents a fresh challenge not only to this old turbine industry, but also to the fundamental sciences.

  5. Tiny bubbles challenge giant turbines: Three Gorges puzzle

    PubMed Central

    Li, Shengcai

    2015-01-01

    Since the birth of the first prototype of the modern reaction turbine, cavitation as conjectured by Euler in 1754 always presents as a challenge. Following his theory, the evolution of modern reaction (Francis and Kaplan) turbines has been completed by adding the final piece of the element ‘draft-tube’ that enables turbines to explore water energy at efficiencies of almost 100%. However, during the last two and a half centuries, with increasing unit capacity and specific speed, the problem of cavitation has been manifested and complicated by the draft-tube surges rather than being solved. Particularly, during the last 20 years, the fierce competition in the international market for extremely large turbines with compact design has encouraged the development of giant Francis turbines of 700–1000 MW. The first group (24 units) of such giant turbines of 700 MW each was installed in the Three Gorges project. Immediately after commission, a strange erosion phenomenon appeared on the guide vane of the machines that has puzzled professionals. From a multi-disciplinary analysis, this Three Gorges puzzle could reflect an unknown type of cavitation inception presumably triggered by turbulence production from the boundary-layer streak transitional process. It thus presents a fresh challenge not only to this old turbine industry, but also to the fundamental sciences. PMID:26442144

  6. Accumulation of floating microplastics behind the Three Gorges Dam.

    PubMed

    Zhang, Kai; Gong, Wen; Lv, Jizhong; Xiong, Xiong; Wu, Chenxi

    2015-09-01

    We investigated the occurrence and distribution of microplastics in surface water from the Three Gorges Reservoir. Nine samples were collected via trawl sampling with a 112 μmmesh net. The abundances of microplastics were from 3407.7 × 10(3) to 13,617.5 × 10(3) items per square kilometer in the main stream of the Yangtze River and from 192.5 × 10(3) to 11,889.7 × 10(3) items per square kilometer in the estuarine areas of four tributaries. The abundance of microplastics in the main stream of the Yangtze River generally increased as moving closer to the Three Gorges Dam. The microplastics are made exclusively of polyethylene (PE), polypropylene (PP), and polystyrene (PS). Together with microplastics, high abundance of coal/fly ash was also observed in the surface water samples. Comparing with previously reported data, microplastics in the TGR were approximately one to three orders of magnitudes greater, suggesting reservoirs as potential hot spot for microplastic pollution.

  7. Local Climate Sensitivity of the Three Gorges Dam

    SciTech Connect

    Miller, Norman L.; Jin, Jiming; Tsang, Chin-Fu

    2005-02-18

    Two simulations, control and land use change, were performed for an eight week period (2 April-16 May 1990) to determine the net sensitivity of the local climate around the Three Gorges Dam. The analysis indicates that the large reservoir acts as a potential evaporating surface that decreases the surface temperature, cools the lower atmosphere, decreasing upward motion, and increasing sinking air mass. Such sinking results in low level moisture divergence, decreasing cloudiness, and increasing net downward radiation, which increases the surface temperature. However, results indicate that evaporative cooling dominates radiative warming in this initial study. The strong evaporation also supplies moisture to the atmosphere, suggesting an increase in precipitation, but the sinking moist air diverges away from the TGD region with no net change in precipitation. This numerical study represents an initial methodology for quantification of the impact of the Three Gorges Dam on the local climate and a more comprehensive, fine-scale set of multi-season simulations with additional observational data is needed for a more complete analysis.

  8. After Three Gorges Dam: What have we learned?

    NASA Astrophysics Data System (ADS)

    Natali, J.; Williams, P.; Wong, R.; Kondolf, G. M.

    2013-12-01

    China is at a critical point in its development path. By investing heavily in large-scale infrastructure, the rewards of economic growth weigh against long-term environmental and social costs. The construction of Three Gorges Dam, the world's largest hydroelectric project, began in 1994. Between 2002 and 2010, its 660 kilometer reservoir filled behind a 181 meter dam, displacing at least 1.4 million people and transforming Asia's longest river (the Yangtze) while generating nearly 100 billion kWh/yr of electricity -- 2.85% of China's current electric power usage. As the mega-project progenitor in a cascade of planned dams, the Three Gorges Dam emerges as a test case for how China will plan, execute and mitigate its development pathway and the transformation of its environment. Post-Project Assessments (PPA) provide a systematic, scientific method for improving the practice of environmental management - particularly as they apply to human intervention in river systems. In 2012, the Department of Landscape Architecture and Environmental Planning at University of California, Berkeley organized a symposium-based PPA for the Three Gorges Dam on the Yangtze River. Prior to this symposium, the twelve invited Chinese scientists, engineers and economists with recent research on Three Gorges Dam had not had the opportunity to present their evaluations together in an open, public forum. With a 50-year planning horizon, the symposium's five sessions centered on impacts on flows, geomorphology, geologic hazards, the environment and socioeconomic effects. Three Gorges' project goals focused on flood control, hydropower and improved navigation. According to expert research, major changes in sediment budget and flow regime from reservoir operation have significantly reduced sediment discharge into the downstream river and estuary, initiating a series of geomorphic changes with ecological and social impacts. While the dam reduces high flow stages from floods originating above the

  9. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

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

    SciTech Connect

    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.

  11. Revealing the nature of the active site on the carbon catalyst for C-H bond activation.

    PubMed

    Sun, XiaoYing; Li, Bo; Su, Dangsheng

    2014-09-28

    A reactivity descriptor for the C-H bond activation on the nanostructured carbon catalyst is proposed. Furthermore the calculations reveal that the single ketone group can be an active site in ODH reaction.

  12. Cellular Active N-Hydroxyurea FEN1 Inhibitors Block Substrate Entry to the Active Site

    PubMed Central

    Exell, Jack C.; Thompson, Mark J.; Finger, L. David; Shaw, Steven J.; Debreczeni, Judit; Ward, Thomas A.; McWhirter, Claire; Siöberg, Catrine L. B.; Martinez Molina, Daniel; Mark Abbott, W.; Jones, Clifford D.; Nissink, J. Willem M.; Durant, Stephen T.; Grasby, Jane A.

    2016-01-01

    The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the first crystal structure of inhibitor-bound hFEN1 and show a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein–substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the unpairing of substrate DNA necessary for reaction. Other compounds were more competitive with substrate. Cellular thermal shift data showed engagement of both inhibitor types with hFEN1 in cells with activation of the DNA damage response evident upon treatment. However, cellular EC50s were significantly higher than in vitro inhibition constants and the implications of this for exploitation of hFEN1 as a drug target are discussed. PMID:27526030

  13. Distribution, sources, and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in surface water in industrial affected areas of the Three Gorges Reservoir, China.

    PubMed

    Zheng, Binghui; Ma, Yingqun; Qin, Yanwen; Zhang, Lei; Zhao, Yanmin; Cao, Wei; Yang, Chenchen; Han, Chaonan

    2016-12-01

    Water samples were collected from wastewater treatment plant (WWTP), drain water (DW), major tributaries (MT), and main course of the Yangtze River (MY) in areas of three industrial parks (IPs) in Chongqing city in the Three Gorges Reservoir (TGR). Sixteen EPA priority polycyclic aromatic hydrocarbon (PAH) pollutants were quantified to identify the effects of industrial activities on water quality of the TGR. The results showed that 11 individual PAHs were quantified and 5 PAHs (naphthalene (Nap), acenaphthylene (Acy), benzo[k]fluoranthene (BkF), indeno[1,2,3-cd]pyrene (InP), and benzo[g,h,i]perylene (BgP)) were under detection limits in all of the water samples. Three-ring and four-ring PAHs were the most detected PAHs. Concentrations of individual PAHs were in the range of not detected (nd) to 24.3 ng/L. Total PAH concentrations for each site ranged from nd to 42.9 ng/L and were lower compared to those in other studies. The mean PAH concentrations for sites WWTP, DW, MT, and MY showed as follows: DW (25.9 ng/L) > MY (15.5 ng/L) > MT (14.0 ng/L) > WWTP (9.3 ng/L), and DW contains the highest PAH concentrations. Source identification ratios showed that petroleum and combustion of biomass coal and petroleum were the main sources of PAHs. The results of potential ecosystem risk assessment indicated that, although PAH concentrations in MT and MY are likely harmless to ecosystem, contaminations of PAHs in DW were listed as middle levels and some management strategies and remediation actions, like strengthen clean production processes and banning illegal sewage discharging activities, etc., should be taken to lighten the ecosystem risk caused by PAHs especially risks caused by water discharging drains.

  14. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  15. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  16. [Research progress on remote sensing of ecological and environmental changes in the Three Gorges Reservoir area, China].

    PubMed

    Teng, Ming-jun; Zeng, Li-xiong; Xiao, Wen-fa; Zhou, Zhi-xiang; Huang, Zhi-lin; Wang, Peng-cheng; Dian, Yuan-yong

    2014-12-01

    The Three Gorges Reservoir area (TGR area) , one of the most sensitive ecological zones in China, has dramatically changes in ecosystem configurations and services driven by the Three Gorges Engineering Project and its related human activities. Thus, understanding the dynamics of ecosystem configurations, ecological processes and ecosystem services is an attractive and critical issue to promote regional ecological security of the TGR area. The remote sensing of environment is a promising approach to the target and is thus increasingly applied to and ecosystem dynamics of the TGR area on mid- and macro-scales. However, current researches often showed controversial results in ecological and environmental changes in the TGR area due to the differences in remote sensing data, scale, and land-use/cover classification. Due to the complexity of ecological configurations and human activities, challenges still exist in the remote-sensing based research of ecological and environmental changes in the TGR area. The purpose of this review was to summarize the research advances in remote sensing of ecological and environmental changes in the TGR area. The status, challenges and trends of ecological and environmental remote-sensing in the TGR area were further discussed and concluded in the aspect of land-use/land-cover, vegetation dynamics, soil and water security, ecosystem services, ecosystem health and its management. The further researches on the remote sensing of ecological and environmental changes were proposed to improve the ecosystem management of the TGR area.

  17. Impact of the Three Gorges Dam on the spawning stock and natural reproduction of Chinese sturgeon in Changjiang River, China

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Lin, Pengcheng; Li, Mingzheng; Duan, Zhonghua; Liu, Huanzhang

    2016-09-01

    Chinese sturgeon ( Acipenser sinensis) is the flagship species of the Changjiang River. The migration route of this species is blocked by the first dam, the Gezhou Dam, and its reproduction is affected by the Three Gorges Dam (TGD), one of the largest dams in the world. We studied the impact of the impoundment of the Three Gorges Reservoir (TGR) since 2003 on the spawning stock and the natural reproduction of the Chinese sturgeon by using our monitoring data from 1997 to 2013. Results indicate that TGR impoundment has delayed the first spawning dates of the fish from middle-late October to late November, decreased the amount of spawning activities from twice to only once each year, and significantly reduced egg production. In particular, the fish did not demonstrate any spawning activities in 2013. Therefore, TGR impoundment significantly affects the natural reproduction of the fish downstream of the TGD. The spawning stock size of the fish is also predicted to further decrease in the future, which will lead to a risk of population extinction. Ecological regulations must be imposed on decreasing the water temperature to 20°C before mid-October and increasing water discharge downstream of the TGD in October to induce spawning of the Chinese sturgeon.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    Not Available

    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.

  20. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins

    PubMed Central

    Yamada, Kazunori D.; Nishi, Hafumi; Nakata, Junichi; Kinoshita, Kengo

    2016-01-01

    Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations. PMID:27924270

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

    PubMed Central

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

    2013-01-01

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

  2. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

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

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    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.

  4. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.

    PubMed

    Stec, Boguslaw

    2012-11-13

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.

  5. Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites

    DTIC Science & Technology

    2013-08-01

    Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites Edward W. Malin, MD, Chaya M. Galin, BSN, RN... microcurrent in comparison to silver-coated dressing with sham microcurrent on wound-closure time for autogenous skin donor sites. Methods: Four...hundred five patients were screened for treatment of their donor sites using a silver-coated nylon dressing with either sham or active microcurrent

  6. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  7. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-26

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  8. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    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...). Title X requires DOE to reimburse eligible uranium and thorium licensees for certain costs...

  9. Hydraulic design of Three Gorges right bank powerhouse turbine for improvement of hydraulic stability

    NASA Astrophysics Data System (ADS)

    Shi, Q.

    2010-08-01

    This paper presents the hydraulic design of Three Gorges Right Bank Powerhouse turbine for improvement of hydraulic stability. The technical challenges faced in the hydraulic design of the turbine are given. The method of hydraulic design for improving the hydraulic stability and particularly for eliminating the upper part load pressure pulsations is clarified. The final hydraulic design results of Three Gorges Right Bank Powerhouse turbine based on modern hydraulic design techniques are presented.

  10. Excavation of Tunnel Valleys and Inner Gorges by Subglacial Meltwater Erosion

    NASA Astrophysics Data System (ADS)

    Beaud, F.; Flowers, G. E.; Venditti, J. G.; Koppes, M. N.

    2015-12-01

    Subglacial meltwater erosion (SME) is thought to contribute to the excavation of tunnel valleys and inner gorges, yet the underpinnings of the formation of these landforms remain obscure. Tunnel valleys are large channel-like features (100s of metres to few kilometres wide and up to 10s of kilometres in length) commonly found in the vicinity of former continental ice-sheet margins. The main question concerning their formation is: does SME excavate them gradually or by large subglacial floods? Inner gorges are V-shaped incisions in an otherwise glacially overprinted landscape. The initial assertion of their fluvial origin has recently been disputed, as they have been shown to persist through multiple glaciations and SME has been invoked to explain some inner gorges in Scandinavia and the Alps. The question is therefore: can SME explain the excavation of an inner gorge? In order to test these hypotheses related to the genesis of tunnel valleys and inner gorges, we use a 1-D model of subglacial hydrology to drive a model of bedrock erosion by total sediment load based on the tools and cover effect. Calculated values of subglacial transport stage in response to ordinary seasonal processes are comparable to those during large floods in rivers. Subglacial floods therefore limit bedrock erosion by transporting sediment farther from the bed, thus inhibiting impacts. Consequently, we find that gradual SME is likely to produce more incision over a glacial cycle. When we simulate the total SME that occurs through a glacial cycle under a synthetic ice-sheet margin, we are able to produce tunnel valleys or inner gorges over the timespan of a glaciation. Based on these results, we propose that (1) tunnel valleys and inner gorges can both be the result of SME, (2) tunnel valleys in bedrock can be formed through gradual processes rather than floods, and (3) SME enhances inner gorge relief.

  11. A model of the rabies virus glycoprotein active site.

    PubMed

    Rustici, M; Bracci, L; Lozzi, L; Neri, P; Santucci, A; Soldani, P; Spreafico, A; Niccolai, N

    1993-06-01

    The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

  12. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

    PubMed Central

    2016-01-01

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

  13. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

    PubMed

    Dingerdissen, Hayley; Motwani, Mona; Karagiannis, Konstantinos; Simonyan, Vahan; Mazumder, Raja

    2013-03-01

    An enzyme's active site is essential to normal protein activity such that any disruptions at this site may lead to dysfunction and disease. Nonsynonymous single-nucleotide variations (nsSNVs), which alter the amino acid sequence, are one type of disruption that can alter the active site. When this occurs, it is assumed that enzyme activity will vary because of the criticality of the site to normal protein function. We integrate nsSNV data and active site annotations from curated resources to identify all active-site-impacting nsSNVs in the human genome and search for all pathways observed to be associated with this data set to assess the likely consequences. We find that there are 934 unique nsSNVs that occur at the active sites of 559 proteins. Analysis of the nsSNV data shows an over-representation of arginine and an under-representation of cysteine, phenylalanine and tyrosine when comparing the list of nsSNV-impacted active site residues with the list of all possible proteomic active site residues, implying a potential bias for or against variation of these residues at the active site. Clustering analysis shows an abundance of hydrolases and transferases. Pathway and functional analysis shows several pathways over- or under-represented in the data set, with the most significantly affected pathways involved in carbohydrate metabolism. We provide a table of 32 variation-substrate/product pairs that can be used in targeted metabolomics experiments to assay the effects of specific variations. In addition, we report the significant prevalence of aspartic acid to histidine variation in eight proteins associated with nine diseases including glycogen storage diseases, lacrimo-auriculo-dento-digital syndrome, Parkinson's disease and several cancers.

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

    SciTech Connect

    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.

  15. All the catalytic active sites of MoS2 for hydrogen evolution

    DOE PAGES

    Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5more » s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

  16. Impacts of the Three Gorges Project on Local Climate

    NASA Astrophysics Data System (ADS)

    Song, Z.; Liang, S.; Feng, L.

    2015-12-01

    Three Gorges Project (TGP) is the largest hydroelectric project in the world and has led to significant land cover changes in Three Gorges Reservoir Area (TGRA). Since its construction the debates on its environmental and climatic impacts have never stopped, especially after the extreme drought and flood in Yangtze River Basin these years. TGP reached its final impounding water level in 2010. However, studies on systematically monitoring the long-term variations in surface and atmospheric parameters in TGRA are still lacking. In this study, three important surface parameters - surface albedo, land surface temperature (LST) and evapotranspiration (ET) and two climatic parameters - air temperature and precipitation were investigated from 2000 to 2013 by combining multiple remote sensing data and ground measurements. Results showed that along the reservoir albedo decreased significantly as a result of water impounding. Correspondingly, in the same region daytime LST decreased in spring and summer and nighttime LST increased in autumn and winter. In the western region of TGRA, albedo increased due to resettlement and LST also changed. The average ET increased by 20% in TGR but kept stable in the whole TGRA. In contrast to LST, air temperature showed less apparent spatial and temporal variability. Only in the region near the dam air temperature experienced a decrease at daytime and an increase at nighttime. Further analysis demonstrated precipitation revealed no apparent changes in TGRA and the precipitation anomaly in northwest of TGRA may not be connected with TGP. All of the findings provide a more substantial clues of local climate change caused by TGP.

  17. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  18. Occurrence and potential health risk of Cryptosporidium and Giardia in the Three Gorges Reservoir, China.

    PubMed

    Xiao, Guosheng; Qiu, Zhiqun; Qi, Junsheng; Chen, Ji-an; Liu, Fengdan; Liu, Wenyi; Luo, Jiaohua; Shu, Weiqun

    2013-05-01

    The Three Gorges Reservoir (TGR) is the biggest lake in the world and a major water source in China. There is no information about occurrence and impact of Cryptosporidium and Giardia on the aquatic ecosystem. 61 surface water samples from 23 monitoring sites and 5 treated effluent samples were collected and analyzed. Cryptosporidium oocysts and Giardia cysts were found, respectively, in 86.4% and 65.2% of a total of 66 water samples, with high concentrations in treated effluent. The mean percent recovery was 29.14% for oocysts and 34.86% for cysts. A seasonal pattern was observed, with positive samples for Cryptosporidium more frequent in flood period and positive samples for Giardia more frequent in impounding period. Counts of enterococci, fecal coliforms and total coliforms, and turbidity were significantly associated with Cryptosporidium concentration in backwater (water in a main river which is backed up by the Three Gorges Dam) areas of tributaries but not Giardia. High associations were also found between oocyst and cyst in backwater areas of tributaries and cities. The risks of infection and illness due to water consumption in four different exposure routes were estimated. The results showed that swimming in the TGR has the highest infection risk with 1.39 × 10(-3) per time (95% confidence interval (CI): 0.05-600.3 × 10(-5)) for Cryptosporidium and 2.08 × 10(-4) per time (95% CI: 0.05-878.87 × 10(-6)) for Giardia, while directly drinking unboiled tap water treated with the conventional process has the highest morbidity with 524.98 per 100,000 population per year (95% CI: 10.35-2040.26) for Cryptosporidium and 5.89 per 100,000 population per year (95% CI: 0.08-22.67) for Giardia. This study provides new useful information for drinking water plants, health care workers and managers to improve the safety of tap water and deduce the risk of surface water contamination in China.

  19. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  20. An active site mutation increases the polymerase activity of the guinea pig-lethal Marburg virus.

    PubMed

    Koehler, Alexander; Kolesnikova, Larissa; Becker, Stephan

    2016-10-01

    Marburg virus (MARV) causes severe, often fatal, disease in humans and transient illness in rodents. Sequential passaging of MARV in guinea pigs resulted in selection of a lethal virus containing 4 aa changes. A D184N mutation in VP40 (VP40D184N), which leads to a species-specific gain of viral fitness, and three mutations in the active site of viral RNA-dependent RNA polymerase L, which were investigated in the present study for functional significance in human and guinea pig cells. The transcription/replication activity of L mutants was strongly enhanced by a substitution at position 741 (S741C), and inhibited by other substitutions (D758A and A759D) in both species. The polymerase activity of L carrying the S741C substitution was eightfold higher in guinea pig cells than in human cells upon co-expression with VP40D184N, suggesting that the additive effect of the two mutations provides MARV a replicative advantage in the new host.

  1. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

  2. Surface energy and radiation budgets in a steppe ecosystem in the Upper Columbia River Gorge

    SciTech Connect

    Whiteman, C.D.; Allwine, K.J.; Bian, X.

    1994-08-01

    Measurements of radiation and surface energy budget components are presented for a semiarid grassland-steppe ecosystem in the Upper Columbia River Gorge (45{degrees}45`25.6 inches N, 120{degrees}01`39.3 inches W, 190 m) for June 2-27, 1991. Over this period, the ratio of sensible to latent heat flux (the Bowen ratio) averaged 5.0, and mean daily surface energy balance totals were: net radiation, 9.23; ground heat flux, 1.25; latent heat flux, 1.32; and sensible heat flux, 6.66 MJ m{sup {minus}2} d{sup {minus}1}, where the mean daily nonradiative fluxes were directed away from the surface, and the mean daily radiative flux was directed toward the surface. On clear days, the site received from 0.71 to 0.76 of the theoretical extraterrestrial solar radiation. Albedo over the 26-d period varied from 0.17 to 0.21. Daily and daytime average values of the components are summarized, and a plot is presented of the 30-min average values of all components for the entire period.

  3. Flood characteristics for the New River in the New River Gorge National River, West Virginia

    USGS Publications Warehouse

    Wiley, J.B.; Cunningham, M.K.

    1994-01-01

    The frequency and magnitude of flooding of the New River in the New River Gorge National River was studied. A steady-state, one-dimensional flow model was applied to the study reach. Rating curves, cross sections, and Manning's roughness coefficients that were used are presented in this report. Manning's roughness coefficients were evaluated by comparing computed elevations (from application of the steady-state, one-dimensional flow model) to rated elevations at U.S. Geological Survey (USGS) streamflow-gaging stations and miscellaneous-rating sites. Manning's roughness coefficients ranged from 0.030 to 0.075 and varied with hydraulic depth. The 2-, 25-, and 100-year flood discharges were esti- mated on the basis of information from flood- insurance studies of Summers County, Fayette County, and the city of Hinton, and flood-frequency analysis of discharge records for the USGS streamflow-gaging stations at Hinton and Thurmond. The 100-year discharge ranged from 107,000 cubic feet per second at Hinton to 150,000 cubic feet per second at Fayette.

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

    SciTech Connect

    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.

  5. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  6. Barium ions selectively activate BK channels via the Ca2+-bowl site.

    PubMed

    Zhou, Yu; Zeng, Xu-Hui; Lingle, Christopher J

    2012-07-10

    Activation of Ca(2+)-dependent BK channels is increased via binding of micromolar Ca(2+) to two distinct high-affinity sites per BK α-subunit. One site, termed the Ca(2+) bowl, is embedded within the second RCK domain (RCK2; regulator of conductance for potassium) of each α-subunit, while oxygen-containing residues in the first RCK domain (RCK1) have been linked to a separate Ca(2+) ligation site. Although both sites are activated by Ca(2+) and Sr(2+), Cd(2+) selectively favors activation via the RCK1 site. Divalent cations of larger ionic radius than Sr(2+) are thought to be ineffective at activating BK channels. Here we show that Ba(2+), better known as a blocker of K(+) channels, activates BK channels and that this effect arises exclusively from binding at the Ca(2+)-bowl site. Compared with previous estimates for Ca(2+) bowl-mediated activation by Ca(2+), the affinity of Ba(2+) to the Ca(2+) bowl is reduced about fivefold, and coupling of binding to activation is reduced from ∼3.6 for Ca(2+) to about ∼2.8 for Ba(2+). These results support the idea that ionic radius is an important determinant of selectivity differences among different divalent cations observed for each Ca(2+)-binding site.

  7. Activation of brown adipose tissue mitochondrial GDP binding sites

    SciTech Connect

    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.

  8. Structure and Reactivity of the Phosphotriesterase Active Site

    DTIC Science & Technology

    2002-01-01

    characterize different catalytic conformations for chorismate mutase . Preliminary evidence for water binding in phosphotriesterase suggests that activity in...MD/QM study of the chorismate mutase catalyzed Claisen rearrangement reaction. 2001.subm. J.Phys.Chem.B 22.Day, P.N.J., J.H.; Gordon,M.S.; Webb,S.P...Claisen rearrangement of an unusual substrate in chorismate mutase . 2001.subm. J.Phys.Chem.B 38.Stevens, W.J., Basch,H., Krauss,M., Compact effective

  9. Multi-Orbit Ps-Insar for Landslide Monitoring in Three Gorges Area (Invited)

    NASA Astrophysics Data System (ADS)

    Liao, M.; Zhang, L.; Balz, T.; Shi, X.; Tantianuparp, P.

    2013-12-01

    The Three Gorges Project, the largest hydroelectric project of the world, became operational in 2003. The construction and operation of the dam significantly increased the number of active landslide bodies in the reservoir area. The reservoir area is huge, with approximately 600 km length along the Yangtze River starting from the dam at Sandouping in China's Hubei province. The dam itself was built on a rather geologically unstable zone, causing many concerns before, during, and after construction. Landslides are activated by the large surface-water level changes in each store-and-release cycle, but also by the construction of new buildings and roads and the deforestation in the area. Landslides are a huge safety concern in the area. To reduce the risks, various methods are applied in the area, such as a GPS networks and terrestrial surveillance. However, this sparse point information cannot cover the vast reservoir area. Furthermore, the area is densely vegetated and has a rough topography with steep mountainsides. Vast areas are practically inaccessible for terrestrial surveillance, due to the difficult terrain. Such a vast and inaccessible area is best to be surveyed using remote sensing techniques. Synthetic Aperture Radar (SAR) can measure long-term and continuous displacement trends using Differential Interferometric SAR (D-InSAR) and Persistent Scatterer Interferometry (PSI). However, the steep mountainside and the dense vegetation are also hindering the use of interferometric SAR techniques. The very dense vegetation causes a strong temporal decorrelation of the interferometric signal in the area. This especially affects shorter wavelength systems, like the X-band systems of TerraSAR-X and COSMO-SkyMed, but also the C-band systems. The longer wavelength L-band of ALOS PALSAR was less affected by the temporal decorrelation in the area, but unfortunately PALSAR is not operational anymore. The steep mountainsides also cause problems in the analysis of the

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

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    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.

  11. Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase

    PubMed Central

    Teixeira, Vitor H.; Baptista, António M.; Soares, Cláudio M.

    2006-01-01

    Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H2), but little is known about the diffusion of H2 toward the active site. Here we analyze pathways for H2 permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H2 easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H2 molecules that reach the active site made their approach from the side of the Ni ion. H2 is able to reach distances of <4 Å from the active site, although after 6 Å permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H2 inside the protein and at lower distances from the active site. This valine can be a control point in the H2 access to the active center. PMID:16731562

  12. Maintenance of plastid RNA editing activities independently of their target sites.

    PubMed

    Tillich, Michael; Poltnigg, Peter; Kushnir, Sergei; Schmitz-Linneweber, Christian

    2006-03-01

    RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.

  13. A Processive Carbohydrate Polymerase That Mediates Bifunctional Catalysis Using a Single Active Site

    PubMed Central

    May, John F.; Levengood, Matthew R.; Splain, Rebecca A.; Brown, Christopher D.; Kiessling, Laura L.

    2012-01-01

    Even in the absence of a template, glycosyltransferases can catalyze the synthesis of carbohydrate polymers of specific sequence. The paradigm has been that one enzyme catalyzes the formation of one type of glycosidic linkage, yet certain glycosyltransferases generate polysaccharide sequences composed of two distinct linkage types. In principle, bifunctional glycosyltransferases can possess separate active sites for each catalytic activity or one active site with dual activities. We encountered the fundamental question of one or two distinct active sites in our investigation of the galactosyltransferase GlfT2. GlfT2 catalyzes the formation of mycobacterial galactan, a critical cell-wall polymer composed of galactofuranose residues connected with alternating, regioisomeric linkages. We found that GlfT2 mediates galactan polymerization using only one active site that manifests dual regioselectivity. Structural modeling of the bifunctional glycosyltransferases hyaluronan synthase and cellulose synthase suggests that these enzymes also generate multiple glycosidic linkages using a single active site. These results highlight the versatility of glycosyltransferases for generating polysaccharides of specific sequence. We postulate that a hallmark of processive elongation of a carbohydrate polymer by a bifunctional enzyme is that one active site can give rise to two separate types of glycosidic bonds. PMID:22217153

  14. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors*

    PubMed Central

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M.; Kenny, Paul J.; Lindstrom, Jon

    2015-01-01

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets. PMID:25869137

  15. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  16. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    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... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  17. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...). (e) For all asbestos-containing waste material received, the owner or operator of the active waste... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  18. Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts.

    PubMed

    Zecchina, Adriano; Rivallan, Mickaël; Berlier, Gloria; Lamberti, Carlo; Ricchiardi, Gabriele

    2007-07-21

    Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed

  19. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    SciTech Connect

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; Nørskov, Jens K.; Studt, Felix

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidation reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.

  20. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    DOE PAGES

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; ...

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidationmore » reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.« less

  1. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    SciTech Connect

    Not Available

    1994-02-01

    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.

  2. The surface chemistry of heterogeneous catalysis: mechanisms, selectivity, and active sites.

    PubMed

    Zaera, Francisco

    2005-01-01

    The role of chemical kinetics in defining the requirements for the active sites of heterogeneous catalysts is discussed. A personal view is presented, with specific examples from our laboratory to illustrate the role of the chemical composition, structure, and electronic properties of specific surface sites in determining reaction activity and selectivity. Manipulation of catalytic behavior via the addition of chemical modifiers and by tuning of the reaction conditions is also introduced.

  3. Nuclear waste: Status of DOE`s nuclear waste site characterization activities

    SciTech Connect

    1987-12-31

    Three potential nuclear waste repository sites have been selected to carry out characterization activities-the detailed geological testing to determine the suitability of each site as a repository. The sites are Hanford in south-central Washington State, Yucca Mountain in southern Nevada, and Deaf Smith in the Texas Panhandle. Two key issues affecting the total program are the estimations of the site characterization completion data and costs and DOE`s relationship with the Nuclear Regulatory Commission which has been limited and its relations with affected states and Indian tribes which continue to be difficult.

  4. Number and locations of agonist binding sites required to activate homomeric Cys-loop receptors.

    PubMed

    Rayes, Diego; De Rosa, María José; Sine, Steven M; Bouzat, Cecilia

    2009-05-06

    Homo-pentameric Cys-loop receptors contain five identical agonist binding sites, each formed at a subunit interface. To determine the number and locations of binding sites required to generate a stable active state, we constructed a receptor subunit with a mutation that disables the agonist binding site and a reporter mutation that alters unitary conductance and coexpressed mutant and nonmutant subunits. Although receptors with a range of different subunit compositions are produced, patch-clamp recordings reveal that the amplitude of each single-channel opening event reports the number and, for certain subunit combinations, the locations of subunits with intact binding sites. We find that receptors with three binding sites at nonconsecutive subunit interfaces exhibit maximal mean channel open time, receptors with binding sites at three consecutive or two nonconsecutive interfaces exhibit intermediate open time, and receptors with binding sites at two consecutive or one interface exhibit brief open time. Macroscopic recordings after rapid application of agonist reveal that channel activation slows and the extent of desensitization decreases as the number of binding sites per receptor decreases. The overall results provide a framework for defining mechanisms of activation and drug modulation for homo-pentameric Cys-loop receptors.

  5. Influence of flocculation on sediment deposition process at the Three Gorges Reservoir.

    PubMed

    Wang, Dangwei; Liu, Xiaofang; Ji, Zuwen; Dong, Zhandi; Hu, Haihua

    2016-01-01

    By comparing the original particle gradation of sediment from the Three Gorges Reservoir with the single particle gradation, the differences in these two particle gradations showed that there is sediment flocculation in the Three Gorges Reservoir, which can accelerate the sediment deposition rate in the reservoir. In order to determine the influence of flocculation on the sediment settling velocity, sediment was collected at the Three Gorges Reservoir, and the indoor quiescent settling experiment was performed to study the mechanism of sediment flocculation. The experimental results showed that sediments aggregated from single particles into floccules in the settling processes. The single particles smaller than 0.022 mm will participate in the formation of floccules, which accounts for 83% of the total amount of sediment in the Three Gorges Reservoir. Moreover, the degree of sediment flocculation and the increase in sediment settling velocity were directly proportional to the sediment concentration. Taking the average particle size and the median particle size as the representative particle size, respectively, the maximum flocculation factors were calculated to be 3.4 and 5.0. Due to the sediment flocculation, the volume of sediment deposition will increase by 66% when the mass settling flux factor of total sediment had a maximum value of 1.66, suggesting that flocculation has a significant influence on the sediment deposition rate in the Three Gorges Reservoir.

  6. Evidence for early Pleistocene Glaciation(s) in tropical Africa: Stratigraphy, Paleomagnetism, Paleosols and Paleoclimate of the Gorges Moraine System, Mount Kenya

    NASA Astrophysics Data System (ADS)

    Mahaney, W. C.; Barendregt, R. W.; Hamilton, T.; Hancock, R.

    2011-12-01

    Moraines marking an Early Pleistocene glaciation on Mt. Kenya are known from several valleys marking the lowermost extent of the Early Pleistocene Gorges Glaciation (2850 m a.s.l.). The lowermost paleosols at these sites formed either in till predating the Gorges Glaciation or in weathered phonolitic bedrock and related lavas, similar to the lithology forming the base of the Mt. Kenya volcanic series of Miocene/Pliocene age. Paleomagnetism and weathering characteristics have been used to refine the age of sediments assigned to the Gorges Glaciation. These deposits are normally magnetized but carry a persistent reversed overprint, suggesting that they were deposited during one of the normal subchrons within the Matuyama Reversed Chron. They are underlain either by a reversely magnetized weathered till (GOR 68), or weathered bedrock (GOR 64 and GOR 69), the latter exhibiting normal magnetization (Gauss?) with reversed overprint (Matuyama?). The sediments are overlain at all three sites by normally magnetized loesses and paleosols of presumable Brunhes age. The normal magnetization and reversed overprint recorded in sediments of the Gorges Glaciation most likely span a considerable portion of the Olduvai subchron (1.78-1.950 Ma.), which persisted for sufficient time to accommodate an extensive montane glaciation and prolonged period of weathering and soil formation. While the somewhat younger Jaramillo subchron cannot be ruled out, the extensive sediment and weathering record is more easily accommodated within the longer-lived Olduvai subchron. The characteristics of the lowermost buried paleosols and weathered bedrock substrate indicate wetter conditions prior to the onset of Pleistocene glaciation, a period that initially may have fostered a higher elevation forest cover of substantial spatial extent. These wetter conditions, punctuated with dry events, depict a progressive transition to alpine grassland at the start of the Quaternary. In light of new paleomagnetic

  7. [Three-dimensional Fluorescence Spectral Characteristics of Different Molecular Weight Fractionations of Dissolved Organic Matter in the Water-level Fluctuation Zones of Three Gorges Reservoir Areas].

    PubMed

    Chen, Xue-shuang; Jiang, Tao; Lu, Song; Wei, Shi-qiang; Wang, Ding-yong; Yan, Jin-long

    2016-03-15

    The study of the molecular weight (MW) fractions of dissolved organic matter (DOM) in aquatic environment is of interests because the size plays an important role in deciding the biogeochemical characteristics of DOM. Thus, using ultrafiltration ( UF) technique combined with three-dimensional fluorescence spectroscopy, DOM samples from four sampling sites in typical water-level fluctuation zones of Three Gorge Reservoir areas were selected to investigate the differences of properties and sources of different DOM MW fractions. The results showed that in these areas, the distribution of MW fractions was highly dispersive, but the approximately equal contributions from colloidal (Mr 1 x 10³-0.22 µm) and true dissolved fraction (Mr < 1 x 10³) to the total DOC concentration were found. Four fluorescence signals (humic-like A and C; protein-like B and T) were observed in all MW fractions including bulk DOM, which showed the same distribution trend: true dissolved > low MW (Mr 1 x 10³-10 x 10³) > medium MW (Mr 10 x 10³-30 x 10³) > high MW (Mr 30 x 10³-0.22 µm). Additionally, with decreasing MW fraction, fluorescence index (FI) and freshness index (BIX) increased suggesting enhanced signals of autochthonous inputs, whereas humification index ( HIX) decreased indicating lowe humification degree. It strongly suggested that terrestrial input mainly affected the composition and property of higher MW fractions of DOM, as compared to lower MW and true dissolved fractions that were controlled by autochthonous sources such as microbial and alga activities, instead of allochthonous sources. Meanwhile, the riparian different land-use types also affected obviously on the characteristics of DOM. Therefore, higher diversity of land-use types, and also higher complexity of ecosystem and landscapes, induced higher heterogeneity of fluorescence components in different MW fraction of DOM.

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

    PubMed

    Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

    2015-04-21

    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 explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

  9. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    SciTech Connect

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B.; Sagi, Irit; Havenith, Martina

    2011-09-18

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

  10. Digital landscapes and Late Pleistocene environments of deglaciation: The use of LiDAR data to test outburst flood hypotheses of lowland river gorge formation

    NASA Astrophysics Data System (ADS)

    Thorndycraft, Varyl; Cripps, Jonathan; Passmore, Dave; Oldknow, Christopher; Eades, Gwilym

    2013-04-01

    We report on the quantitative interrogation of DEMs developed from airborne LiDAR data for the identification and reconstruction of Late Pleistocene glacial lake outburst floods (GLOFs). There is much importance attached to the quantification of geomorphic processes associated with deglaciation given global warming and current observations of rapidly melting glaciers and ice caps (e.g. Greenland). Given the period of direct observation is short, recourse can be made to the study of past ice sheets and associated landforms in order to reconstruct the rates and magnitudes of change during deglaciation. Meltwater channels, lakes and outflow channels are examples of landforms that can be used to identify the position, timing and retreat of former ice margins. With regards lake drainage there is a need to distinguish 'instantaneous' outburst floods from long term downcutting in order to improve our interpretations on the rates and magnitudes of geomorphic processes. There has been success in this regards at the megaflood scale but less attention has been paid to low magnitude outburst floods that can nevertheless have important regional implications for geomorphic processes. Here we use 5m DEMs and 2m resolution LiDAR data using ArcMap10, in combination with fieldwork, to investigate outflow channels in lowland environments of northern England, and develop methodological guidelines to aid the identification of GLOF events in previously glaciated landscapes. We identified a suite of distinguishing landforms from the 2m LiDAR data, not always identifiable in the 5m DEM, that indicate rapid erosion as opposed to long-term incision: 1) abandoned head cuts; 2) spillways representing sudden incision events once a downstream blockage has failed; 3) headcut extension of incised gorges upstream of the breach site; and 4) sedimentary deposits of 'chaotic' poorly sorted, water-lain sediments mapped at low elevations in the gorge; and run-up bars at higher elevations. All of these

  11. Two interacting binding sites for quinacrine derivatives in the active site of trypanothione reductase – a template for drug design

    PubMed Central

    Saravanamuthu, Ahilan; Vickers, Tim J.; Bond, Charles S.; Peterson, Mark R.; Hunter, William N.; Fairlamb, Alan H.

    2012-01-01

    SUMMARY Trypanothione reductase is a key enzyme in the trypanothione-based redox metabolism of pathogenic trypanosomes. Since this system is absent in humans, being replaced with glutathione and glutathione reductase, it offers a target for selective inhibition. The rational design of potent inhibitors requires accurate structures of enzyme-inhibitor complexes, but this is lacking for trypanothione reductase. We therefore used quinacrine mustard, an alkylating derivative of the competitive inhibitor quinacrine, to probe the active site of this dimeric flavoprotein. Quinacrine mustard irreversibly inactivates Trypanosoma cruzi trypanothione reductase, but not human glutathione reductase, in a time-dependent manner with a stoichiometry of two inhibitors bound per monomer. The rate of inactivation is dependent upon the oxidation state of trypanothione reductase, with the NADPH-reduced form being inactivated significantly faster than the oxidised form. Inactivation is slowed by clomipramine and a melarsen oxide-trypanothione adduct (both are competitive inhibitors) but accelerated by quinacrine. The structure of the trypanothione reductase-quinacrine mustard adduct was determined to 2.7 Å, revealing two molecules of inhibitor bound in the trypanothione-binding site. The acridine moieties interact with each other through π-stacking effects, and one acridine interacts in a similar fashion with a tryptophan residue. These interactions provide a molecular explanation for the differing effects of clomipramine and quinacrine on inactivation by quinacrine mustard. Synergism with quinacrine occurs as a result of these planar acridines being able to stack together in the active site cleft, thereby gaining an increased number of binding interactions, whereas antagonism occurs with non-planar molecules, such as clomipramine, where stacking is not possible. PMID:15102853

  12. The three Mycobacterium tuberculosis antigen 85 isoforms have unique substrates and activities determined by non-active site regions.

    PubMed

    Backus, Keriann M; Dolan, Michael A; Barry, Conor S; Joe, Maju; McPhie, Peter; Boshoff, Helena I M; Lowary, Todd L; Davis, Benjamin G; Barry, Clifton E

    2014-09-05

    The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro(216)-Phe(228) loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors.

  13. Kokanee Stock Status and Contribution of Cabinet Gorge Hatchery, Lake Pend Oreille, Idaho, 1987 Annual Progress Report.

    SciTech Connect

    Bowles, Edward C.

    1988-05-01

    Estimated kokanee Oncorhynchus nerka abundance in Lake Pend Oreille was 6.01 million during late summer 1987. This estimate is 40% higher than the 1986 estimate and is the second largest population estimate since 1977. Higher abundance is predominantly a result of enhanced fry survival and recruitment. Hatchery-reared fry contribution was 22% of total fry recruitment in 1987, compared to 8% in 1986, and resulted from a fivefold increase in survival. Much of this improvement can be attributed to the large (52 mm) fry produced at Cabinet Gorge Hatchery in 1987 and represents the first measurable contribution of the new hatchery to the kokanee rehabilitation program. Survival of hatchery-reared fry released into Clark Fork River was nearly one-half that of fry released into Sullivan Springs due to poor flow conditions and potentially high predation during migration from Cabinet Gorge Hatchery to Lake Pend Oreille. Wild fry survival was enhanced by early availability of forage (cladocern zooplankton) during fry emergence in late spring. Cladoceran production began three weeks earlier in 1987 than 1986, which resulted from reduced Mysis abundance and earlier thermal stratification of Lake Pend Oreille, which helped segregate cladocerans from mysid predation. Kokanee dry otolith coding was evaluated to provide a reliable long-term mark. Analysis of daily growth increments on otoliths was used successfully in 1987 to differentiate fry from various release sites. The technique will be refined during 1988 to include coding fry otoliths with water temperature fluctuations during hatchery residence. 23 refs., 20 figs., 2 tabs.

  14. [Distribution of Mercury in Plants at Water-Level-Fluctuating Zone in the Three Gorges Reservoir].

    PubMed

    Liang, Li; Wang, Yong-min; Li, Xian-yuan; Tang, Zhen-ya; Zhang, Xiang; Zhang, Cheng; WANG, Ding-yong

    2015-11-01

    The mercury (Hg) distribution and storage in plants at water-level-fluctuating zone (WLFZ) in the Three Gorges Reservoir were investigated by analyzing the total mercury(THg) and methylmercury ( MeHg) levels in different parts of plants collected from three typical sites including Shibaozhai, Zhenxi and Hanfeng Lake in WLFZ. The results indicated that THg and MeHg concentrations in plants ranged from (1.62 ± 0.57) to (49.42 ± 3.93) μg x kg(-1) and from (15.27 ± 7.09) to (1 974.67 ± 946.10) ng x kg(-1), respectively. In addition, THg levels in different plant parts followed the trend: root > leaf > stem, and similar trend for MeHg was observed with the highest level in root. An obvious spatial distribution was also found with the THg and MeHg levels in plants in Hanfeng higher than those in the same plants in the other two sampling sites (Shibaozhai and Zhenxi), and there was a difference of THg and MeHg storage in plants in various attitudes. The corresponding THg and MeHg storages were 145.3, 166.4, 124.3 and 88.2 mg x hm(-2), and 1.9, 2.7, 3.6 and 3.2 mg x hm(-2) in 145-150, 150-160, 160-170 and 170-175 m attitudes. The accumulation ability of dominant plants in WLFZ for THg (bioaccumulation factor, BAF < 1) was weaker than that for MeHg (BAF > 1).

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

    SciTech Connect

    Carra,J.; McHugh, C.; Mulligan, S.; Machiesky, L.; Soares, A.; Millard, C.

    2007-01-01

    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 geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding to a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.

  16. Amphitheater-headed canyons formed by megaflooding at Malad Gorge, Idaho.

    PubMed

    Lamb, Michael P; Mackey, Benjamin H; Farley, Kenneth A

    2014-01-07

    Many bedrock canyons on Earth and Mars were eroded by upstream propagating headwalls, and a prominent goal in geomorphology and planetary science is to determine formation processes from canyon morphology. A diagnostic link between process and form remains highly controversial, however, and field investigations that isolate controls on canyon morphology are needed. Here we investigate the origin of Malad Gorge, Idaho, a canyon system cut into basalt with three remarkably distinct heads: two with amphitheater headwalls and the third housing the active Wood River and ending in a 7% grade knickzone. Scoured rims of the headwalls, relict plunge pools, sediment-transport constraints, and cosmogenic ((3)He) exposure ages indicate formation of the amphitheater-headed canyons by large-scale flooding ∼46 ka, coeval with formation of Box Canyon 18 km to the south as well as the eruption of McKinney Butte Basalt, suggesting widespread canyon formation following lava-flow diversion of the paleo-Wood River. Exposure ages within the knickzone-headed canyon indicate progressive upstream younging of strath terraces and a knickzone propagation rate of 2.5 cm/y over at least the past 33 ka. Results point to a potential diagnostic link between vertical amphitheater headwalls in basalt and rapid erosion during megaflooding due to the onset of block toppling, rather than previous interpretations of seepage erosion, with implications for quantifying the early hydrosphere of Mars.

  17. Amphitheater-headed canyons formed by megaflooding at Malad Gorge, Idaho

    PubMed Central

    Lamb, Michael P.; Mackey, Benjamin H.; Farley, Kenneth A.

    2014-01-01

    Many bedrock canyons on Earth and Mars were eroded by upstream propagating headwalls, and a prominent goal in geomorphology and planetary science is to determine formation processes from canyon morphology. A diagnostic link between process and form remains highly controversial, however, and field investigations that isolate controls on canyon morphology are needed. Here we investigate the origin of Malad Gorge, Idaho, a canyon system cut into basalt with three remarkably distinct heads: two with amphitheater headwalls and the third housing the active Wood River and ending in a 7% grade knickzone. Scoured rims of the headwalls, relict plunge pools, sediment-transport constraints, and cosmogenic (3He) exposure ages indicate formation of the amphitheater-headed canyons by large-scale flooding ∼46 ka, coeval with formation of Box Canyon 18 km to the south as well as the eruption of McKinney Butte Basalt, suggesting widespread canyon formation following lava-flow diversion of the paleo-Wood River. Exposure ages within the knickzone-headed canyon indicate progressive upstream younging of strath terraces and a knickzone propagation rate of 2.5 cm/y over at least the past 33 ka. Results point to a potential diagnostic link between vertical amphitheater headwalls in basalt and rapid erosion during megaflooding due to the onset of block toppling, rather than previous interpretations of seepage erosion, with implications for quantifying the early hydrosphere of Mars. PMID:24344293

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

    SciTech Connect

    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.

  19. All the catalytic active sites of MoS2 for hydrogen evolution

    SciTech Connect

    Li, Guoqing; Zhang, Du; Qiao, Qiao; Yu, Yifei; Peterson, David; Zafar, Abdullah; Kumar, Raj; Curtarolo, Stefano; Hunte, Frank; Shannon, Steve; Zhu, Yimei; Yang, Weitao; Cao, Linyou

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5 s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.

  20. Three Gorges Reservoir Area: soil erosion under natural condition vs. soil erosion under current land use

    NASA Astrophysics Data System (ADS)

    Schönbrodt, Sarah; Behrens, Thorsten; Scholten, Thomas

    2010-05-01

    Apparently, the current most prominent human-induced example for large scale environmental impact is the Three Gorges Dam in China. The flooding alongside the Yangtze River, and its tributaries results in a vast loss of settlement and farmland area with productive, fertile valley soils. Due to the associated high land use dynamic on uphill-sites, the soil resources are underlying high land use pressure. Within our study, the soil erosion under natural conditions is compared to the soil erosion under current land use after the impoundment. Both were modeled using the empirical Universal Soil Loss Equation (USLE) which is able to predict long-term annual soil loss with limited data. The database consists of digital terrain data (45 m resolution DEM, erosive slope length based on Monte-Carlo-Aggregation according to Behrens et al. (2008)), field investigations of recent erosion forms, and literature studies. The natural disposition to soil erosion was calculated considering the USLE factors R, S, and K. The soil erosion under current land use was calculated taking into account all USLE factors. The study area is the catchment of the Xiangxi River in the Three Gorges Reservoir area. Within the Xiangxi Catchment (3,200 km²) the highly dynamic backwater area (580 km²), and two micro-scale study sites (Xiangjiaba with 2.8 km², and Quyuan with 88 km²) are considered more detailed as they are directly affected by the river impoundment. Central features of the Xiangxi Catchment are the subtropical monsoon climate, an extremely steep sloping relief (mean slope angle 39°, SD 22.8°) artificially fractured by farmland terraces, and a high soil erodibility (mean K factor 0.37, SD 0.13). On the catchment scale the natural disposition to soil erosion makes up to mean 518.0 t ha-1 a-1. The maximum potential soil loss of 1,730.1 t ha-1 a-1 under natural conditions is reached in the Quyuan site (mean 635.8 t ha-1 a-1) within the backwater area (mean 582.9 t ha-1 a-1). In the

  1. A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime.

    PubMed

    Legler, Patricia M; Soojhawon, Iswarduth; Millard, Charles B

    2015-09-01

    As part of ongoing efforts to design improved nerve agent antidotes, two X-ray crystal structures of Torpedo californica acetylcholinesterase (TcAChE) bound to the bis-pyridinium oxime, Ortho-7, or its experimental bis-imidazolium analogue, 2BIM-7, were determined. Bis-oximes contain two oxime groups connected by a hydrophobic linker. One oxime group of Ortho-7 binds at the entrance to the active-site gorge near Trp279, and the second binds at the bottom near Trp84 and Phe330. In the Ortho-7-TcAChE complex the oxime at the bottom of the gorge was directed towards the nucleophilic Ser200. In contrast, the oxime group of 2BIM-7 was rotated away from Ser200 and the oxime at the entrance induced a significant conformational change in the peripheral anionic site (PAS) residue Trp279. The conformational change alters the surface of the PAS and positions the imidazolium oxime of 2BIM-7 further from Ser200. The relatively weaker binding and poorer reactivation of VX-inhibited, tabun-inhibited or sarin-inhibited human acetylcholinesterase by 2BIM-7 compared with Ortho-7 may in part be owing to the unproductively bound states caught in crystallo. Overall, the reactivation efficiency of 2BIM-7 was comparable to that of 2-pyridine aldoxime methyl chloride (2-PAM), but unlike 2-PAM the bis-imidazolium oxime lacks a fixed charge, which may affect its membrane permeability.

  2. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  3. Monitoring Ground Surface Displacements in the Three Gorges Area, Crustal Tectonic Movement in Tibet and Subsidence in South China

    NASA Astrophysics Data System (ADS)

    Sun, L.; Muller, J.-P.; Singleton, A.; Li, Z.; Liu, D.; Riedel, B.; Niemeier, W.; Liang, C.; Zeng, Q.; Jiao, J.; Ye, Y.; Green, B.; Zhang, F.; Wang, Q.; Zhang, J.; Xiao, R.; He, X.; Xiong, S.

    2014-11-01

    During the first half of the DRAGON-3 project, various projects have been running through collaborations between research groups focusing on different geographical studies in the Three Gorges Region (3G), Tibet, Coal Mining areas in West China, Daduhe River and Southeast China. Stimulated by the interest and concerns of demonstrated and potential geo-hazards in the 3G Region, research has been undertaken focusing on deformation monitoring using SAR images with much higher spatial and temporal sampling. The use of different strategies including sub-Pixel Offset Tracking (sPOT) have been evaluated in challenging areas with steep slopes and dense vegetative cover. In addition to the development and validation of algorithms to improve previous attempts using InSAR, studies have been conducted on environmental impacts included mapping of subsidence caused by mining activities; assessment of building collapse after earthquakes using polarized SAR; landslide monitoring of a hydraulic engineering resettlement zone using GPS and InSAR, etc.

  4. [Zoning of water environment protection in Three Gorges Reservoir watershed].

    PubMed

    Wang, Li-jing; Xi, Chun-yan; Zheng, Bing-hui

    2011-04-01

    Regional differences in socio-economic development, land use, vegetation cover, and relative location of water body within a watershed bring about significant effects on the water environment quality of the watershed. Concerning about the core demands of water body protection, it is important and necessary to carry out zoning water environment protection for whole watershed. With a view to the spatial differences in regional characteristics of eco-environment and water body pressure-respond features, this paper studied the zoning of water environment protection in the Three Gorges Reservoir watershed, based on the methods of ecological factors overlay and ecological sensitivity analysis. The factors considered included hydrothermal conditions, terrain topography, administrative unit, and ecological sensitivity. Three regions in the watershed were zoned, i. e., 1) red region, namely strictly protected region, with an area of 2924 km2 and occupying 5.1% of the total; 2) yellow region, namely first class protection region, with an area of 10477 km2 and occupying 18.4%; and 3) blue region, namely second class protection region, with an area of 43599 km2 and occupying 76.5%. The key environmental problems of the regions were identified, and the strategies for the regions' development and water environment protection were proposed.

  5. Predictability of wind ramps in the Columbia River Gorge

    NASA Astrophysics Data System (ADS)

    Smith, C.

    2013-12-01

    Wind generation capacity in the Bonneville Power Administration (BPA) system, which stands at 4,500 MW currently, can at time account for 70% of total electricity demand. With 2,500 additional MW of wind generation capacity expected by 2015, increasingly accurate forecasts are required to avoid water quality issues associated with hydropower dam overspill. Wind ramps, or large increases or decreases in wind generation over a short period of time, are particularly difficult to accurately forecast in the Columbia River Gorge area. Industry standard computational resources, combined with turbulence grey-zone issues associated with planetary boundary (PBL) schemes, suggest a leveling off of numerical weather prediction (NWP) model skill score with respect to increasing grid resolution until eddy resolving scales are resolved. However, we show that dispersion errors, which associated with wind ramps, continue to decrease for locations and seasons in which meso-scale and topographically forced diurnal motions account for a significant portion of the power spectral density of hub-height wind speeds.

  6. China`s Three Gorges Dam: Mammoth opportunities - and risks

    SciTech Connect

    Maize, K.P.

    1996-05-01

    China is embarking on an infrastructure project of almost unimaginable proportions. If it succeeds, it will be one of the modern wonders of the world. If it fails, the Chinese government could be impoverished for a generation. The Three Gorges Dam represents an audacious gamble for infrastructure-starved China. Like some U.S. utilities in the 1970`s and 1980`s, China is taking a giant roll of the dice on a single generating project. If it succeeds, the dam will be one of the modern wonders of the world. If it fails, China`s government could be impoverished for a generation. The scope of the project is breathtaking. Designed for flood control, navigation and hydropower, the dam will rise 185 meters, spanning a two-kilometer gap and creating a reservoir that will reach 600 kilometers westward to Chongqing. Twin five stage ship locks will lift river boats with 10,000 tonnes of cargo capacity, tripling the size of the vessels that can reach Chongqing.

  7. Modeling the ecological impacts of Flaming Gorge Dam operations

    SciTech Connect

    Yin, S.C.L.; LaGory, K.E.; Hayse, J.W.; Hlohowskyj, I.; Van Lonkhuyzen, R.A.; Cho, H.E.

    1996-05-01

    Hydropower operations at Flaming Gorge Dam on the Green River in Utah, US, can produce rapid downstream changes in flow and stage during a day. These changes can, in turn, affect ecological resources below the dam, including riparian vegetation, trout, and endangered fish. Four hydropower operational scenarios featuring varying degrees of hydropower-induced flow fluctuation were evaluated with hydrologic models and multispectral aerial videography of the river. Year-round high fluctuations would support the least amount of stable spawning habitat for trout and nursery habitat for endangered fish, and would have the greatest potential for reducing growth and over winter survival of fish. Seasonally, adjusted moderate fluctuation and seasonally adjusted steady flow scenarios could increase food production and over winter survival and would provide the greatest amount of spawning and nursery habitat for fish. The year-round high fluctuation, seasonally adjusted high fluctuation, and seasonally adjusted moderate fluctuation scenarios would result in a 5% decrease in upper riparian zone habitat. the seasonally adjusted steady flow scenario would result in an 8% increase in upper riparian zone habitat. Lower riparian zone habitat would increase by about 17% for year-round and seasonally adjusted high fluctuating flow scenarios but decrease by about 24% and 69% for seasonally adjusted moderate fluctuating and steady flow scenarios, respectively.

  8. Acoustic Emission Parameters of Three Gorges Sandstone during Shear Failure

    NASA Astrophysics Data System (ADS)

    Xu, Jiang; Liu, Yixin; Peng, Shoujian

    2016-12-01

    In this paper, an experimental investigation of sandstone samples from the Three Gorges during shear failure was conducted using acoustic emission (AE) and direct shear tests. The AE count rate, cumulative AE count, AE energy, and amplitude of the sandstone samples were determined. Then, the relationships among the AE signals and shearing behaviors of the samples were analyzed in order to detect micro-crack initiation and propagation and reflect shear failure. The results indicated that both the shear strength and displacement exhibited a logarithmic relationship with the displacement rate at peak levels of stress. In addition, the various characteristics of the AE signals were apparent in various situations. The AE signals corresponded with the shear stress under different displacement rates. As the displacement rate increased, the amount of accumulative damage to each specimen decreased, while the AE energy peaked earlier and more significantly. The cumulative AE count primarily increased during the post-peak period. Furthermore, the AE count rate and amplitude exhibited two peaks during the peak shear stress period due to crack coalescence and rock bridge breakage. These isolated cracks later formed larger fractures and eventually caused ruptures.

  9. Long-distance carcass transport at Olduvai Gorge? A quantitative examination of Bed I skeletal element abundances.

    PubMed

    Faith, J Tyler; Domínguez-Rodrigo, Manuel; Gordon, Adam D

    2009-03-01

    Relative abundances of skeletal elements at Plio-Pleistocene archaeological sites have long been interpreted to represent selective transport of portions of large prey. Models from optimal foraging theory suggest that the degree of carcass transport selectivity reflects transport constraints, particularly transport distance. A quantitative analysis of skeletal element abundances in five bone assemblages from Bed I, Olduvai Gorge, indicates that within the subset of elements most likely to resist attritional processes, there is no evidence for preferential transport of small or large mammals. The results suggest relatively low carcass transport costs and are most consistent with site formation models favoring short-distance carcass transport. The data are also consistent with the possibility that hominins were not responsible for transporting bones at some sites. Several Bed I assemblages, with the exception of FLK-Zinjanthropus, lack evidence of a functional relationship between flaked stone artifacts and the faunal remains, such as cut-marks or percussion-marks on bone. In conjunction with the skeletal part data, this suggests that hominin involvement with the bone assemblages was minimal at all sites but FLK-Zinjanthropus. The patterning at Bed I contrasts strongly with Middle Stone Age and Middle Paleolithic assemblages, which provide clear evidence for selective transport, suggesting higher transport costs and longer transport distances.

  10. Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet.

    PubMed

    Wang, Ping; Scherler, Dirk; Liu-Zeng, Jing; Mey, Jürgen; Avouac, Jean-Philippe; Zhang, Yunda; Shi, Dingguo

    2014-11-21

    The Himalayan mountains are dissected by some of the deepest and most impressive gorges on Earth. Constraining the interplay between river incision and rock uplift is important for understanding tectonic deformation in this region. We report here the discovery of a deeply incised canyon of the Yarlung Tsangpo River, at the eastern end of the Himalaya, which is now buried under more than 500 meters of sediments. By reconstructing the former valley bottom and dating sediments at the base of the valley fill, we show that steepening of the Tsangpo Gorge started at about 2 million to 2.5 million years ago as a consequence of an increase in rock uplift rates. The high erosion rates within the gorge are therefore a direct consequence of rapid rock uplift.

  11. Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet

    NASA Astrophysics Data System (ADS)

    Wang, Ping; Scherler, Dirk; Liu-Zeng, Jing; Mey, Jürgen; Avouac, Jean-Philippe; Zhang, Yunda; Shi, Dingguo

    2014-11-01

    The Himalayan mountains are dissected by some of the deepest and most impressive gorges on Earth. Constraining the interplay between river incision and rock uplift is important for understanding tectonic deformation in this region. We report here the discovery of a deeply incised canyon of the Yarlung Tsangpo River, at the eastern end of the Himalaya, which is now buried under more than 500 meters of sediments. By reconstructing the former valley bottom and dating sediments at the base of the valley fill, we show that steepening of the Tsangpo Gorge started at about 2 million to 2.5 million years ago as a consequence of an increase in rock uplift rates. The high erosion rates within the gorge are therefore a direct consequence of rapid rock uplift.

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

    SciTech Connect

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    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.

  13. Synergistic effect between defect sites and functional groups on the hydrolysis of cellulose over activated carbon.

    PubMed

    Foo, Guo Shiou; Sievers, Carsten

    2015-02-01

    The chemical oxidation of activated carbon by H2 O2 and H2 SO4 is investigated, structural and chemical modifications are characterized, and the materials are used as catalysts for the hydrolysis of cellulose. Treatment with H2 O2 enlarges the pore size and imparts functional groups such as phenols, lactones, and carboxylic acids. H2 SO4 treatment targets the edges of carbon sheets primarily, and this effect is more pronounced with a higher temperature. Adsorption isotherms demonstrate that the adsorption of oligomers on functionalized carbon is dominated by van der Waals forces. The materials treated chemically are active for the hydrolysis of cellulose despite the relative weakness of most of their acid sites. It is proposed that a synergistic effect between defect sites and functional groups enhances the activity by inducing a conformational change in the glucan chains if they are adsorbed at defect sites. This activates the glycosidic bonds for hydrolysis by in-plane functional groups.

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

    PubMed Central

    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 fluorescence results were in agreement and both paralleled enzymatic activity of papain with respect to both the variation in pH and denaturation. These results strongly suggest that SL-PMB and Acrylodan labels can be used to characterize the physical state of the active site of the enzyme. PMID:1657229

  15. Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site

    PubMed Central

    Ma, Yi; Zhang, Beilei; Wang, Meng; Ou, Yanghui

    2016-01-01

    The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) with 5′-3′ DNA polymerase activity while in absence of 5′-3′ exonuclease activity possesses high thermal stability and polymerase activity. Bst DNA polymerase was employed in isothermal multiple self-matching initiated amplification (IMSA) which amplified the interest sequence with high selectivity and was widely applied in the rapid detection of human epidemic diseases. However, the detailed information of commercial Bst DNA polymerase is unpublished and well protected by patents, which makes the high price of commercial kits. In this study, wild-type Bst DNA polymerase (WT) and substitution mutations for improving the efficiency of DNA polymerization were expressed and purified in E. coli. Site-directed substitutions of four conserved residues (Gly310, Arg412, Lys416, and Asp540) in the activity site of Bst DNA polymerase influenced efficiency of polymerizing dNTPs. The substitution of residue Gly310 by alanine or leucine and residue Asp540 by glutamic acid increased the efficiency of polymerase activity. All mutants with higher polymerizing efficiency were employed to complete the rapid detection of EV71-associated hand, foot, and mouth disease (HFMD) by IMSA approach with relatively shorter period which is suitable for the primary diagnostics setting in rural and underdeveloped areas. PMID:27981047

  16. Geomorphic evolution of the Yangtze Gorges and the time of their formation

    NASA Astrophysics Data System (ADS)

    Li, Jijun; Xie, Shiyou; Kuang, Mingsheng

    2001-11-01

    The Three Gorges of the Yangtze link its upper rocky valley to downstream alluvial sections. A series of stepped landforms exist in the Three Gorges area, the Sichuan Basin upstream and the Jianghan Basin downstream. These landforms are characterized by two planation surfaces, one erosional surface, and up to seven terraces. The higher planation surface (named the Exi Surface, ~1800-2000 m a.s.l.) and the lower planation surface (1200-1500 m) were probably formed in the Tertiary (prior to 3.4-3.6 Ma B.P.). No correlation seems to exist between the drainage networks of earlier period with the present Yangtze system. It is suggested that the erosional surface found in the study area at 800-1200 m in elevation above sea level was formed in Late Pliocene of Early Pleistocene. During this period following the last planation event, the ancestral Yangtze might have begun to adjust its drainage network. The seven terraces, well developed along the eastern Sichuan Basin and the Three Gorges, date from Early to Late Pleistocene (1.16-0.01 Ma B.P). The chronostratigraphic evidence and diagnostic sediments are generally comparable in time and space from the Sichuan Basin, through the Three Gorges, to the Jianghan Basin. Therefore, the present study proposes that the Three Gorges were cut not later than the initiation of the earliest terrace. The fluvial landforms in the Yangtze Gorges are characterized also by valley-in-valley cross-sections, i.e. an older U-shaped valley cut by a younger V-shaped valley. A tectonic rise accompanied by a rapid downcutting of the river channels predominated in the region.

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

    PubMed

    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.

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

    PubMed

    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.

  19. Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen

    PubMed Central

    Phillips, John D.; Warby, Christy A.; Whitby, Frank G.; Kushner, James P.; Hill, Christopher P.

    2009-01-01

    Summary 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 the four acetate side chains on 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 (scURO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposible with wild-type activity and have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of scURO-D resulted in approximately half of wild-type activity. The distribution of reaction intermediates was the same for mutant and wild-type sequences, and was unaltered in a competition experiment using the 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 create a large active site cleft. PMID:19362562

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

    SciTech Connect

    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.

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

    SciTech Connect

    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

    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.

  2. Transcriptional activation by LR1 at the Eµ enhancer and switch region sites

    PubMed Central

    Hanakahi, L. A.; Maizels, Nancy

    2000-01-01

    LR1 is a B cell-specific, sequence-specific duplex DNA binding activity which is induced in B cells carrying out class switch recombination. Here we identify several properties of LR1 which enable it to function in transcriptional regulation. We show that LR1 contributes to transcriptional activation by the Eµ immunoglobulin heavy chain intron enhancer by binding to a site within the enhancer core. We further show that LR1 bends DNA upon binding. In addition, we show that LR1 is itself a bona fide transcriptional activator, as multimerized LR1 sites produce an element which can enhance transcription from a minimal promoter. In order for class switch recombination to occur, an activating signal must be transmitted via the Eµ core, and both S regions targeted for recombination must be actively transcribed. The properties of LR1 that we have identified suggest distinct potential functions of LR1 duplex DNA binding activity in class switch recombination. First, LR1 may contribute to recombinational activation by the Eµ core. Second, there are multiple potential LR1 duplex binding sites in each of the G-rich switch regions, and LR1 bound at contiguous sites may enhance recombination by stimulating transcription of the S regions. PMID:10908319

  3. Regulation of Dpp activity by tissue-specific cleavage of an upstream site within the prodomain

    PubMed Central

    Sopory, Shailaja; Kwon, Sunjong; Wehrli, Marcel; Christian, Jan L.

    2010-01-01

    BMP4 is synthesized as an inactive precursor that is cleaved at two sites during maturation: initially at a site (S1) adjacent to the ligand domain, and then at an upstream site (S2) within the prodomain. Cleavage at the second site regulates the stability of mature BMP4 and this in turn influences its signaling intensity and range of action. The Drosophila ortholog of BMP4, Dpp, functions as a long- or short-range signaling molecule in the wing disc or embryonic midgut, respectively but mechanisms that differentially regulate its bioactivity in these tissues have not been explored. In the current studies we demonstrate, by dpp mutant rescue, that cleavage at the S2 site of proDpp is required for development of the wing and leg imaginal discs, whereas cleavage at the S1 site is sufficient to rescue Dpp function in the midgut. Both the S1 and S2 site of proDpp are cleaved in the wing disc, and S2-cleavage is essential to generate sufficient ligand to exceed the threshold for pMAD activation at both short- and long-range in most cells. By contrast, proDpp is cleaved at the S1 site alone in the embryonic mesoderm and this generates sufficient ligand to activate physiological target genes in neighboring cells. These studies provide the first biochemical and genetic evidence that that selective cleavage of the S2 site of proDPP provides a tissue-specific mechanism for regulating Dpp activity, and that differential cleavage can contribute to, but is not an absolute determinant of signaling range. PMID:20659445

  4. Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR).

    PubMed

    Menon, Binuraj R K; Hardman, Samantha J O; Scrutton, Nigel S; Heyes, Derren J

    2016-08-01

    Protochlorophyllide oxidoreductase (POR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), an essential, regulatory step in chlorophyll biosynthesis. The unique requirement of the enzyme for light has provided the opportunity to investigate how light energy can be harnessed to power biological catalysis and enzyme dynamics. Excited state interactions between the Pchlide molecule and the protein are known to drive the subsequent reaction chemistry. However, the structural features of POR and active site residues that are important for photochemistry and catalysis are currently unknown, because there is no crystal structure for POR. Here, we have used static and time-resolved spectroscopic measurements of a number of active site variants to study the role of a number of residues, which are located in the proposed NADPH/Pchlide binding site based on previous homology models, in the reaction mechanism of POR. Our findings, which are interpreted in the context of a new improved structural model, have identified several residues that are predicted to interact with the coenzyme or substrate. Several of the POR variants have a profound effect on the photochemistry, suggesting that multiple residues are important in stabilizing the excited state required for catalysis. Our work offers insight into how the POR active site geometry is finely tuned by multiple active site residues to support enzyme-mediated photochemistry and reduction of Pchlide, both of which are crucial to the existence of life on Earth.

  5. Valencia gorge: possible Messinian refill channel for the western Mediterranean Sea

    USGS Publications Warehouse

    Field, M.E.; Gardner, J.V.

    1991-01-01

    A deeply incised gorge is buried nearly 800 m beneath the floor of the Valencia Trough in the western Mediterranean Sea. The gorge is steeply cut more than 200 m into Messinian evaporite deposits and has been mapped for more than 40 km. Published and unpublished seismic profiles show the total length to be nearly 300 km. It may have been connected near Valencia with the Betic Strait, the portal in southern Spain proposed to link the Atlantic and the western Mediterranean. -from Authors

  6. An Electromagnetic Interference Study of Potential Transmitter Sites for the HF Active Auroral Research Program (HAARP)

    DTIC Science & Technology

    1993-07-19

    heating . The measurements described in this report were conducted at a number of candidate HAARP transmitter sites in the vicinity of Fairbanks...employ the High Power Auroral Stimulation (HIPAS) RF heating facility [1], located in the Chena River valley area near Fairbanks. HAARP will be an...Potential Transmitter Sites for the HF Active Auroral Research Program ( HAARP ) JOSEP11 A. GOLDSTEIN EDWARD 1. KENNEDY ADRIAN S. ELEY 4 IMICHlAEL A. RuPAR C

  7. Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues.

    PubMed

    Kuhn, Isabelle; Kellenberger, Esther; Cakir-Kiefer, Céline; Muller-Steffner, Hélène; Schuber, Francis

    2014-07-01

    Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.

  8. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy.

    PubMed

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-09-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides.

  9. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  10. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.

    PubMed

    Wang, Beibei; Sexton, Rachel E; Feig, Michael

    2017-04-01

    During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.

  11. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

    PubMed Central

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-01-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides. PMID:27704049

  12. Gamma exposure rates due to neutron activation of soil: site of Hood detonation, Operation Plumbbob

    SciTech Connect

    Auxier, J.A.; Ohnesorge, W.F.

    1980-06-01

    This paper is the result of some recent discussions of exposure rates within the first few hours of the Hood detonation of the Plumbbob series due to neutron activation of soil. We estimated the exposure rates from 1/2 to 3 h after the detonation from ground zero to 1000 yards from ground zero. The area was assumed to be uncontaminated by fallout. Soil samples from the area of the Nevada Test Site at which the Hood device was detonated were sent to ORNL by Dr. John Malik of Los Alamos and by Mr. Gordon Jacks of the Nevada Test Site. These samples were irradiated at the DOSAR facility and the resulting activity analyzed. Calculations of exposure rates were then made based on the analyzed activity and the measured thermal neutron fluences at DOSAR and at the Hood Site.

  13. Systematic mutagenesis of the active site omega loop of TEM-1 beta-lactamase.

    PubMed Central

    Petrosino, J F; Palzkill, T

    1996-01-01

    Beta-Lactamase is a bacterial protein that provides resistance against beta-lactam antibiotics. TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Normally, this enzyme has high levels of hydrolytic activity for penicillins, but mutant beta-lactamases have evolved with activity toward a variety of beta-lactam antibiotics. It has been shown that active site substitutions are responsible for changes in the substrate specificity. Since mutant beta-lactamases pose a serious threat to antimicrobial therapy, the mechanisms by which mutations can alter the substrate specificity of TEM-1 beta-lactamase are of interest. Previously, screens of random libraries encompassing 31 of 55 active site amino acid positions enabled the identification of the residues responsible for maintaining the substrate specificity of TEM-1 beta-lactamase. In addition to substitutions found in clinical isolates, many other specificity-altering mutations were also identified. Interestingly, many nonspecific substitutions in the N-terminal half of the active site omega loop were found to increase ceftazidime hydrolytic activity and decrease ampicillin hydrolytic activity. To complete the active sight study, eight additional random libraries were constructed and screened for specificity-altering mutations. All additional substitutions found to alter the substrate specificity were located in the C-terminal half of the active site loop. These mutants, much like the N-terminal omega loop mutants, appear to be less stable than the wild-type enzyme. Further analysis of a 165-YYG-167 triple mutant, selected for high levels of ceftazidime hydrolytic activity, provides an example of the correlation which exists between enzyme instability and increased ceftazidime hydrolytic activity in the ceftazidime-selected omega loop mutants. PMID:8606154

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

    PubMed

    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.

  15. A mutational analysis of the active site of human type II inosine 5'-monophosphate dehydrogenase.

    PubMed

    Futer, Olga; Sintchak, Michael D; Caron, Paul R; Nimmesgern, Elmar; DeCenzo, Maureen T; Livingston, David J; Raybuck, Scott A

    2002-01-31

    The oxidation of IMP to XMP is the rate-limiting step in the de novo synthesis of guanine ribonucleotides. This NAD-dependent reaction is catalyzed by the enzyme inosine monophosphate dehydrogenase (IMPDH). Based upon the recent structural determination of IMPDH complexed to oxidized IMP (XMP*) and the potent uncompetitive inhibitor mycophenolic acid (MPA), we have selected active site residues and prepared mutants of human type II IMPDH. The catalytic parameters of these mutants were determined. Mutations G326A, D364A, and the active site nucleophile C331A all abolish enzyme activity to less than 0.1% of wild type. These residues line the IMP binding pocket and are necessary for correct positioning of the substrate, Asp364 serving to anchor the ribose ring of the nucleotide. In the MPA/NAD binding site, significant loss of activity was seen by mutation of any residue of the triad Arg322, Asn303, Asp274 which form a hydrogen bonding network lining one side of this pocket. From a model of NAD bound to the active site consistent with the mutational data, we propose that these resides are important in binding the ribose ring of the nicotinamide substrate. Additionally, mutations in the pair Thr333, Gln441, which lies close to the xanthine ring, cause a significant drop in the catalytic activity of IMPDH. It is proposed that these residues serve to deliver the catalytic water molecule required for hydrolysis of the cysteine-bound XMP* intermediate formed after oxidation by NAD.

  16. Tool-using strategies by early hominids at bed II, Olduvai Gorge, Tanzania.

    PubMed

    Kimura, Y

    1999-12-01

    This study examines the current prevailing model of Oldowan technology-the opportunistic, least-effort strategy of stone tool making and using by early hominids. The sample includes the MNK chert factory site and three contemporaneous assemblages from Olduvai Gorge, all dated between 1.65 and 1.53 m.y.a. The analysis suggests that early hominids at Olduvai may have been selective, applying distinctive strategies in making and using tools depending on the different types of raw materials available to them. The preponderance of lava cores and near absence of flakes associated with the cores suggest that lava cores at Olduvai did not provide a source of flakes. They were primarily heavy-duty core tools, despite the fact that the majority of Olduvai lava is of excellent quality for flaking. Contrary to this pattern, the abundance of chert flakes and the lack of large chert cores suggest that the production of flakes was the most important strategy applied to chert. Original forms and flaking mechanics of the raw materials may have been important factors in the simultaneous application of the different, complementary strategies. The Oldowan tool-using strategy was dynamic and flexible, in response to changes in raw material availability. The use of chert between 1.65 and 1.53 m.y.a. was apparently related to the drastic decrease in flake production in lava and quartz. Finally, lack of initial reduction episodes of lava material challenges the idea of the stone cache strategy at Olduvai between 1.65 to 1.53 m.y.a.

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

    SciTech Connect

    Fitzner, R.E.; Weiss, S.G.; Stegen, J.A.

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  19. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation.

    PubMed

    Immormino, Robert M; Silversmith, Ruth E; Bourret, Robert B

    2016-10-04

    Two-component regulatory systems, minimally composed of a sensor kinase and a response regulator protein, are common mediators of signal transduction in microorganisms. All response regulators contain a receiver domain with conserved active site residues that catalyze the signal activating and deactivating phosphorylation and dephosphorylation reactions. We explored the impact of variable active site position T+1 (one residue C-terminal to the conserved Thr/Ser) on reaction kinetics and signaling fidelity, using wild type and mutant Escherichia coli CheY, CheB, and NarL to represent the three major sequence classes observed across response regulators: Ala/Gly, Ser/Thr, and Val/Ile/Met, respectively, at T+1. Biochemical and structural data together suggested that different amino acids at T+1 impacted reaction kinetics by altering access to the active site while not perturbing overall protein structure. A given amino acid at position T+1 had similar effects on autodephosphorylation in each protein background tested, likely by modulating access of the attacking water molecule to the active site. Similarly, rate constants for CheY autophosphorylation with three different small molecule phosphodonors were consistent with the steric constraints on access to the phosphorylation site arising from combination of specific phosphodonors with particular amino acids at T+1. Because other variable active site residues also influence response regulator phosphorylation biochemistry, we began to explore how context (here, the amino acid at T+2) affected the influence of position T+1 on CheY autocatalytic reactions. Finally, position T+1 affected the fidelity and kinetics of phosphotransfer between sensor kinases and response regulators but was not a primary determinant of their interaction.

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

    NASA Astrophysics Data System (ADS)

    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.

    2016-08-01

    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.

  1. Seasonal succession of phytoplankton in response to the variation of environmental factors in the Gaolan River, Three Gorges Reservoir, China

    NASA Astrophysics Data System (ADS)

    Peng, Chengrong; Zhang, Lang; Zheng, Yangzhong; Li, Dunhai

    2013-07-01

    To understand the responses of a freshwater ecosystem to the impoundment of the Three Gorges Reservoir (TGR), phytoplankton was monitored in the tributaries of the TGR area. From August 2010 to July 2011, algal species composition, abundance, chlorophyll a and other environmental parameters were investigated in the Gaolan River, which is a tributary of Xiangxi River. Thirty-one algal genera from seven phyla were identified. Results show that the lowest concentrations of total phosphorus (TP) and total nitrogen (TN) were 0.06 mg/L and 1.08 mg/L, respectively. The values of TP and TN exceeded the threshold concentration of the eutrophic state suggested for freshwater bodies. In the Gaolan River, the succession of phytoplankton showed clear seasonal characteristics. Different dominant species were observed among seasons under the control of environment factors. In spring and summer, the dominant species were Nitzschia sp. and Aphanizomenon flos-aquae (L.) Ralfs, the limiting nutrient was NO{3/-}-N, and the key environmental factor for phytoplankton population succession was water temperature (WT). In autumn and winter, the dominant species were A. flos-aquae and Chlorella sp., the limiting nutrient was PO{4/3-}-P, and the key environmental factors were transparency and WT. This study illustrates the influence of physical and chemical factors on phytoplankton seasonal succession in a tributary of TGR since the downstream regions of Xiangxi River and Gaolan River became reservoirs after impoundment of the Three Gorges Dam. We suggest that this activity has significantly affected water quality in the dam area.

  2. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri.

    PubMed

    Dutta, Saheb; Nandi, Nilashis

    2015-08-27

    Aminoacyl tRNA synthetases (aaRSs) carry out the first step of protein biosynthesis. Several aaRSs are multimeric, and coordination between the dynamics of active sites present in each monomer is a prerequisite for the fast and accurate aminoacylation. However, important lacunae of understanding exist concerning the conformational dynamics of multimeric aaRSs. Questions remained unanswered pertaining to the dynamics of the active site. Little is known concerning the conformational dynamics of the active sites in response to the substrate binding, reorganization of the catalytic residues around reactants, time-dependent changes at the reaction center, which are essential for facilitating the nucleophilic attack, and interactions at the interface of neighboring monomers. In the present work, we carried out all-atom molecular dynamics simulation of dimeric (mk)SerRS from Methanopyrus kandleri bound with tRNA using an explicit solvent system. Two dimeric states of seryl tRNA synthetase (open, substrate bound, and adenylate bound) and two monomeric states (open and substrate bound) are simulated with bound tRNA. The aim is to understand the conformational dynamics of (mk)SerRS during its reaction cycle. While the present results provide a clear dynamical perspective of the active sites of (mk)SerRS, they corroborate with the results from the time-averaged experimental data such as crystallographic and mutation analysis of methanogenic SerRS from M. kandleri and M. barkeri. It is observed from the present simulation that the motif 2 loop gates the active site and its Glu351 and Arg360 stabilizes ATP in a bent state favorable for nucleophilic attack. The flexibility of the walls of the active site gradually reduces near reaction center, which is a more organized region compared to the lid region. The motif 2 loop anchors Ser and ATP using Arg349 in a hydrogen bonded geometry crucial for nucleophilic attack and favorably influences the electrostatic potential at the

  3. Paleoenvironmental and paleoecological reconstruction of a freshwater oasis in savannah grassland at FLK North, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Ashley, Gail M.; Barboni, Doris; Dominguez-Rodrigo, Manuel; Bunn, Henry T.; Mabulla, Audax Z. P.; Diez-Martin, Fernando; Barba, Rebeca; Baquedano, Enrique

    2010-11-01

    The records of early hominins are commonly localized both temporally and spatially even in archaeologically rich basins like Olduvai Gorge, Tanzania. The FLK North site was discovered in 1960, but the reason for the exact location of this dense concentration of fossils and stone tools on a lake-margin flat has not been explained. We present new geological and geochemical information from six excavations in upper Bed I, which revealed up to 1.4-m-thick carbonate deposits, attesting to the presence of freshwater springs in the area surrounding FLK North. The δ 18O signatures of the tufa are typical for meteoric water that has evolved during evaporation. Tuff IF that caps the sequence was deposited on uneven topography with the highest area a low-relief ridge between two faults at the archaeological site and lowest areas being sites of groundwater discharge. The model proposed here is that rainfall on adjacent highlands was transported to the basin where faults acted as conduits for water. Similar hydrogeological settings at modern lakes Manyara and Eyasi, currently support lush groundwater forest and woodland despite arid climate. FLK North may have been an "oasis" offering freshwater and shelter for consuming meat by both carnivores and hominins.

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

    SciTech Connect

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

    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.

  5. Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase.

    PubMed

    Collman, James P; Decréau, Richard A

    2008-11-07

    A functional analog of the active site in the respiratory enzyme, cytochrome c oxidase (CcO) reproduces every feature in CcO's active site: a myoglobin-like heme (heme a3), a distal tridentate imidazole copper complex (Cu(B)), a phenol (Tyr244), and a proximal imidazole. When covalently attached to a liquid-crystalline SAM film on an Au electrode, this functional model continuously catalyzes the selective four-electron reduction of dioxygen at physiological potential and pH, under rate-limiting electron flux (as occurs in CcO).

  6. New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase

    PubMed Central

    Cecchini, Davide A; Serra, Immacolata; Ubiali, Daniela; Terreni, Marco; Albertini, Alessandra M

    2007-01-01

    Background Immobilized Penicillin G Acylase (PGA) derivatives are biocatalysts that are industrially used for the hydrolysis of Penicillin G by fermentation and for the kinetically controlled synthesis of semi-synthetic β-lactam antibiotics. One of the most used supports for immobilization is glyoxyl-activated agarose, which binds the protein by reacting through its superficial Lys residues. Since in E. coli PGA Lys are also present near the active site, an immobilization that occurs through these residues may negatively affect the performance of the biocatalyst due to the difficult diffusion of the substrate into the active site. A preferential orientation of the enzyme with the active site far from the support surface would be desirable to avoid this problem. Results Here we report how it is possible to induce a preferential orientation of the protein during the binding process on aldehyde activated supports. A superficial region of PGA, which is located on the opposite side of the active site, is enriched in its Lys content. The binding of the enzyme onto the support is consequently forced through the Lys rich region, thus leaving the active site fully accessible to the substrate. Different mutants with an increasing number of Lys have been designed and, when active, immobilized onto glyoxyl agarose. The synthetic performances of these new catalysts were compared with those of the immobilized wild-type (wt) PGA. Our results show that, while the synthetic performance of the wt PGA sensitively decreases after immobilization, the Lys enriched mutants have similar performances to the free enzyme even after immobilization. We also report the observations made with other mutants which were unable to undergo a successful maturation process for the production of active enzymes or which resulted toxic for the host cell. Conclusion The desired orientation of immobilized PGA with the active site freely accessible can be obtained by increasing the density of Lys residues

  7. Wetland Diagenesis and Traces of Early Hominids, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Deocampo, Daniel M.; Blumenschine, Robert J.; Ashley, Gail M.

    2002-03-01

    Lateral variations in whole-rock and clay geochemistry of basal Bed II claystones in Olduvai Gorge, Tanzania, reflect water quality differences across the Eastern Lacustrine Plain ∼1.75 myr ago. Bulk Ba/Sr and (Na2O+K2O+MgO)/Al2O3 range from 1.4 to 4.2 and from 0.7 to 1.4, respectively, and indicate leaching of lacustrine claystones beneath freshwater wetlands at times following lake retreat. Bulk MgO/Al2O3 (0.3-1.0) and molar Mg/Al (0.5-3.9) ratios of <0.2-μm clays reflect alteration of Mg-rich lacustrine clays. These indicators point to freshest conditions near Locality 43 of Hay (1976; HWK-East; Leakey, 1971), moderate conditions to the east (Locality 40-MCK), and high salinity and alkalinity to the west (Localities 85-VEK, 45-FLK). Clay geochemistry and artifact abundances are well correlated (r=-0.67, p<0.005), suggesting a relationship between paleo-water quality and hominid paleoecology. This pattern is consistent with predictions of greatest artifact discard/loss around freshwater sources where scavanging opportunities were greatest for hominids. This quantifies a relationship between artifact density distribution and a paleoecological proxy over landscape scales for the first time in Early Stone Age archaeology. In contrast, fossil bone abundance is uncorrelated (r=0.14, p=0.6), reflecting more complex taphonomic processes. Quantitative tests of landscape-scale land-use models are important for understanding early hominid behavior and its evolution.

  8. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

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

    PubMed Central

    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 Thr998 in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr890, Ser893 and Thr894) 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, Thr890, Ser893, Thr894 and Thr899, 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

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

    PubMed

    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.

  11. Kv3 channel assembly, trafficking and activity are regulated by zinc through different binding sites.

    PubMed

    Gu, Yuanzheng; Barry, Joshua; Gu, Chen

    2013-05-15

    Zinc, a divalent heavy metal ion and an essential mineral for life, regulates synaptic transmission and neuronal excitability via ion channels. However, its binding sites and regulatory mechanisms are poorly understood. Here, we report that Kv3 channel assembly, localization and activity are regulated by zinc through different binding sites. Local perfusion of zinc reversibly reduced spiking frequency of cultured neurons most likely by suppressing Kv3 channels. Indeed, zinc inhibited Kv3.1 channel activity and slowed activation kinetics, independent of its site in the N-terminal T1 domain. Biochemical assays surprisingly identified a novel zinc-binding site in the Kv3.1 C-terminus, critical for channel activity and axonal targeting, but not for the zinc inhibition. Finally, mutagenesis revealed an important role of the junction between the first transmembrane (TM) segment and the first extracellular loop in sensing zinc. Its mutant enabled fast spiking with relative resistance to the zinc inhibition. Therefore, our studies provide novel mechanistic insights into the multifaceted regulation of Kv3 channel activity and localization by divalent heavy metal ions.

  12. Active-Site Monovalent Cations Revealed in a 1.55 Å Resolution Hammerhead Ribozyme Structure

    PubMed Central

    Anderson, Michael; Schultz, Eric P.; Martick, Monika; Scott, William G.

    2013-01-01

    We have obtained a 1.55 Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni in conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical to that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest resolution ribozyme structure in the protein data bank. PMID:23711504

  13. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites.

    PubMed

    Colombo, Matteo; Girard, Eric; Franzetti, Bruno

    2016-02-08

    TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn(2+), hyperthermophilic TETs prefers Co(2+). Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.

  14. Fluvial incision into bedrock: Insights from morphometric analysis and numerical modeling of gorges incising glacial hanging valleys (Western Alps, France)

    NASA Astrophysics Data System (ADS)

    Valla, Pierre G.; van der Beek, Peter A.; Lague, Dimitri

    2010-06-01

    Bedrock gorges incising glacial hanging valleys potentially allow measurements of fluvial bedrock incision in mountainous relief. Using digital elevation models, topographic maps, and field reconnaissance, we identified and characterized 30 tributary hanging valleys incised by gorges near their confluence with trunk streams in the Romanche watershed, French Western Alps. Longitudinal profiles of these tributaries are all convex and have abrupt knickpoints at the upper limit of oversteepened gorge reaches. We reconstructed initial glacial profiles from glacially polished bedrock knobs surrounding the gorges in order to quantify the amount of fluvial incision and knickpoint retreat. From morphometric analyses, we find that mean channel gradients and widths, as well as knickpoint retreat rates, display a drainage area dependence modulated by bedrock lithology. However, there appears to be no relation between horizontal retreat and vertical downwearing of knickpoints. Assuming a postglacial origin of these gorges, our results imply high postglacial fluvial incision (0.5-15 mm yr-1) and knickpoint retreat (1-200 mm yr-1) rates that are, however, consistent with previous estimates. Numerical modeling was used to test the capacity of different fluvial incision models to predict the inferred evolution of the gorges. Results from simple end-member models suggest transport-limited behavior of the bedrock gorges. A more sophisticated model including dynamic width adjustment and sediment-dependent incision rates predicts present-day channel geometry only if a significant supply of sediment from the gorge sidewalls (˜10 mm yr-1) is triggered by gorge deepening, combined with pronounced inhibition of bedrock incision by sediment transport and deposition.

  15. Docking and molecular dynamics studies at trypanothione reductase and glutathione reductase active sites.

    PubMed

    Iribarne, Federico; Paulino, Margot; Aguilera, Sara; Murphy, Miguel; Tapia, Orlando

    2002-05-01

    A theoretical docking study on the active sites of trypanothione reductase (TR) and glutathione reductase (GR) with the corresponding natural substrates, trypanothione disulfide (T[S]2) and glutathione disulfide (GSSG), is reported. Molecular dynamics simulations were carried out in order to check the robustness of the docking results. The energetic results are in agreement with previous experimental findings and show the crossed complexes have lower stabilization energies than the natural ones. To test DOCK3.5, four nitro furanic compounds, previously designed as potentially active anti-chagasic molecules, were docked at the GR and TR active sites with the DOCK3.5 procedure. A good correlation was found between differential inhibitory activity and relative interaction energy (affinity). The results provide a validation test for the use of DOCK3.5 in connection with the design of anti-chagasic drugs.

  16. The Short-Term Impact of Involuntary Migration in China's Three Gorges: A Prospective Study

    ERIC Educational Resources Information Center

    Hwang, Sean-Shong; Cao, Yue; Xi, Juan

    2011-01-01

    The aim of this study is to measure the short-term impact of involuntary migration resulting from China's Three Gorges Dam project on the 1.3 million persons being displaced. We focus on the social, economic, and mental and physical health impact using three sets of indicators. Using a prospective research design, we gathered information about…

  17. Spatial Forecast of Landslides in Three Gorges Based On Spatial Data Mining

    PubMed Central

    Wang, Xianmin; Niu, Ruiqing

    2009-01-01

    The Three Gorges is a region with a very high landslide distribution density and a concentrated population. In Three Gorges there are often landslide disasters, and the potential risk of landslides is tremendous. In this paper, focusing on Three Gorges, which has a complicated landform, spatial forecasting of landslides is studied by establishing 20 forecast factors (spectra, texture, vegetation coverage, water level of reservoir, slope structure, engineering rock group, elevation, slope, aspect, etc). China-Brazil Earth Resources Satellite (Cbers) images were adopted based on C4.5 decision tree to mine spatial forecast landslide criteria in Guojiaba Town (Zhigui County) in Three Gorges and based on this knowledge, perform intelligent spatial landslide forecasts for Guojiaba Town. All landslides lie in the dangerous and unstable regions, so the forecast result is good. The method proposed in the paper is compared with seven other methods: IsoData, K-Means, Mahalanobis Distance, Maximum Likelihood, Minimum Distance, Parallelepiped and Information Content Model. The experimental results show that the method proposed in this paper has a high forecast precision, noticeably higher than that of the other seven methods. PMID:22573999

  18. EPA Will Remove Contaminated Soil at Ithaca Falls Creek Gorge, N.Y.

    EPA Pesticide Factsheets

    (New York, N.Y) The U.S. Environmental Protection Agency will remove lead contaminated soil this month at a property between the base of a cliff wall and a walkway at the Falls Creek Gorge in Ithaca, N.Y.

  19. The Three Gorges Dam of China: Technology to Bridge Two Centuries

    ERIC Educational Resources Information Center

    Wahby, Wafeek S.

    2003-01-01

    Some of the most sophisticated 20th-century technologies have been applied to build the largest hydroelectric dam in the world, the Three Gorges Dam Project (TGDP) of China. The author administered a study abroad course in China from May 27 to June 10, 2000, to study the massive project as it approached the halfway mark of its second and most…

  20. Spatial forecast of landslides in three gorges based on spatial data mining.

    PubMed

    Wang, Xianmin; Niu, Ruiqing

    2009-01-01

    The Three Gorges is a region with a very high landslide distribution density and a concentrated population. In Three Gorges there are often landslide disasters, and the potential risk of landslides is tremendous. In this paper, focusing on Three Gorges, which has a complicated landform, spatial forecasting of landslides is studied by establishing 20 forecast factors (spectra, texture, vegetation coverage, water level of reservoir, slope structure, engineering rock group, elevation, slope, aspect, etc). China-Brazil Earth Resources Satellite (Cbers) images were adopted based on C4.5 decision tree to mine spatial forecast landslide criteria in Guojiaba Town (Zhigui County) in Three Gorges and based on this knowledge, perform intelligent spatial landslide forecasts for Guojiaba Town. All landslides lie in the dangerous and unstable regions, so the forecast result is good. The method proposed in the paper is compared with seven other methods: IsoData, K-Means, Mahalanobis Distance, Maximum Likelihood, Minimum Distance, Parallelepiped and Information Content Model. The experimental results show that the method proposed in this paper has a high forecast precision, noticeably higher than that of the other seven methods.

  1. Hydrothermal alteration of the Ediacaran Doushantuo Formation in the Yangtze Gorges area (South China)

    NASA Astrophysics Data System (ADS)

    Derkowski, Arkadiusz; Bristow, Thomas F.; Wampler, J. M.; Środoń, Jan; Marynowski, Leszek; Elliott, W. Crawford; Chamberlain, C. Page

    2013-04-01

    The geochemical and fossil record preserved in the Ediacaran age (635-551 Ma) Doushantuo Formation of South China has been extensively examined to explore the impact of changing climate and the oxidation state of the oceans on the development and distribution of early multicellular life. In the Yangtze Gorges area, this formation shows many of the geochemical trends and features thought to typify global ocean chemistry in the Ediacaran Period, but there are indications that post-sedimentary processes modified these signals. This study of clay minerals and organic matter builds a more detailed picture of the type and degree of post-sedimentary alteration at different stratigraphic levels of the formation and focuses on how this alteration influenced stable carbon and oxygen isotope records. In the cratonward Jiulongwan and Huajipo sections of the Doushantuo Formation, its lower part (Members 1 and 2) consists largely of dolomitic shale, rich in authigenic saponite that crystallized in an alkaline sedimentary basin. Saponite has been altered to chlorite via corrensite across tens of meters of strata in lower Member 2, with increased alteration downward toward the cap dolostone. The greater chloritization is accompanied by lower δ18O and higher δD values of trioctahedral clays. This pattern of alteration of trioctahedral clays is likely due to hydrothermal fluid activity in the underlying, relatively permeable Nantuo Formation and cap dolostone. A concomitant increase of solid bitumen reflectance toward the base of the formation supports this idea. In the uppermost part of the formation in the Yangtze Gorges area (Member 4), a typical open water marine dolomitic shale rich in illite and organic matter, increases in the methylphenanthrenes ratio index and solid bitumen reflectance correlate with decrease of the bulk rock K/Al ratio upward, providing evidence for hot fluid migration above the nearly impermeable shale. Clay from the upper part of the formation is

  2. Active layer dynamics in three sites with contrasted topography in the Byers Peninsula (Livingston Island, Antarctica)

    NASA Astrophysics Data System (ADS)

    Oliva, Marc; Ruiz-Fernández, Jesús; Vieira, Gonçalo

    2015-04-01

    Topography exerts a key role on permafrost distribution in areas where mean annual temperatures are slightly negative. This is the case of low-altitude environments in Maritime Antarctica, namely in the South Shetland Islands, where permafrost is marginal to discontinuous until elevations of 20-40 m asl turning to continuous at higher areas. Consequently, the active layer dynamics is also strongly conditioned by the geomorphological setting. In January 2014 we installed three sites for monitoring the active layer dynamics across the Byers Peninsula (Livingston Island, South Shetland Islands) in different geomorphological environments at elevations between 60 and 100 m. The purpose was to examine the role of the topography and microclimatic conditions on the active layer dynamics. At each site a set of loggers was set up to monitor: air temperatures, snow thickness, ground temperatures until 80 cm together with the coupling atmosphere-ground temperatures. During the first year of monitoring the mean annual air temperatures show similar values in the three sites, in all cases slightly below freezing. The snowy conditions during this year in this archipelago have resulted in a late melting of snow, which has also conditioned the duration of frozen conditions in the uppermost soil layers. Topography has a strong influence on snow cover duration, which in turn affects frozen ground conditions. The Domo site is located in a higher position with respect to the central plateau of Byers; here, the wind is stronger and snow cover thinner, which has conditioned a longer thawing season than in the other two sites (Cerro Negro, Escondido). These two sites are located in topographically protected areas favouring snow accumulation. The longer persistence of snow conditions a longer duration of negative temperatures in the active layer of the permafrost. This research was financially supported by the HOLOANTAR project (Portuguese Science Foundation) and the AXA Research Fund.

  3. 78 FR 8190 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF THE INTERIOR 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...

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

    ERIC Educational Resources Information Center

    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…

  5. Penicillin Use in Meningococcal Disease Management: Active Bacterial Core Surveillance Sites, 2009

    PubMed Central

    Blain, Amy E.; Mandal, Sema; Wu, Henry; MacNeil, Jessica R.; Harrison, Lee H.; Farley, Monica M.; Lynfield, Ruth; Miller, Lisa; Nichols, Megin; Petit, Sue; Reingold, Arthur; Schaffner, William; Thomas, Ann; Zansky, Shelley M.; Anderson, Raydel; Harcourt, Brian H.; Mayer, Leonard W.; Clark, Thomas A.; Cohn, Amanda C.

    2016-01-01

    In 2009, in the Active Bacterial Core surveillance sites, penicillin was not commonly used to treat meningococcal disease. This is likely because of inconsistent availability of antimicrobial susceptibility testing and ease of use of third-generation cephalosporins. Consideration of current practices may inform future meningococcal disease management guidelines. PMID:27704009

  6. 77 FR 5830 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-06

    ... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the Atlantic... of involving Federal agencies, states, tribes, local governments, offshore wind energy developers, and the public in the Department of the Interior's (DOI) ``Smart from the Start'' wind...

  7. Penicillin Use in Meningococcal Disease Management: Active Bacterial Core Surveillance Sites, 2009.

    PubMed

    Blain, Amy E; Mandal, Sema; Wu, Henry; MacNeil, Jessica R; Harrison, Lee H; Farley, Monica M; Lynfield, Ruth; Miller, Lisa; Nichols, Megin; Petit, Sue; Reingold, Arthur; Schaffner, William; Thomas, Ann; Zansky, Shelley M; Anderson, Raydel; Harcourt, Brian H; Mayer, Leonard W; Clark, Thomas A; Cohn, Amanda C

    2016-09-01

    In 2009, in the Active Bacterial Core surveillance sites, penicillin was not commonly used to treat meningococcal disease. This is likely because of inconsistent availability of antimicrobial susceptibility testing and ease of use of third-generation cephalosporins. Consideration of current practices may inform future meningococcal disease management guidelines.

  8. The active site of cytochrome P-450 nifedipine oxidase: a model-building study.

    PubMed

    Ferenczy, G G; Morris, G M

    1989-12-01

    A model of the active site of cytochrome P-450 nifedipine oxidase is built on the basis of sequence homology with cytochrome P-450CAM. Substrates are docked into the binding pocket, and molecular mechanical energy minimization is performed to analyze the forces between the substrates and the enzyme.

  9. 77 FR 74218 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-13

    ... identified in the document entitled, Commercial Leasing for Wind Power on the Outer Continental Shelf... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the Atlantic... agencies, states, tribes, local governments, offshore wind energy developers, and the public in...

  10. Archaeological Activity Report: Post-Review Discoveries Within 45BN431 at Solid Waste Site 128-F-2

    SciTech Connect

    T. E. Marceau; J. J. Sharpe

    2006-12-21

    During monitoring of remedial activities at Solid Waste Site 128-F-2 on August 19, 2005, a concentration of mussel shell was discovered in the west wall of a trench in the northen section of the waste site.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Kinetic and Spectroscopic Studies of Bicupin Oxalate Oxidase and Putative Active Site Mutants

    PubMed Central

    Moomaw, Ellen W.; Hoffer, Eric; Moussatche, Patricia; Salerno, John C.; Grant, Morgan; Immelman, Bridget; Uberto, Richard; Ozarowski, Andrew; Angerhofer, Alexander

    2013-01-01

    Ceriporiopsis subvermispora oxalate oxidase (CsOxOx) is the first bicupin enzyme identified that catalyzes manganese-dependent oxidation of oxalate. In previous work, we have shown that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated. CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC) and the 241-244DASN region of the N-terminal Mn binding domain of CsOxOx is analogous to the lid region of OxDC that has been shown to determine reaction specificity. We have prepared a series of CsOxOx mutants to probe this region and to identify the carboxylate residue implicated in catalysis. The pH profile of the D241A CsOxOx mutant suggests that the protonation state of aspartic acid 241 is mechanistically significant and that catalysis takes place at the N-terminal Mn binding site. The observation that the D241S CsOxOx mutation eliminates Mn binding to both the N- and C- terminal Mn binding sites suggests that both sites must be intact for Mn incorporation into either site. The introduction of a proton donor into the N-terminal Mn binding site (CsOxOx A242E mutant) does not affect reaction specificity. Mutation of conserved arginine residues further support that catalysis takes place at the N-terminal Mn binding site and that both sites must be intact for Mn incorporation into either site. PMID:23469254

  13. Transfer hydrogenation over sodium-modified ceria: Enrichment of redox sites active for alcohol dehydrogenation

    DOE PAGES

    Nelson, Nicholas C.; Boote, Brett W.; Naik, Pranjali; ...

    2017-01-17

    Ceria (CeO2) and sodium-modified ceria (Ce-Na) were prepared through combustion synthesis. Palladium was deposited onto the supports (Pd/CeO2 and Pd/Ce-Na) and their activity for the aqueous-phase transfer hydrogenation of phenol using 2-propanol under liquid flow conditions was studied. Pd/Ce-Na showed a marked increase (6×) in transfer hydrogenation activity over Pd/CeO2. Material characterization indicated that water-stable sodium species were not doped into the ceria lattice, but rather existed as subsurface carbonates. Modification of ceria by sodium provided more adsorption and redox active sites (i.e. defects) for 2-propanol dehydrogenation. This effect was an intrinsic property of the Ce-Na support and independent ofmore » Pd. The redox sites active for 2-propanol dehydrogenation were thermodynamically equivalent on both supports/catalysts. At high phenol concentrations, the reaction was limited by 2-propanol adsorption. Furthermore, the difference in catalytic activity was attributed to the different numbers of 2-propanol adsorption and redox active sites on each catalyst.« less

  14. The effects of overwinter flowson the spring condition of rainbow and brown trout size classes in the Green River downstream of Flaming Gorge Dam, Utah.

    SciTech Connect

    Magnusson, A. K.; LaGory, K. E.; Hayse, J. W.; Environmental Science Division

    2010-06-25

    Flaming Gorge Dam, a hydroelectric facility operated by the Bureau of Reclamation (Reclamation), is located on the Green River in Daggett County, northeastern Utah. Until recently, and since the early 1990s, single daily peak releases or steady flows have been the operational pattern of the dam during the winter period. However, releases from Flaming Gorge Reservoir followed a double-peak pattern (two daily flow peaks) during the winters of 2006-2007 and 2008-2009. Because there is little recent long-term history of double-peaking at Flaming Gorge Dam, the potential effects of double-peaking operations on trout body condition in the dam's tailwater are not known. A study plan was developed that identified research activities to evaluate potential effects from winter double-peaking operations (Hayse et al. 2009). Along with other tasks, the study plan identified the need to conduct a statistical analysis of historical trout condition and macroinvertebrate abundance to evaluate the potential effects of hydropower operations. The results from analyses based on the combined size classes of trout (85-630 mm) were presented in Magnusson et al. (2008). The results of this earlier analysis suggested possible relationships between trout condition and flow, but concern that some of the relationships resulted from size-based effects (e.g., apparent changes in condition may have been related to concomitant changes in size distribution, because small trout may have responded differently to flow than large trout) prompted additional analysis of within-size class relationships. This report presents the results of analyses of three different size classes of trout (small: 200-299 mm, medium: 300-399 mm, and large: {ge}400 mm body length). We analyzed historical data to (1) describe temporal patterns and relationships among flows, benthic macroinvertebrate abundance, and condition of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in the tailwaters of Flaming

  15. Site-directed mutagenesis of the Anabaena sp. strain PCC 7120 nitrogenase active site to increase photobiological hydrogen production.

    PubMed

    Masukawa, Hajime; Inoue, Kazuhito; Sakurai, Hidehiro; Wolk, C Peter; Hausinger, Robert P

    2010-10-01

    Cyanobacteria use sunlight and water to produce hydrogen gas (H₂), which is potentially useful as a clean and renewable biofuel. Photobiological H₂ arises primarily as an inevitable by-product of N₂ fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In Anabaena sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H₂ production by this strain, six nitrogenase amino acid residues predicted to reside within 5 Å of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N₂. Most of the 49 variants examined were deficient in N₂-fixing growth and exhibited decreases in their in vivo rates of acetylene reduction. Of greater interest, several variants examined under an N₂ atmosphere significantly increased their in vivo rates of H₂ production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H₂ compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H₂ in an aerobic, nitrogen-containing environment.

  16. Site-specific profiles of estrogenic activity in agricultural areas of California's inland waters.

    PubMed

    Lavado, Ramon; Loyo-Rosales, Jorge E; Floyd, Emily; Kolodziej, Edward P; Snyder, Shane A; Sedlak, David L; Schlenk, Daniel

    2009-12-15

    To evaluate the occurrence and sources of compounds capable of feminizing fish in agriculturally impacted waterways of the Central Valley of California, water samples were extracted and subjected to chemical analyses as well as in vitro and in vivo measurements of vitellogenin in juvenile rainbow trout (Oncorhynchus mykiss). Among the 16 sites sampled, 6 locations frequently exhibited elevated concentrations of estrogenic substances with 17beta-estradiol equivalents up to 242 ng/L in vitro and 12 microg/kg in vivo. The patterns of activity varied among sites, with two sites showing elevated activity only in vitro, two showing elevated activity only in vivo, and two showing elevated activity in both assays. Sequential elution of solid-phase extraction (SPE) disks followed by bioassay-guided fractionation was used to characterize water samples from the two locations where activity was observed in both bioassays. The highest estrogenic activity was observed in the most nonpolar fractions (80-100% methanol eluent) from the Napa River, while most of the activity in the Sacramento River Delta eluted in the 60% methanol eluent. Quantitative analyses of SPE extracts and additional HPLC fractionation of the SPE extracts by GC-MS/MS and LC-MS/MS indicated concentrations of steroid hormones, alkylphenol polyethoxylates, and herbicides that were at least 1-3 orders of magnitude below bioassay 17beta-estradiol equivalent calculations. Given the different patterns of activity and chemical properties of the estrogenic compounds, it appears that estrogenic activity in these agriculturally impacted surface waters is attributable to multiple compounds. Further investigation is needed to identify the compounds causing the estrogenic activity and to determine the potential impacts of these compounds on feral fish.

  17. Regional Impact of Climate on Japanese Encephalitis in Areas Located near the Three Gorges Dam

    PubMed Central

    Mao, Deqiang; Luo, Chao; He, Yuanyuan; Liang, Guodong; Lu, Bo; Bisesi, Michael S.; Sun, Qinghua; Xu, Xinyi; Yang, Weizhong; Liu, Qiyong

    2014-01-01

    Background In this study, we aim to identify key climatic factors that are associated with the transmission of Japanese encephalitis virus in areas located near the Three Gorges Dam, between 1997 and 2008. Methods We identified three geographical regions of Chongqing, based on their distance from the Three Gorges Dam. Collectively, the three regions consisted of 12 districts from which study information was collected. Zero-Inflated Poisson Regression models were run to identify key climatic factors of the transmission of Japanese encephalitis virus for both the whole study area and for each individual region; linear regression models were conducted to examine the fluctuation of climatic variables over time during the construction of the Three Gorges Dam. Results Between 1997 and 2008, the incidence of Japanese encephalitis decreased throughout the entire city of Chongqing, with noticeable variations taking place in 2000, 2001 and 2006. The eastern region, which is closest to the Three Gorges Dam, suffered the highest incidence of Japanese encephalitis, while the western region experienced the lowest incidence. Linear regression models revealed that there were seasonal fluctuations of climatic variables during this period. Zero-Inflated Poisson Regression models indicated a significant positive association between temperature (with a lag of 1 and 3 months) and Japanese encephalitis incidence, and a significant negative association between rainfall (with a lag of 0 and 4 months) and Japanese encephalitis incidence. Conclusion The spatial and temporal trends of Japanese encephalitis incidence that occurred in the City of Chongqing were associated with temperature and rainfall. Seasonal fluctuations of climatic variables during this period were also observed. Additional studies that focus on long-term data collection are needed to validate the findings of this study and to further explore the effects of the Three Gorges Dam on Japanese encephalitis and other related

  18. Evaluation of laboratory test method for determining the potential alkali contribution from aggregate and the ASR safety of the Three-Gorges dam concrete

    SciTech Connect

    Lu Duyou . E-mail: duyoulu@njut.edu.cn; Zhou, Xiaoling; Xu Zhongzi; Lan Xianghui; Tang Mingshu; Fournier, Benoit

    2006-06-15

    The releasable alkali from granite, which was used in the Three-Gorges concrete dam project in China, and from gneiss and feldspar was estimated by extraction in distilled water and super-saturated Ca(OH){sub 2} solution. Results show that: i) the finer the particles and the higher the temperature, the greater and faster the release of alkali; ii) compared with extraction by distilled water, super-saturated Ca(OH){sub 2} solution had a stronger activation on feldspar than on granite and gneiss; iii) for the three rocks tested, thermal activation had the largest effect on gneiss and a lower and similar effect on granite and feldspar. For very fine particles, temperature had a similar effect on the release of alkali by all three rocks. Because the aggregate used in the Three-Gorges dam concrete is non-reactive and a low calcium fly ash was used in the concrete, ASR would not be an issue for the dam, despite the release of alkali from the aggregate into the concrete.

  19. Site-directed mutagenesis of an alkaline phytase: influencing specificity, activity and stability in acidic milieu.

    PubMed

    Tran, Thuy T; Mamo, Gashaw; Búxo, Laura; Le, Nhi N; Gaber, Yasser; Mattiasson, Bo; Hatti-Kaul, Rajni

    2011-07-10

    Site-directed mutagenesis of a thermostable alkaline phytase from Bacillus sp. MD2 was performed with an aim to increase its specific activity and activity and stability in an acidic environment. The mutation sites are distributed on the catalytic surface of the enzyme (P257R, E180N, E229V and S283R) and in the active site (K77R, K179R and E227S). Selection of the residues was based on the idea that acid active phytases are more positively charged around their catalytic surfaces. Thus, a decrease in the content of negatively charged residues or an increase in the positive charges in the catalytic region of an alkaline phytase was assumed to influence the enzyme activity and stability at low pH. Moreover, widening of the substrate-binding pocket is expected to improve the hydrolysis of substrates that are not efficiently hydrolysed by wild type alkaline phytase. Analysis of the phytase variants revealed that E229V and S283R mutants increased the specific activity by about 19% and 13%, respectively. Mutation of the active site residues K77R and K179R led to severe reduction in the specific activity of the enzyme. Analysis of the phytase mutant-phytate complexes revealed increase in hydrogen bonding between the enzyme and the substrate, which might retard the release of the product, resulting in decreased activity. On the other hand, the double mutant (K77R-K179R) phytase showed higher stability at low pH (pH 2.6-3.0). The E227S variant was optimally active at pH 5.5 (in contrast to the wild type enzyme that had an optimum pH of 6) and it exhibited higher stability in acidic condition. This mutant phytase, displayed over 80% of its initial activity after 3h incubation at pH 2.6 while the wild type phytase retained only about 40% of its original activity. Moreover, the relative activity of this mutant phytase on calcium phytate, sodium pyrophosphate and p-nitro phenyl phosphate was higher than that of the wild type phytase.

  20. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase*

    PubMed Central

    Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W.

    2016-01-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites. PMID:26893379

  1. Multiple DNA binding activities of the novel site-specific recombinase, Piv, from Moraxella lacunata.

    PubMed

    Tobiason, D M; Lenich, A G; Glasgow, A C

    1999-04-02

    The recombinase, Piv, is essential for site-specific DNA inversion of the type IV pilin DNA segment in Moraxella lacunata and Moraxella bovis. Piv shows significant homology with the transposases of the IS110/IS492 family of insertion elements, but, surprisingly, Piv contains none of the conserved amino acid motifs of the lambda Int or Hin/Res families of site-specific recombinases. Therefore, Piv may mediate site-specific recombination by a novel mechanism. To begin to determine how Piv may assemble a synaptic nucleoprotein structure for DNA cleavage and strand exchange, we have characterized the interaction of Piv with the DNA inversion region of M. lacunata. Gel shift and nuclease/chemical protection assays, competition and dissociation rate analyses, and cooperativity studies indicate that Piv binds two distinct recognition sequences. One recognition sequence, found at multiple sites within and outside of the invertible segment, is bound by Piv protomers with high affinity. The second recognition sequence is located at the recombination cross-over sites at the ends of the invertible element; Piv interacts with this sequence as an oligomer with apparent low affinity. A model is proposed for the role of the different Piv binding sites of the M. lacunata inversion region in the formation of an active synaptosome.

  2. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase.

    PubMed

    Kalamajski, Sebastian; Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W

    2016-04-08

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites.

  3. Use of single-grain geochemistry of cryptic tuffs and volcaniclastic sandstones improves the tephrostratigraphic framework of Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    McHenry, Lindsay J.; Stollhofen, Harald; Stanistreet, Ian G.

    2013-09-01

    Single-grain geochemical composition of volcaniclastic sandstones can be a potential tool to improve correlations of mixed pyroclastic/epiclastic deposits. To test this, trachytic tuffs of the paleoanthropologically important FLK, FLK N, and FLK NN sites of Pleistocene Olduvai Gorge Bed I (Tanzania) are used as an established tephrostratigraphic framework against which to test volcaniclastic sandstone correlations. Fluvio-lacustrine sandstones and tuff samples were collected from eight archeological trenches between Tuffs IB and ID across a 500-m transect, including Leakey's famous Zinjanthropus (FLK) and OH 7/OH 8 (FLK NN) sites. A previously unknown, thin, fine, mineralogically unique, black trachyandesitic fallout ash was discovered below Tuff IC. Compositions of individual augite, feldspar and titanomagnetite grains from sandstones between Tuffs IB and IC reveal some IB-equivalent material, and a new compositional assemblage distinct from the sandwiching marker tuffs. Mineral compositions of the "tripartite" volcaniclastic sandstone between Tuffs IC and ID are similar to ID. Volcaniclastic sandstone grain fingerprints further refine correlations between fluvio-lacustrine sections within the area, providing support for proposed high-resolution stratigraphic reconstruction of the Zinjanthropus and OH 7/OH 8 land surfaces. This method might be applied to other sections where pyroclastic particles are admixed but distinct tuffs are not preserved.

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

    PubMed Central

    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 the level and type of activity influences forelimb muscle architecture of spinodeltoideus, acromiodeltoideus, and superficial pectoralis, bone growth rate and gross morphology of their insertion sites. Over an 11-week period, we collected data on activity levels in one control group and two experimental activity groups (running, climbing) of female wild-type mice. Our results show that both activity type and level increased bone growth rates influenced muscle architecture, including differences in potential muscular excursion (fibre length) and potential force production (physiological cross-sectional area). However, despite significant influences on muscle architecture and bone development, activity had no observable effect on enthesis morphology. These results suggest that the gross morphology of entheses is less reliable than internal bone structure for making inferences about an individual’s past behaviour. PMID:25467113

  5. Roles of s3 site residues of nattokinase on its activity and substrate specificity.

    PubMed

    Wu, Shuming; Feng, Chi; Zhong, Jin; Huan, Liandong

    2007-09-01

    Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.

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

    PubMed

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

    2015-01-01

    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 the level and type of activity influences forelimb muscle architecture of spinodeltoideus, acromiodeltoideus, and superficial pectoralis, bone growth rate and gross morphology of their insertion sites. Over an 11-week period, we collected data on activity levels in one control group and two experimental activity groups (running, climbing) of female wild-type mice. Our results show that both activity type and level increased bone growth rates influenced muscle architecture, including differences in potential muscular excursion (fibre length) and potential force production (physiological cross-sectional area). However, despite significant influences on muscle architecture and bone development, activity had no observable effect on enthesis morphology. These results suggest that the gross morphology of entheses is less reliable than internal bone structure for making inferences about an individual's past behaviour.

  7. Interaction of aspartic acid-104 and proline-287 with the active site of m-calpain.

    PubMed Central

    Arthur, J S; Elce, J S

    1996-01-01

    In an ongoing study of the mechanisms of calpain catalysis and Ca(2+)-induced activation, the effects of Asp-104-->Ser and Pro-287-->Ser large subunit mutations on m-calpain activity, the pH-activity profile, Ca(2+)-sensitivity, and autolysis were measured. The importance of these positions was suggested by sequence comparisons between the calpain and papain families of cysteine proteinases. Asp-104 is adjacent to the active-site Cys-105, and Pro-287 is adjacent to the active-site Asn-286 and probably to the active-site His-262; both Asp-104 and Pro-287 are absolutely conserved in the known calpains, but are replaced by highly conserved serine residues in the papains. The single mutants had approx. 10-15% of wild-type activity, due mainly to a decrease in kcat, since Km was only slightly increased. The Pro-287-->Ser mutation appeared to cause a local perturbation of the catalytic Cys-105/His-262 catalytic ion pair, reducing its efficiency without major effect on the conformation and stability of the enzyme. The Asp-104-->Ser mutation caused a marked narrowing of the pH-activity curve, a 9-fold increase in Ca2+ requirement, and an acceleration of autolysis, when compared with the wild-type enzyme. The results indicated that Asp-104 alters the nature of its interaction with the catalytic ion pair during Ca(2+)-induced conformational change in calpain. This interaction may be direct or indirect, but is important in activation of the enzyme. PMID:8912692

  8. Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase.

    PubMed

    Irani, Seema; Yogesha, S D; Mayfield, Joshua; Zhang, Mengmeng; Zhang, Yong; Matthews, Wendy L; Nie, Grace; Prescott, Nicholas A; Zhang, Yan Jessie

    2016-03-01

    Changes in the phosphorylation status of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII) correlate with the process of eukaryotic transcription. The yeast protein regulator of transcription 1 (Rtr1) and the human homolog RNAPII-associated protein 2 (RPAP2) may function as CTD phosphatases; however, crystal structures of Kluyveromyces lactis Rtr1 lack a consensus active site. We identified a phosphoryl transfer domain in Saccharomyces cerevisiae Rtr1 by obtaining and characterizing a 2.6 Å resolution crystal structure. We identified a putative substrate-binding pocket in a deep groove between the zinc finger domain and a pair of helices that contained a trapped sulfate ion. Because sulfate mimics the chemistry of a phosphate group, this structural data suggested that this groove represents the phosphoryl transfer active site. Mutagenesis of the residues lining this groove disrupted catalytic activity of the enzyme assayed in vitro with a fluorescent chemical substrate, and expression of the mutated Rtr1 failed to rescue growth of yeast lacking Rtr1. Characterization of the phosphatase activity of RPAP2 and a mutant of the conserved putative catalytic site in the same chemical assay indicated a conserved reaction mechanism. Our data indicated that the structure of the phosphoryl transfer domain and reaction mechanism for the phosphoryl transfer activity of Rtr1 is distinct from those of other phosphatase families.

  9. Mutational analysis of the lac regulatory region: second-site changes that activate mutant promoters.

    PubMed Central

    Rothmel, R K; LeClerc, J E

    1989-01-01

    Second-site mutations that restored activity to severe lacP1 down-promoter mutants were isolated. This was accomplished by using a bacteriophage f1 vector containing a fusion of the mutant E. coli lac promoters with the structural gene for chloramphenicol acetyltransferase (CAT), so that a system was provided for selecting phage revertants (or pseudorevertants) that conferred resistance of phage-infected cells to chloramphenicol. Among the second-site changes that relieved defects in mutant lac promoters, the only one that restored lacP1 activity was a T----G substitution at position -14, a weakly conserved site in E. coli promoters. Three other sequence changes, G----A at -2, A----T at +1, and C----A at +10, activated nascent promoters in the lac regulatory region. The nascent promoters conformed to the consensus rule, that activity is gained by sequence changes toward homology with consensus sequences at the -35 and -10 regions of the promoter. However, the relative activities of some promoters cannot be explained solely by consideration of their conserved sequence elements. Images PMID:2660105

  10. Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase

    PubMed Central

    Mayfield, Joshua; Zhang, Mengmeng; Zhang, Yong; Matthews, Wendy L.; Nie, Grace; Prescott, Nicholas A.; Zhang, Yan Jessie

    2016-01-01

    Changes in the phosphorylation status of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII) correlate with the process of eukaryotic transcription. The yeast protein regulator of transcription 1 (Rtr1) and the human homolog RNAPII-associated protein 2 (RPAP2) may function as CTD phosphatases; however, crystal structures of Kluyveromyces lactis Rtr1 lack a consensus active site. We identified a phosphoryl transfer domain in Saccharomyces cerevisiae Rtr1 by obtaining and characterizing a 2.6 Å resolution crystal structure. We identified a putative substrate-binding pocket in a deep groove between the zinc finger domain and a pair of helices that contained a trapped sulfate ion. Because sulfate mimics the chemistry of a phosphate group, this structural data suggested that this groove represents the phosphoryl transfer active site. Mutagenesis of the residues lining this groove disrupted catalytic activity of the enzyme assayed in vitro with a fluorescent chemical substrate, and expression of the mutated Rtr1 failed to rescue growth of yeast lacking Rtr1. Characterization of the phosphatase activity of RPAP2 and a mutant of the conserved putative catalytic site in the same chemical assay indicated a conserved reaction mechanism. Our data indicated that the structure of the phosphoryl transfer domain and reaction mechanism for the phosphoryl transfer activity of Rtr1 is distinct from those of other phosphatase families. PMID:26933063

  11. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

    PubMed Central

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H.

    2016-01-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes. PMID:27581526

  12. Characterization of heavy metal contamination in the soil and sediment of the Three Gorges Reservoir, China.

    PubMed

    Wang, Tujin; Pan, Jin; Liu, Xuelian

    2017-02-23

    This paper analyzes the concentration, distribution, bioavailability, and potential heavy metal contamination risk of Cu, Pb, Cd, Zn, and Cr in the soil and sediment of the Three Gorges Reservoir (TGR). In this paper, 14 stations that cover the upper reaches to the lower reaches of the TGR were selected. The spatial distribution of heavy metals in the TGR showed that the average concentrations of Cu, Pb, Cd, Zn, and Cr were higher in the upper and lower reaches than those in the middle reaches because of industrial and agricultural activities as well as natural processes (e.g., soil erosion, rock weathering). The results also indicated that multiple pollution sources and complex geomorphological, geochemical and biological processes resulted in remarkably higher heavy metal concentrations in the soils of the water-level-fluctuation zone (WLFZ) than in the soils of the banks. The Cu, Pb, Cd, Zn, and Cr concentrations in the soils of the TGR did not exceed their respective maximum allowable concentration (MAC) values for agricultural soils in China, indicating that the soil in the TGR was not seriously contaminated with Cu, Pb, Cd, Zn, or Cr. However, the mean concentrations of all the studied metals in the sediments were higher than the geochemical background values and much higher than those in the soils, thus indicating the effect of the pollution sources and the altered hydrologic conditions that occurred after the impoundment of the TGR. A geoaccumulation index analysis indicated that the TGR sediments were moderately polluted with Cu and Cd, unpolluted to moderately polluted with Pb and Cr, and unpolluted with Zn. Fractionation studies indicated that Cd was mainly present in the non-residual fractions and exhibited great instability and bioavailability; furthermore, the alternating wetting and drying of the WFLZ soils enhance the mobility and bioavailability of Cd. Thus, greater attention should be paid to Cd pollution in the TGR because of its higher risk

  13. Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents.

    PubMed

    Reddi, Ravikumar; Arya, Tarun; Kishor, Chandan; Gumpena, Rajesh; Ganji, Roopa J; Bhukya, Supriya; Addlagatta, Anthony

    2014-09-01

    Methionine aminopeptidases (MetAPs) cleave initiator methionine from ~ 70% of the newly synthesized proteins in every living cell, and specific inhibition or knockdown of this function is detrimental. MetAPs are metalloenzymes, and are broadly classified into two subtypes, type I and type II. Bacteria contain only type I MetAPs, and the active site of these enzymes contains a conserved cysteine. By contrast, in type II enzymes the analogous position is occupied by a conserved glycine. Here, we report the reactivity of the active site cysteine in a type I MetAP, MetAP1c, of Mycobacterium tuberculosis (MtMetAP1c) towards highly selective cysteine-specific reagents. The authenticity of selective modification of Cys105 of MtMetAP1c was established by using site-directed mutagenesis and crystal structure determination of covalent and noncovalent complexes. On the basis of these observations, we propose that metal ions in the active site assist in the covalent modification of Cys105 by orienting the reagents appropriately for a successful reaction. These studies establish, for the first time, that the conserved cysteine of type I MetAPs can be targeted for selective inhibition, and we believe that this chemistry can be exploited for further drug discovery efforts regarding microbial MetAPs.

  14. The Ribotoxin Restrictocin Recognizes Its RNA Substrate by Selective Engagement of Active Site Residues

    PubMed Central

    2011-01-01

    Restrictocin and related fungal endoribonucleases from the α-sarcin family site-specifically cleave the sarcin/ricin loop (SRL) on the ribosome to inhibit translation and ultimately trigger cell death. Previous studies showed that the SRL folds into a bulged-G motif and tetraloop, with restrictocin achieving a specificity of ∼1000-fold by recognizing both motifs only after the initial binding step. Here, we identify contacts within the protein−RNA interface and determine the extent to which each one contributes to enzyme specificity by examining the effect of protein mutations on the cleavage of the SRL substrate compared to a variety of other RNA substrates. As with other biomolecular interfaces, only a subset of contacts contributes to specificity. One contact of this subset is critical, with the H49A mutation resulting in quantitative loss of specificity. Maximum catalytic activity occurs when both motifs of the SRL are present, with the major contribution involving the bulged-G motif recognized by three lysine residues located adjacent to the active site: K110, K111, and K113. Our findings support a kinetic proofreading mechanism in which the active site residues H49 and, to a lesser extent, Y47 make greater catalytic contributions to SRL cleavage than to suboptimal substrates. This systematic and quantitative analysis begins to elucidate the principles governing RNA recognition by a site-specific endonuclease and may thus serve as a mechanistic model for investigating other RNA modifying enzymes. PMID:21417210

  15. Computational approaches to find the active binding sites of biological targets against busulfan.

    PubMed

    Karthick, T; Tandon, Poonam

    2016-06-01

    Determination of electrophilic and nucleophilic sites of a molecule is the primary task to find the active sites of the lead molecule. In the present study, the active sites of busulfan have been predicted by molecular electrostatic potential surface and Fukui function analysis with the help of dispersion corrected density functional theory. Similarly, the identification of active binding sites of the proteins against lead compound plays a vital role in the field of drug discovery. Rigid and flexible molecular docking approaches are used for this purpose. For rigid docking, Hex 8.0.0 software employing fast Fourier transform (FFT) algorithm has been used. The partial flexible blind docking simulations have been performed with AutoDock 4.2 software; where a Lamarckian genetic algorithm is employed. The results showed that the most electrophilic atoms of busulfan bind with the targets. It is clear from the docking studies that busulfan has inhibition capability toward the targets 12CA and 1BZM. Graphical Abstract Docking of ligand and protein.

  16. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  17. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  18. Lymphokine-activated killer (LAK) cells can be focused at sites of tumor growth by products of macrophage activation

    SciTech Connect

    Migliori, R.J.; Gruber, S.A.; Sawyer, M.D.; Hoffman, R.; Ochoa, A.; Bach, F.H.; Simmons, R.L.

    1987-08-01

    Successful adoptive cancer immunotherapy presumably depends on the accumulation of tumoricidal leukocytes at the sites of tumor growth. Large numbers of lymphokine-activated killer (LAK) cells can be generated in vitro by growth in high concentrations of interleukin-2 (IL-2), but relatively few arrive at the tumor site after intravenous injection. We hypothesize that the delivery of LAK cells to tumor sites may be augmented by previously demonstrated lymphocyte-recruiting factors, including activated macrophage products such as interleukin-1 (IL-1) and tumor necrosis factor. /sup 111/Indium-labeled LAK cells were injected intravenously into syngeneic mice bearing the macrophage activator endotoxin (LPS) in one hind footpad, and saline solution was injected into the contralateral footpad. Significantly more activity was recovered from the LPS-bearing footpad at all times during a 96-hour period. Recombinant IL-1 also attracted more LAK cells after injection into tumor-free hind footpads. Furthermore, LAK cells preferentially homed to hind footpads that were bearing 3-day established sarcomas after intralesional injections of LPS, IL-1, or tumor necrosis factor when compared with contralateral tumor-bearing footpads injected with saline solution alone. In preliminary experiments, mice with hind-footpad tumors appeared to survive longer after combined systemic IL-2 and LAK therapy if intralesional LPS was administered. These studies demonstrate that macrophage activation factors that have been shown capable of attracting circulating normal lymphocytes can also effectively attract LAK cells from the circulation. By the stimulation of macrophages at the sites of tumor growth, more LAK cells can be attracted. It is hoped that by focusing the migration of LAK cells to tumors, LAK cells and IL-2 would effect tumor regression more efficiently and with less toxicity.

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

    SciTech Connect

    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.

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

    SciTech Connect

    Petersen, C.A.

    1996-09-20

    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 waste, for disposal is a deep geologic repository. The remainder of the waste would be considered `incidental` waste and could be disposed onsite.

  1. Particle Size Distribution Data From Existing Boreholes at the Immobilized Low-Activity Waste Site

    SciTech Connect

    Valenta, Michelle M.; Martin, Maria B.; Moreno, Jorge R.; Ferri, Rosalie M.; Horton, Duane G.; Reidel, Stephen P.

    2000-09-25

    This report provides particle size distribution data for samples near the Immobilized Low-Activity Waste (ILAW) Site that were archived in the Hanford Geotechnical Sample Library. Seventy-nine sediment samples were analyzed from four boreholes. Samples were collected from every ten feet in the boreholes. Eightly percent of the samples were classified as slightly gravelly sand. Fifteen percent were classified as gravelly sand, gravelly silty sand, or sandy gravels. These data indicate that the particle size of the sediment is consistent across the ILAW site and is dominated by sand in the upper part of the Hanford formation with more gravel rich units in the lower part.

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

    SciTech Connect

    Parker, Shane M.; Shiozaki, Toru

    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.

  3. Controlling activation site density by low-energy far-field stimulation in cardiac tissue.

    PubMed

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites ("virtual electrodes") in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  4. Probing Oxygen Activation Sites in Two Flavoprotein Oxidases Using Chloride as an Oxygen Surrogate

    SciTech Connect

    Kommoju, Phaneeswara-Rao; Chen, Zhi-wei; Bruckner, Robert C.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2011-08-16

    A single basic residue above the si-face of the flavin ring is the site of oxygen activation in glucose oxidase (GOX) (His516) and monomeric sarcosine oxidase (MSOX) (Lys265). Crystal structures of both flavoenzymes exhibit a small pocket at the oxygen activation site that might provide a preorganized binding site for superoxide anion, an obligatory intermediate in the two-electron reduction of oxygen. Chloride binds at these polar oxygen activation sites, as judged by solution and structural studies. First, chloride forms spectrally detectable complexes with GOX and MSOX. The protonated form of His516 is required for tight binding of chloride to oxidized GOX and for rapid reaction of reduced GOX with oxygen. Formation of a binary MSOX-chloride complex requires Lys265 and is not observed with Lys265Met. Binding of chloride to MSOX does not affect the binding of a sarcosine analogue (MTA, methylthioactetate) above the re-face of the flavin ring. Definitive evidence is provided by crystal structures determined for a binary MSOX-chloride complex and a ternary MSOX-chloride-MTA complex. Chloride binds in the small pocket at a position otherwise occupied by a water molecule and forms hydrogen bonds to four ligands that are arranged in approximate tetrahedral geometry: Lys265:NZ, Arg49:NH1, and two water molecules, one of which is hydrogen bonded to FAD:N5. The results show that chloride (i) acts as an oxygen surrogate, (ii) is an effective probe of polar oxygen activation sites, and (iii) provides a valuable complementary tool to the xenon gas method that is used to map nonpolar oxygen-binding cavities.

  5. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.

    PubMed

    Armstrong, Michelle; van Hoorebeke, Christopher; Horn, Thomas; Deschamps, Joshua; Freedman, J Cody; Kalyanaraman, Chakrapani; Jacobson, Matthew P; Holman, Theodore

    2016-11-01

    Human 15-lipoxygenase-1 (h15-LOX-1 or h12/15-LOX) reacts with polyunsaturated fatty acids and produces bioactive lipid derivatives that are implicated in many important human diseases. One such disease is stroke, which is the fifth leading cause of death and the first leading cause of disability in America. The discovery of h15-LOX-1 inhibitors could potentially lead to novel therapeutics in the treatment of stroke, however, little is known about the inhibitor/active site interaction. This study utilizes site-directed mutagenesis, guided in part by molecular modeling, to gain a better structural understanding of inhibitor interactions within the active site. We have generated eight mutants (R402L, R404L, F414I, F414W, E356Q, Q547L, L407A, I417A) of h15-LOX-1 to determine whether these active site residues interact with two h15-LOX-1 inhibitors, ML351 and an ML094 derivative, compound 18. IC50 values and steady-state inhibition kinetics were determined for the eight mutants, with four of the mutants affecting inhibitor potency relative to wild type h15-LOX-1 (F414I, F414W, E356Q and L407A). The data indicate that ML351 and compound 18, bind in a similar manner in the active site to an aromatic pocket close to F414 but have subtle differences in their specific binding modes. This information establishes the binding mode for ML094 and ML351 and will be leveraged to develop next-generation inhibitors.

  6. Controlling activation site density by low-energy far-field stimulation in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites (“virtual electrodes”) in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  7. Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

    PubMed Central

    Lee, Tai-Sung; Giambaşu, George M.; Sosa, Carlos P.; Martick, Monika; Scott, William G.; York, Darrin M.

    2009-01-01

    The relationship between formation of active in-line attack conformations and monovalent (Na+) and divalent (Mg2+) metal ion binding in the hammerhead ribozyme has been explored with molecular dynamics simulations. To stabilize repulsions between negatively charged groups, different requirements of threshold occupancy of metal ions were observed in the reactant and activated precursor states both in the presence or absence of a Mg2+ in the active site. Specific bridging coordination patterns of the ions are correlated with the formation of active in-line attack conformations and can be accommodated in both cases. Furthermore, simulation results suggest that the hammerhead ribozyme folds to form an electronegative recruiting pocket that attracts high local concentrations of positive charge. The present simulations help to reconcile experiments that probe the metal ion sensitivity of hammerhead ribozyme catalysis and support the supposition that Mg2+, in addition to stabilizing active conformations, plays a specific chemical role in catalysis. PMID:19265710

  8. Localization of the active site of an enzyme, bacterial luciferase, using two-quantum affinity modification

    NASA Astrophysics Data System (ADS)

    Benimetskaya, L. Z.; Gitelzon, I. I.; Kozionov, Andrew L.; Novozhilov, S. Y.; Petushkov, V. N.; Rodionova, N. S.; Stockman, Mark I.

    1991-11-01

    For the first time the method of two-quantum affinity modification has been employed to probe the structure of an enzyme, bacterial luciferase. Position of the flavin-binding site of this enzyme, which was previously unknown, has been established. The obtained data indicate that the flavin site is positioned on the (alpha) -subunit. The closest contact of the protein chain of the enzyme with the chromophoric group of the flavin takes place near 80 +/- 10 and 120 +/- 10 amino acid residues; the regions 50 +/- 10 and 215 +/- 10 are also close to the flavin. The established localization does not contradict suggestions on positions of the flavin and phosphate sites of the bacterial luciferase, which had earlier been made from the data on evolutionary stability of various luciferases. The present method can, in principle, be applied to a great number of enzymes, including all flavin-dependent enzymes. Enzymatic catalysis has high speed and specificity. Creation of a method of determination of the elements of the primary structure of a protein, making up the active site (in which substratum conversion occurs), could be a significant advance in clearing up mechanisms of enzymatic catalysis. It was proposed to localize active sites of the enzymes, whose substrata are chromophores, using this method of two-quantum affinity modification. An enzyme- substratum complex is irradiated with laser light of sufficiently long wavelength ((lambda) 300 nm) which is not directly absorbed by the enzyme. Two-quantum quasiresonant excitation of the substratum activates it to the state with energy 5-7 eV, which is then radiativelessly transferred to neighboring protein groups. This energy exceeds the energy of activation of peptide bond breakage. Therefore, the enzyme will be disrupted in the vicinity of its active site. In the present paper the above approach has been implemented for the first time. Information has been obtained about the position of the flavin-binding site of bacterial

  9. Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity

    PubMed Central

    Zorrilla de San Martin, Javier; Jalil, Abdelali

    2015-01-01

    Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABAARs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABAA autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca2+ photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl−]i, autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30–150 GABAA channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Nav-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABAA autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity. PMID:26621773

  10. Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity.

    PubMed

    de San Martin, Javier Zorrilla; Jalil, Abdelali; Trigo, Federico F

    2015-12-01

    Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABA(A)Rs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABA(A) autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca(2+) photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl(-)](i), autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30-150 GABA(A) channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Na(v)-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABA(A) autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity.

  11. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  12. Active-site modifications of adenylation domains lead to hydrolysis of upstream nonribosomal peptidyl thioester intermediates.

    PubMed

    Uguru, Gabriel C; Milne, Claire; Borg, Matthew; Flett, Fiona; Smith, Colin P; Micklefield, Jason

    2004-04-28

    Site-directed mutagenesis of nonribosomal peptide synthetase (NRPS) adenylation (A) domains was investigated as a means to engineer new calcium-dependent antibiotics (CDA) in Streptomyces coelicolor. Single- and double-point mutants of the CDA NRPS module 7, A-domain were generated, which were predicted to alter the specificity of this domain from Asp to Asn. The double-point mutant produced a new peptide CDA2a-7N containing Asn at position 7 as expected. However, in both the single- and the double-point mutants, significant hydrolysis of the CDA-6mer intermediate was evident. One explanation for this is that the mutant module 7 A-domain activates Asn instead of Asp; however, the Asn-thioester intermediate is only weakly recognized by the upstream C-domain acceptor site (a), allowing a water molecule to intercept the hexapeptidyl intermediate in the donor site (d).

  13. Novel active comb-shaped dry electrode for EEG measurement in hairy site.

    PubMed

    Huang, Yan-Jun; Wu, Chung-Yu; Wong, Alice May-Kuen; Lin, Bor-Shyh

    2015-01-01

    Electroencephalography (EEG) is an important biopotential, and has been widely applied in clinical applications. The conventional EEG electrode with conductive gels is usually used for measuring EEG. However, the use of conductive gel also encounters with the issue of drying and hardening. Recently, many dry EEG electrodes based on different conductive materials and techniques were proposed to solve the previous issue. However, measuring EEG in the hairy site is still a difficult challenge. In this study, a novel active comb-shaped dry electrode was proposed to measure EEG in hairy site. Different form other comb-shaped or spike-shaped dry electrodes, it can provide more excellent performance of avoiding the signal attenuation, phase distortion, and the reduction of common mode rejection ratio. Even under walking motion, it can effectively acquire EEG in hairy site. Finally, the experiments for alpha rhythm and steady-state visually evoked potential were also tested to validate the proposed electrode.

  14. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase.

    PubMed

    Mercaldi, Gustavo F; Pereira, Humberto M; Cordeiro, Artur T; Michels, Paul A M; Thiemann, Otavio H

    2012-06-01

    Phosphoglycerate mutases (PGAMs) participate in both the glycolytic and the gluconeogenic pathways in reversible isomerization of 3-phosphoglycerate and 2-phosphoglycerate. PGAMs are members of two distinct protein families: enzymes that are dependent on or independent of the 2,3-bisphosphoglycerate cofactor. We determined the X-ray structure of the monomeric Trypanosoma brucei independent PGAM (TbiPGAM) in its apoenzyme form, and confirmed this observation by small angle X-ray scattering data. Comparing the TbiPGAM structure with the Leishmania mexicana independent PGAM structure, previously reported with a phosphoglycerate molecule bound to the active site, revealed the domain movement resulting from active site occupation. The structure reported here shows the interaction between Asp319 and the metal bound to the active site, and its contribution to the domain movement. Substitution of the metal-binding residue Asp319 by Ala resulted in complete loss of independent PGAM activity, and showed for the first time its involvement in the enzyme's function. As TbiPGAM is an attractive molecular target for drug development, the apoenzyme conformation described here provides opportunities for its use in structure-based drug design approaches. Database Structural data for the Trypanosoma brucei 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) has been deposited with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank under code 3NVL.

  15. Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism.

    PubMed

    Guo, H; Cui, Q; Lipscomb, W N; Karplus, M

    2001-07-31

    Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer.

  16. How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

    PubMed Central

    Hytönen, Vesa P; Vogel, Viola

    2008-01-01

    Upon cell adhesion, talin physically couples the cytoskeleton via integrins to the extracellular matrix, and subsequent vinculin recruitment is enhanced by locally applied tensile force. Since the vinculin binding (VB) sites are buried in the talin rod under equilibrium conditions, the structural mechanism of how vinculin binding to talin is force-activated remains unknown. Taken together with experimental data, a biphasic vinculin binding model, as derived from steered molecular dynamics, provides high resolution structural insights how tensile mechanical force applied to the talin rod fragment (residues 486–889 constituting helices H1–H12) might activate the VB sites. Fragmentation of the rod into three helix subbundles is prerequisite to the sequential exposure of VB helices to water. Finally, unfolding of a VB helix into a completely stretched polypeptide might inhibit further binding of vinculin. The first events in fracturing the H1–H12 rods of talin1 and talin2 in subbundles are similar. The proposed force-activated α-helix swapping mechanism by which vinculin binding sites in talin rods are exposed works distinctly different from that of other force-activated bonds, including catch bonds. PMID:18282082

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

    SciTech Connect

    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.

  18. Structure-based drug design: exploring the proper filling of apolar pockets at enzyme active sites.

    PubMed

    Zürcher, Martina; Diederich, François

    2008-06-20

    The proper filling of apolar pockets at enzyme active sites is central for increasing binding activity and selectivity of hits and leads in medicinal chemistry. In our structure-based design approach toward the generation of potent enzyme inhibitors, we encountered a variety of challenges in gaining suitable binding affinity from the occupation of such pockets. We summarize them here for the first time. A fluorine scan of tricyclic thrombin inhibitors led to the discovery of favorable orthogonal dipolar C-F...CO interactions. Efficient cation-pi interactions were established in the S4 pocket of factor Xa, another serine protease from the blood coagulation cascade. Changing from mono- to bisubstrate inhibitors of catechol O-methyltransferase, a target in the L-Dopa-based treatment of Parkinson's disease, enabled the full exploitation of a previously unexplored hydrophobic pocket. Conformational preorganization of a pocket at an enzyme active site is crucial for harvesting binding affinity. This is demonstrated for two enzymes from the nonmevalonate pathway of isoprenoid biosynthesis, IspE and IspF, which are pursued as antimalarial targets. Disrupting crystallographically defined water networks on the way into a pocket might cost all of the binding free enthalpy gained from its occupation, as revealed in studies with tRNA-guanine transglycosylase, a target against shigellosis. Investigations of the active site of plasmepsin II, another antimalarial target, showed that principles for proper apolar cavity filling, originally developed for synthetic host-guest systems, are also applicable to enzyme environments.

  19. Pose prediction accuracy in docking studies and enrichment of actives in the active site of GSK-3beta.

    PubMed

    Gadakar, Pravin Kumar; Phukan, Samiron; Dattatreya, Prasanna; Balaji, V N

    2007-01-01

    We present molecular docking studies on the inhibitors of GSK-3beta kinase in the enzyme binding sites of the X-ray complexes (1H8F, 1PYX, 1O9U, 1Q4L, 1Q5K, and 1UV5) using the Schrödinger docking tool Glide. Cognate and cross-docking studies using standard precision (SP) and extraprecision (XP) algorithms have been carried out. Cognate docking studies demonstrate that docked poses similar to X-ray poses (root-mean-square deviations of less than 2 A) are found within the top four ranks of the GlideScore and E-model scores. However, cross-docking studies typically produce poses that are significantly deviated from X-ray poses in all but a couple of cases, implying potential for induced fit effects in ligand binding. In this light, we have also carried out induced fit docking studies in the active sites of 1O9U, 1Q4L, and 1Q5K. Specifically, conformational changes have been effected in the active sites of these three protein structures to dock noncognate ligands. Thus, for example, the active site of 1O9U has been induced to fit the ligands of 1Q4L, 1Q5K, and 1UV5. These studies produce ligand docked poses which have significantly lower root-mean-square deviations relative to their X-ray crystallographic poses, when compared to the corresponding values from the cross-docking studies. Furthermore, we have used an ensemble of the induced fit models and X-ray structures to enhance the retrieval of active GSK-3beta inhibitors seeded in a decoy database, normally used in Glide validation studies. Thus, our studies provide valuable insights into computational strategies useful for the identification of potential GSK-3beta inhibitors.

  20. A NMR and MD study of the active site of factor Xa by selective inhibitors

    NASA Astrophysics Data System (ADS)

    Doan, B. T.; Fraternali, F.; Do, Q. T.; Atkinson, R. A.; Palmas, P.; Sklenar, V.; Wildgoose, P.; Strop, P.; Saudek, V.

    1998-02-01

    The structure of two selective inhibitors obtained by the screening of a vast combinatorial library, Ac-Tyr-Ile-Arg-Ile-NH2 and Ac-(4-amino-Phe)-(Cyc.-Gly)-NH2, in the active site of the blood clotting enzyme factor Xa was determined using transferred NOE NMR and simulated annealing (SA) under NMR constraints. The refined structures of the inhibitors were docked in the active site and SA was performed inside the enzyme which has been kept as a rigid charged template. The final structures were optimised by molecular dynamics simulation of the complexes in water. The inhibitors assume a compact, very well defined conformation embedded in the binding site without blocking the catalysis. The model allows to explain the mode of action, affinity and specificity. L'étude structurale d'inhibiteurs du facteur Xa, une enzyme de coagulation, obtenus par chimie combinatoire : Ac-Tyr-Ile-Arg-Ile-NH2, Ac-(4-amino-Phe)-(Cyc.-Gly)-NH2, a été réalisée par RMN NOE de transfert et modélisation moléculaire. Les structures ont été calculées sous contraintes RMN : géométrie de distance, recuit simulé et minimisation, affinées par une recherche conformationnelle et recuit de l'inhibiteur placé dans le site actif et optimisées par simulation de dynamique moléculaire du complexe dans l'eau. L'inhibiteur présente une structure compacte positionnée dans le site d'interaction hors d'accès du site catalytique. Ce modèle permet d'expliquer le mode d'action, l'affinité et la spécificité des peptides.

  1. A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies

    NASA Astrophysics Data System (ADS)

    Mayer, Dorica; Naylor, Christopher B.; Motoc, Ioan; Marshall, Garland R.

    1987-04-01

    Previous structure-activity studies of captopril and related active angiotensin-converting enzyme (ACE) inhibitors have led to the conclusion that the basic structural requirements for inhibition of ACE involve (a) a terminal carboxyl group; (b) an amido carbonyl group; and (c) different types of effective zinc (Zn) ligand functional groups. Such structural requirements common to a set of compounds acting at the same receptor have been used to define a pharmacophoric pattern of atoms or groups of atoms mutually oriented in space that is necessary for ACE inhibition from a stereochemical point of view. A unique pharmacophore model (within the resolution of approximately 0.15 Å) was observed using a method for systematic search of the conformational hyperspace available to the 28 structurally different molecules under study. The method does not assume a common molecular framework, and, therefore, allows comparison of different compounds that is independent of their absolute orientation. Consequently, by placing the carboxyl binding group, the binding site for amido carbonyl, and the Zn atom site in positions determined by ideal binding geometry with the inhibitors' functional groups, it was possible to clearly specify a geometry for the active site of ACE.

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

    SciTech Connect

    Oliver, S. A.; Harris, V. G.; Hamdeh, H. H.; Ho, J. C.

    2000-05-08

    The cation site occupancy of a mechanically activated nanocrystalline zinc ferrite powder was determined as (Zn{sub 0.55}{sup 2+}Fe{sub 0.18}{sup 3+}){sub tet}[Zr{sub 0.45}{sup 2+}Fe{sub 1.82}{sup 3+}]{sub oct}O{sub 4} 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 Fe{sup 3+} on both sites is consistent with the measured room temperature magnetic properties. (c) 2000 American Institute of Physics.

  3. Identification of a novel K311 ubiquitination site critical for androgen receptor transcriptional activity.

    PubMed

    McClurg, Urszula L; Cork, David M W; Darby, Steven; Ryan-Munden, Claudia A; Nakjang, Sirintra; Mendes Côrtes, Leticia; Treumann, Achim; Gaughan, Luke; Robson, Craig N

    2016-11-29

    The androgen receptor (AR) is the main driver of prostate cancer (PC) development and progression, and the primary therapeutic target in PC. To date, two functional ubiquitination sites have been identified on AR, both located in its C-terminal ligand binding domain (LBD). Recent reports highlight the emergence of AR splice variants lacking the LBD that can arise during disease progression and contribute to castrate resistance. Here, we report a novel N-terminal ubiquitination site at lysine 311. Ubiquitination of this site plays a role in AR stability and is critical for its transcriptional activity. Inactivation of this site causes AR to accumulate on chromatin and inactivates its transcriptional function as a consequence of inability to bind to p300. Additionally, mutation at lysine 311 affects cellular transcriptome altering the expression of genes involved in chromatin organization, signaling, adhesion, motility, development and metabolism. Even though this site is present in clinically relevant AR-variants it can only be ubiquitinated in cells when AR retains LBD suggesting a role for AR C-terminus in E2/E3 substrate recognition. We report that as a consequence AR variants lacking the LBD cannot be ubiquitinated in the cellular environment and their protein turnover must be regulated via an alternate pathway.

  4. Foreign Glycoproteins Can Be Actively Recruited to Virus Assembly Sites during Pseudotyping▿

    PubMed Central

    Jorgenson, Rebecca L.; Vogt, Volker M.; Johnson, Marc C.

    2009-01-01

    Retroviruses like human immunodeficiency virus type 1 (HIV-1), as well as many other enveloped viruses, can efficiently produce infectious virus in the absence of their own surface glycoprotein if a suitable glycoprotein from a foreign virus is expressed in the same cell. This process of complementation, known as pseudotyping, often can occur even when the glycoprotein is from an unrelated virus. Although pseudotyping is widely used for engineering chimeric viruses, it has remained unknown whether a virus can actively recruit foreign glycoproteins to budding sites or, alternatively, if a virus obtains the glycoproteins through a passive mechanism. We have studied the specificity of glycoprotein recruitment by immunogold labeling viral glycoproteins and imaging their distribution on the host plasma membrane using scanning electron microscopy. Expressed alone, all tested viral glycoproteins were relatively randomly distributed on the plasma membrane. However, in the presence of budding HIV-1 or Rous sarcoma virus (RSV) particles, some glycoproteins, such as those encoded by murine leukemia virus and vesicular stomatitis virus, were dramatically redistributed to viral budding sites. In contrast, the RSV Env glycoprotein was robustly recruited only to the homologous RSV budding sites. These data demonstrate that viral glycoproteins are not in preformed membrane patches prior to viral assembly but rather that glycoproteins are actively recruited to certain viral assembly sites. PMID:19224995

  5. Barriers to physical activity in an on-site corporate fitness center.

    PubMed

    Schwetschenau, Heather M; O'Brien, William H; Cunningham, Christopher J L; Jex, Steve M

    2008-10-01

    Many corporations provide employees the option of participating in on-site fitness centers, but utilization rates are low. Perceived barriers to physical activity have been established as important correlates of physical activity, and recent research indicates that barriers may vary across settings. Work-site fitness centers may present unique barriers to participation, but there are currently no standardized measures that assess such barriers. Eighty-eight employees of a midwestern corporation completed a survey designed to identify and evaluate the extent to which barriers influence participation in an on-site corporate fitness center. Regression analyses revealed that external environmental barriers (e.g., inadequate exercise facilities) significantly accounted for not joining the fitness center, and for decreased duration of visits to the facility among members. Internal barriers (e.g., feeling embarrassed to exercise around coworkers) significantly accounted for frequency of fitness center visits among members. This corporate specific measure may lead to more effective interventions aimed to increase use of on-site corporate fitness centers.

  6. Den site activity patterns of adult male and female swift foxes, Vulpes velox, in Northwestern Texas

    USGS Publications Warehouse

    Lemons, P.R.; Ballard, W.B.; Sullivan, R.M.; Sovada, M.A.

    2003-01-01

    Activity of Swift Foxes (Vulpes velox) at den sites was studied in northwestern Texas during pup rearing seasons in 2000 and 2001 to determine role of males in parental care. Twenty-four percent of radio-collared females with a potential to breed successfully raised pups to eight weeks of age. We intensively monitored presence and absence of male and female Swift Foxes at two den sites each year. Females were present >2.6 times more at den sites than males during the pup rearing season. Female and male Swift Foxes largely stayed at dens during diurnal hours and were active away from dens during nocturnal and crepuscular hours. Females and males spent 12.4% and 3.0% more time at dens before pups emerged, than after pups emerged, respectively. Following depredation of one male parent, the female spent 29% less time at the den site. Decrease in time spent at the den by the female following loss of her mate suggested that loss of one parent might severely impact recruitment of Swift Foxes. Our observations indicated that intense Coyote (Canis latrans) depredation may severely impact pup-rearing success as well as the parental care within Swift Fox family groups.

  7. Crustal structure across the Three Gorges area of the Yangtze platform, central China, from seismic refraction/wide-angle reflection data

    USGS Publications Warehouse

    Zhang, Z.; Bai, Z.; Mooney, W.; Wang, C.; Chen, X.; Wang, E.; Teng, J.; Okaya, N.

    2009-01-01

    We present active-source seismic data recorded along a 300??km-long profile across the Three Gorges area of the western Yangtze platform, central China. From west to east, the profile crosses the Zigui basin, Huangling dome and Jianghan basin. The derived crustal P-wave velocity structure changes significantly across the Tongchenghe fault that lies at the transition from the Huangling dome to the Jianghan basin. West of the Tongchenghe fault, beneath the Zigui basin and the Huangling dome, we observe a ~ 42??km thick crust of relatively low average velocity (6.3-6.4??km/s). In contrast, east of the Tongchenghe fault, beneath the Jianghan basin, the crust is only 30??km thick and has a high average velocity (6.6-6.7??km/s). A west-east variation in crustal composition along the Tongchenghe fault is also inferred. West of the fault, P-wave velocities suggest a felsic composition with an intermediate layer at the base of the crust, whilst, east of the fault, felsic, intermediate, and mafic crustal layers are apparent. Our results suggest that the crust beneath the Jianghan basin has been thinned by rifting, accompanied by intrusion of the lower crust by mafic dikes and sills. The west-to-east division of the crust in the Three Gorges area coincides with first-order geophysical contrasts in gravity, topography, crustal and lithospheric thickness. ?? 2009 Elsevier B.V.

  8. The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis.

    PubMed Central

    Okoniewska, M; Tanaka, T; Yada, R Y

    2000-01-01

    Glycine residues are known to contribute to conformational flexibility of polypeptide chains, and have been found to contribute to flexibility of some loops associated with enzymic catalysis. A comparison of porcine pepsin in zymogen, mature and inhibited forms revealed that a loop (a flap), consisting of residues 71--80, located near the active site changed its position upon substrate binding. The loop residue, glycine-76, has been implicated in the catalytic process and thought to participate in a hydrogen-bond network aligning the substrate. This study investigated the role of glycine-76 using site-directed mutagenesis. Three mutants, G76A, G76V and G76S, were constructed to increase conformational restriction of a polypeptide chain. In addition, the serine mutant introduced a hydrogen-bonding potential at position 76 similar to that observed in human renin. All the mutants, regardless of amino acid size and polarity, had lower catalytic efficiency and activated more slowly than the wild-type enzyme. The slower activation process was associated directly with altered proteolytic activity. Consequently, it was proposed that a proteolytic cleavage represents a limiting step of the activation process. Lower catalytic efficiency of the mutants was explained as a decrease in the flap flexibility and, therefore, a different pattern of hydrogen bonds responsible for substrate alignment and flap conformation. The results demonstrated that flap flexibility is essential for efficient catalytic and activation processes. PMID:10861225

  9. Improving the activity of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    PubMed

    Weng, Meizhi; Deng, Xiongwei; Bao, Wei; Zhu, Li; Wu, Jieyuan; Cai, Yongjun; Jia, Yan; Zheng, Zhongliang; Zou, Guolin

    2015-09-25

    Nattokinase (NK), a bacterial serine protease from Bacillus subtilis var. natto, is a potential cardiovascular drug exhibiting strong fibrinolytic activity. To broaden its commercial and medical applications, we constructed a single-mutant (I31L) and two double-mutants (M222A/I31L and T220S/I31L) by site-directed mutagenesis. Active enzymes were expressed in Escherichia coli with periplasmic secretion and were purified to homogeneity. The kinetic parameters of enzymes were examined by spectroscopy assay and isothermal titration calorimetry (ITC), and their fibrinolytic activities were determined by fibrin plate method. The substitution of Leu(31) for Ile(31) resulted in about 2-fold enhancement of catalytic efficiency (Kcat/KM) compared with wild-type NK. The specific activities of both double-mutants (M222A/I31L and T220S/I31L) were significantly increased when compared with the single-mutants (M222A and T220S) and the oxidative stability of M222A/I31L mutant was enhanced with respect to wild-type NK. This study demonstrates the feasibility of improving activity of NK by site-directed mutagenesis and shows successful protein engineering cases to improve the activity of NK as a potent therapeutic agent.

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

    SciTech Connect

    Beres, Christopher M.; Fort, E. Joseph; Boyle, James D.

    2013-07-01

    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)

  11. PARP promoter-mediated activation of a VSG expression site promoter in insect form Trypanosoma brucei.

    PubMed

    Urményi, T P; Van der Ploeg, L H

    1995-03-25

    In trypanosomes the rRNA, PARP and VSG gene promoters mediate alpha-amanitin-resistant transcription of protein coding genes, presumably by RNA polymerase (pol) I. We compared the activity of PARP and VSG promoters integrated at one of the alleles of the largest subunit of pol II genes in insect form trypanosomes. Even though both promoters are roughly equally active in transient transformation assays in insect form trypanosomes, only the PARP promoter functioned effectively when integrated at the pol II largest subunit or other loci. Promoter activity in transient transformation assays is therefore not necessarily predictive of transcriptional activity once integrated into the trypanosome genome. The integrated fully active PARP promoter could upregulate in cis an otherwise poorly active integrated VSG promoter. The PARP promoter nucleotide sequence elements responsible for VSG promoter activation coincided with most of the important PARP promoter elements mapped previously by linker scanning mutagenesis, indicating that it is not a single unique promoter element that was responsible for VSG promoter activation. The data suggest that PARP promoter-mediated activation of the VSG promoter does not result from complementation of the VSG promoter with a single insect form-specific transcription factor whose binding site is missing from the VSG promoter and present in the PARP promoter. We favor a model in which chromatin structure at the locus is altered by the PARP promoter, allowing VSG promoter activation in insect form trypanosomes. We discuss the significance of these observations for the control of VSG promoters in insect form trypanosomes.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Mutation of active site residues in synthetic T4-lysozyme gene and their effect on lytic activity.

    PubMed

    Anand, N N; Stephen, E R; Narang, S A

    1988-06-16

    The active site amino acids (Glu11 and Asp20) in T4-lysozyme have been mutated to their isosteric residues Gln or Asn and/or acidic residues such as Glu----Asp or Asp----Glu by the oligonucleotide-replacement method. Out of eight mutants so generated the mutant T4-lysozyme obtained from pTLY.Asp11 retains maximum amount of activity (approximately 16%), pTLY.Asn20 the least (0.9%) whereas pTLY.Gln11 lost completely. A systematic study of the active and inactive mutants thus generated supports the important role of Glu11 and Asp20 in T4-lysozyme activity as predicted in earlier studies.

  14. 78 FR 21352 - Update on Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    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,...

  15. Discovery of Active Hydrothermal Sites Along the Mariana Volcanic Arc, Western Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Baker, E. T.; Embley, R. W.; Resing, J. A.; Lupton, J. E.; Massoth, G. J.; de Ronde, C. E.; Nakamura, K.; Walker, S. L.

    2003-12-01

    Some 20,000 km of volcanic arcs, roughly one-third the total length of the global midocean ridge (MOR) system, rim the western Pacific Ocean. But compared to 25 years of hydrothermal investigations along MORs, exploration of similar activity on the estimated 600 submarine arc volcanoes is only beginning. In February 2003, as part of the Submarine Ring of Fire project funded by NOAA's Ocean Exploration Program, we made the first systematic survey of hydrothermal activity along the 1270-km-long Mariana intraoceanic volcanic arc, which lies almost entirely within the US EEZ. Prior fieldwork had documented active (but low-temperature) hydrothermal discharge on only three volcanoes: Kasuga 2, Kasuga 3, and Esmeralda Bank. During the cruise, we conducted 70 CTD operations over more than 50 individual volcanoes from 13° N to 23° N, plus a continuous CTD survey along 75 km of the back-arc spreading center (13° 15'N to 13° 41'N) adjacent to the southern end of the arc. We found evidence for active hydrothermal venting at 11 submarine volcanoes with summit (or caldera floor) depths ranging from 50 to 1550 m. Two additional sites were identified on the back-arc spreading center. Ongoing analyses of collected water samples could increase these totals. Our results confirmed continuing hydrothermal activity at Kasuga 2 (but not Kasuga 3) and Esmeralda Bank, in addition to newly discovered sites on nine other volcanoes. Many of these sites produce intense and widely dispersed plumes indicative of vigorous, high-temperature discharge. The volcanoes with active hydrothermal systems are about equally divided between those with and without summit calderas. The addition of the Marianas data greatly improves our view of hydrothermal sources along arcs. The 20,000 km of Pacific arcs can be divided between 6380 km of intraoceanic (i.e., mostly submarine) arcs and 13,880 km of island (i.e., mostly subaerial) arcs. At present, ˜15% of the total length of Pacific arcs has been surveyed

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

    SciTech Connect

    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).

  17. Dynamics and Mechanism of Efficient DNA Repair Reviewed by Active-Site Mutants

    NASA Astrophysics Data System (ADS)

    Tan, Chuang; Liu, Zheyun; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases repair the UV-induced pyrimidine dimers in damage DNA via a photoreaction which includes a series of light-driven electron transfers between the two-electron-reduced flavin cofactor FADH^- and the dimer. We report here our systematic studies of the repair dynamics in E. coli photolyase with mutation of several active-site residues. With femtosecond resolution, we observed the significant change in the forward electron transfer from the excited FADH^- to the dimer and the back electron transfer from the repaired thymines by mutation of E274A, R226A, R342A, N378S and N378C. We also found that the mutation of E274A accelerates the bond-breaking of the thymine dimer. The dynamics changes are consistent with the quantum yield study of these mutants. These results suggest that the active-site residues play a significant role, structurally and chemically, in the DNA repair photocycle.

  18. Extreme electric fields power catalysis in the active site of ketosteroid isomerase.

    PubMed

    Fried, Stephen D; Bagchi, Sayan; Boxer, Steven G

    2014-12-19

    Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI's rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme's catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.

  19. The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.

    PubMed Central

    Rudd, M D; Izban, M G; Luse, D S

    1994-01-01

    RNA polymerase II may become arrested during transcript elongation, in which case the ternary complex remains intact but further RNA synthesis is blocked. To relieve arrest, the nascent transcript must be cleaved from the 3' end. RNAs of 7-17 nt are liberated and transcription continues from the newly exposed 3' end. Factor SII increases elongation efficiency by strongly stimulating the transcript cleavage reaction. We show here that arrest relief can also occur by the addition of pyrophosphate. This generates the same set of cleavage products as factor SII, but the fragments produced with pyrophosphate have 5'-triphosphate termini. Thus, the active site of RNA polymerase II, in the presence of pyrophosphate, appears to be capable of cleaving phosphodiester linkages as far as 17 nt upstream of the original site of polymerization, leaving the ternary complex intact and transcriptionally active. Images PMID:8058756

  20. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold

    NASA Astrophysics Data System (ADS)

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-01

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  1. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  2. 13C-Methyl isocyanide as an NMR probe for cytochrome P450 active sites

    PubMed Central

    McCullough, Christopher R.; Pullela, Phani Kumar; Im, Sang-Choul; Waskell, Lucy

    2012-01-01

    The cytochromes P450 (CYPs) play a central role in many biologically important oxidation reactions, including the metabolism of drugs and other xenobiotic compounds. Because they are often assayed as both drug targets and anti-targets, any tools that provide: (a) confirmation of active site binding and (b) structural data, would be of great utility, especially if data could be obtained in reasonably high throughput. To this end, we have developed an analog of the promiscuous heme ligand, cyanide, with a 13CH3-reporter attached. This 13C-methyl isocyanide ligand binds to bacterial (P450cam) and membrane-bound mammalian (CYP2B4) CYPs. It can be used in a rapid 1D experiment to identify binders, and provides a qualitative measure of structural changes in the active site. PMID:19199046

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase".

    PubMed

    Natarajan, Aditya; Yabukarski, Filip; Lamba, Vandana; Schwans, Jason P; Sunden, Fanny; Herschlag, Daniel

    2015-08-28

    Fried et al. (Reports, 19 December 2014, p. 1510) demonstrated a strong correlation between reaction rate and the carbonyl stretching frequency of a product analog bound to ketosteroid isomerase oxyanion hole mutants and concluded that the active-site electric field provides 70% of catalysis. Alternative comparisons suggest a smaller contribution, relative to the corresponding solution reaction, and highlight the importance of atomic-level descriptions.

  6. Disposal Activities and the Unique Waste Streams at the Nevada National Security Site (NNSS)

    SciTech Connect

    Arnold, P.

    2012-10-31

    This slide show documents waste disposal at the Nevada National Security Site. Topics covered include: radionuclide requirements for waste disposal; approved performance assessment (PA) for depleted uranium disposal; requirements; program approval; the Waste Acceptance Review Panel (WARP); description of the Radioactive Waste Acceptance Program (RWAP); facility evaluation; recent program accomplishments, nuclear facility safety changes; higher-activity waste stream disposal; and, large volume bulk waste streams.

  7. Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements

    PubMed Central

    Sumner, Isaiah; Iyengar, Srinivasan S.

    2010-01-01

    We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the “transition state” towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further “tailor” the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process. PMID:22933858

  8. Non-specific binding sites help to explain mixed inhibition in mushroom tyrosinase activities.

    PubMed

    Hassani, Sorour; Haghbeen, Kamahldin; Fazli, Mostafa

    2016-10-21

    Inhibition and activation studies of tyrosinase could prove beneficial to agricultural, food, cosmetic, and pharmaceutical industries. Although non-competitive and mixed-inhibition are frequent modes observed in kinetics studies on mushroom tyrosinase (MT) activities, the phenomena are left unexplained. In this study, dual effects of phthalic acid (PA) and cinnamic acid (CA) on MT during mono-phenolase activity were demonstrated. PA activated and inhibited MT at concentrations lower and higher than 150 μM, respectively. In contrast, CA inhibited and activated MT at concentrations lower and higher than 5 μM. The mode of inhibition for both effectors was mixed-type. Complex kinetics of MT in the presence of a modulator could partly be ascribed to its mixed-cooperativity. However, to explain mixed-inhibition mode, it is necessary to demonstrate how the ternary complex of substrate/enzyme/effector is formed. Therefore, we looked for possible non-specific binding sites using MT tropolone-bound PDB (2Y9X) in the computational studies. When tropolone was in MTPa (active site), PA and CA occupied different pockets (named MTPb and MTPc, respectively). The close Moldock scores of PA binding posed in MTPb and MTPa suggested that MTPb could be a secondary binding site for PA. Similar results were obtained for CA. Ensuing results from 10 ns molecular dynamics simulations for 2Y9X-effector complexes indicated that the structures were gradually stabilized during simulation. Tunnel analysis by using CAVER Analyst and CHEXVIS resulted in identifying two distinct channels that assumingly participate in exchanging the effectors when the direct channel to MTPa is not accessible.

  9. Crystal Structure of Albaflavenone Monooxygenase Containing a Moonlighting Terpene Synthase Active Site*

    PubMed Central

    Zhao, Bin; Lei, Li; Vassylyev, Dmitry G.; Lin, Xin; Cane, David E.; Kelly, Steven L.; Yuan, Hang; Lamb, David C.; Waterman, Michael R.

    2009-01-01

    Albaflavenone synthase (CYP170A1) is a monooxygenase catalyzing the final two steps in the biosynthesis of this antibiotic in the soil bacterium, Streptomyces coelicolor A3(2). Interestingly, CYP170A1 shows no stereo selection forming equal amounts of two albaflavenol epimers, each of which is oxidized in turn to albaflavenone. To explore the structural basis of the reaction mechanism, we have studied the crystal structures of both ligand-free CYP170A1 (2.6 Å) and complex of endogenous substrate (epi-isozizaene) with CYP170A1 (3.3 Å). The structure of the complex suggests that the proximal epi-isozizaene molecules may bind to the heme iron in two orientations. In addition, much to our surprise, we have found that albaflavenone synthase also has a second, completely distinct catalytic activity corresponding to the synthesis of farnesene isomers from farnesyl diphosphate. Within the cytochrome P450 α-helical domain both the primary sequence and x-ray structure indicate the presence of a novel terpene synthase active site that is moonlighting on the P450 structure. This includes signature sequences for divalent cation binding and an α-helical barrel. This barrel is unusual because it consists of only four helices rather than six found in all other terpene synthases. Mutagenesis establishes that this barrel is essential for the terpene synthase activity of CYP170A1 but not for the monooxygenase activity. This is the first bifunctional P450 discovered to have another active site moonlighting on it and the first time a terpene synthase active site is found moonlighting on another protein. PMID:19858213

  10. Quantifying the growth of a rapidly eroding bedrock gorge using repeat terrestrial Lidar

    NASA Astrophysics Data System (ADS)

    Cook, K. L.

    2012-12-01

    The Da'an River Gorge in western Taiwan provides a unique opportunity to observe the formation and evolution of a natural bedrock gorge. The 1.2 km long and up to 20 m deep gorge has formed since 1999 in response to uplift of the riverbed during the Chi-Chi earthquake. The extremely rapid pace of erosion enables us to observe both downcutting and channel widening over short time periods. We have monitored the evolution of the gorge since 2009 using repeat RTK GPS surveys and terrestrial Lidar scans. GPS surveys of the channel profile are conducted frequently, with 24 surveys to date, while Lidar scans are conducted after major floods, or after 5-9 months without a flood, for a total of 8 scans to date. The Lidar data are most useful for recording erosion of channel walls, which is quite episodic and highly variable along the channel. By quantifying the distribution of wall erosion in space and time, we can improve our understanding of channel widening processes and of the development of the channel planform, particularly the growth of bends. During the summer of 2012, the Da'an catchment experienced two large storm events, a meiyu (plum rain) event on June 10-13 that brought 800 mm of rain, and a typhoon on August 1-3 that brought 650 mm of rain. The resulting floods had significant geomorphic effects on the Da'an gorge, including up to 10s of meters of erosion on some sections of the gorge walls. We quantify these changes using Lidar surveys conducted on June 7, July 3, and in mid-August. Channel wall collapses also occur in the absence of large floods, and we use scans from August 23, 2011 and June 7, 2012 to quantify erosion during a period that included a number of small floods, but no large ones. This allows us to compare the impact of 9 months of normal conditions to the impact of short-duration extreme events.Before June flood After June flood

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

    SciTech Connect

    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.

    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

  12. Site-specific mutagenesis and functional analysis of active sites of sulfur oxygenase reductase from Gram-positive moderate thermophile Sulfobacillus acidophilus TPY.

    PubMed

    Zhang, Huijun; Guo, Wenbin; Xu, Changan; Zhou, Hongbo; Chen, Xinhua

    2013-12-14

    Sequence alignments revealed that the conserved motifs of SORSa which formed an independent branch between archaea and Gram-negative bacteria SORs according to the phylogenetic relationship were similar with the archaea and Gram-negative bacteria SORs. In order to investigate the active sites of SORSa, cysteines 31, 101 and 104 (C31, C101, C104), histidines 86 and 90 (H86 and H90) and glutamate 114 (E114) of SORSa were chosen as the target amino acid residues for site-specific mutagenesis. The wild type and six mutant SORs were expressed in E. coli BL21, purified and confirmed by SDS-PAGE and Western blotting analysis. Enzyme activity determination revealed that the active sites of SORSa were identical with the archaea and Gram-negative bacteria SORs reported. Replacement of any cysteine residues reduced SOR activity by 53-100%, while the mutants of H86A, H90A and E114A lost their enzyme activities largely, only remaining 20%, 19% and 32% activity of the wild type SOR respectively. This study will enrich our awareness for active sites of SOR in a Gram-positive bacterium.

  13. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes

    PubMed Central

    Herschlag, Daniel

    2016-01-01

    Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes. PMID:27501145

  14. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    NASA Astrophysics Data System (ADS)

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-01

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5‧-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  15. Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

    PubMed

    Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

    2015-12-11

    Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases.

  16. A Relaxed Active Site After Exon Ligation by the Group I Intron

    SciTech Connect

    Lipchock,S.; Strobel, S.

    2008-01-01

    During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

  17. Kinetic Study of the Active Site Structure of β-Amylase from Bacillus cereus var. mycoides.

    PubMed

    Nitta, Y; Shirakawa, M; Takasaki, Y

    1996-01-01

    The subsite affinities of the active site of β-amylase from Bacillus cereus var. mycoides were evaluated based on Hiromi's theory, using (14)C-radiolabeled maltooligosaccharides as substrate. It was estimated that the active site consisted of six subsites, and all subsite affinities could be evaluated. The active site had a common subsite arrangement with those of β -amylases from soybean and wheat bran. The intrinsic breakdown rate constant of α-1,4 glucosidic linkage (kint) was five to seven times as large as those of the other enzymes.From the pH dependence of log[k0/Km], pK values of two functional ionizable groups were pK1 =4.0 and pK2 = 8.4. The pK values were 0.5-0.6 units for pK1 and 0.2-0.3 units for pK2 larger than those of the other enzymes. For the affinity-labeling of this enzyme by 2, 3 epoxypropyl α-D-glucopyranoside (α-EPG), the binding affinity of α-EPG was 1-1.6kcal/mol larger than those of the other β-amylases.

  18. Identification of active site residues of Fenugreek β-amylase: chemical modification and in silico approach.

    PubMed

    Srivastava, Garima; Singh, Vinay K; Kayastha, Arvind M

    2014-10-01

    The amino acid sequence of Fenugreek β-amylase is not available in protein data bank. Therefore, an attempt has been made to identify the catalytic amino acid residues of enzyme by employing studies of pH dependence of enzyme catalysis, chemical modification and bioinformatics. Treatment of purified Fenugreek β-amylase with EDAC in presence of glycine methyl ester and sulfhydryl group specific reagents (IAA, NEM and p-CMB), followed a pseudo first-order kinetics and resulted in effective inactivation of enzyme. The reaction with EDAC in presence of NTEE (3-nitro-l-tyrosine ethylester) resulted into modification of two carboxyl groups per molecule of enzyme and presence of one accessible sulfhydryl group at the active site, per molecule of enzyme was ascertained by titration with DTNB. The above results were supported by the prevention of inactivation of enzyme in presence of substrate. Based on MALDI-TOF analysis of purified Fenugreek β-amylase and MASCOT search, β-amylase of Medicago sativa was found to be the best match. To further confirm the amino acid involved in catalysis, homology modelling of β-amylase of M. sativa was performed. The sequence alignment, superimposition of template and target models, along with study of interactions involved in docking of sucrose and maltose at the active site, led to identification of Glu187, Glu381 and Cys344 as active site residues.

  19. Active site structure and catalytic mechanism of phosphodiesterase for degradation of intracellular second messengers

    NASA Astrophysics Data System (ADS)

    Zhan, Chang-Guo

    2002-03-01

    Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulate intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it was uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand has been determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.

  20. Aerosol measurements at a high-elevation site: composition, size, and cloud condensation nuclei activity

    SciTech Connect

    Friedman, Beth; Zelenyuk, Alla; Beranek, Josef; Kulkarni, Gourihar R.; Pekour, Mikhail S.; Hallar, Anna G.; McCubbin, Ian; Thornton, Joel A.; Cziczo, D. J.

    2013-12-09

    We present measurements of CCN concentrations and associated aerosol composition and size properties at a high-elevation research site in March 2011. CCN closure and aerosol hygroscopicity were assessed using simplified assumptions of bulk aerosol properties as well as a new method utilizing single particle composition and size to assess the importance of particle mixing state in CCN activation. Free troposphere analysis found no significant difference between the CCN activity of free tropospheric aerosol and boundary layer aerosol at this location. Closure results indicate that using only size and number information leads to adequate prediction, in the majority of cases within 50%, of CCN concentrations, while incorporating the hygroscopicity parameters of the individual aerosol components measured by single particle mass spectrometry adds to the agreement, in most cases within 20%, between predicted and measured CCN concentrations. For high-elevation continental sites, with largely aged aerosol and low amounts of local area emissions, a lack of chemical knowledge and hygroscopicity may not hinder models in predicting CCN concentrations. At sites influenced by fresh emissions or more heterogeneous particle types, single particle composition information may be more useful in predicting CCN concentrations and understanding the importance of particle mixing state on CCN activation.

  1. Thermal regime of active layer at two lithologically contrasting sites on James Ross Island, Antarctic Peninsula.

    NASA Astrophysics Data System (ADS)

    Hrbáček, Filip; Nývlt, Daniel; Láska, Kamil

    2016-04-01

    Antarctic Peninsula region (AP) represents one of the most rapidly warming parts of our planet in the last 50 years. Despite increasing research activities along both western and eastern sides of AP in last decades, there is still a lot of gaps in our knowledge relating to permafrost, active layer and its thermal and physical properties. This study brings new results of active layer monitoring on James Ross Island, which is the largest island in northern AP. Its northern part, Ulu Peninsula, is the largest ice-free area (more than 200 km2) in the region. Due its large area, we focused this study on sites located in different lithologies, which would affect local thermal regime of active layer. Study site (1) at Abernethy Flats area (41 m a.s.l.) lies ~7 km from northern coast. Lithologically is formed by disintegrated Cretaceous calcareous sandstones and siltstones of the Santa Marta Formation. Study site (2) is located at the northern slopes of Berry Hill (56 m a.s.l.), about 0.4 km from northern coastline. Lithology is composed of muddy to intermediate diamictites, tuffaceous siltstones to fine grained sandstones of the Mendel Formation. Data of air temperature at 2 meters above ground and the active layer temperatures at 75 cm deep profiles were obtained from both sites in period 1 January 2012 to 31 December 2014. Small differences were found when comparing mean air temperatures and active temperatures at 5 and 75 cm depth in the period 2012-2014. While the mean air temperatures varied between -7.7 °C and -7.0 °C, the mean ground temperatures fluctuated between -6.6 °C and -6.1 °C at 5 cm and -6.9 °C and -6.0 °C at 75 cm at Abernethy Flats and Berry Hill slopes respectively. Even though ground temperature differences along the profiles weren't pronounced during thawing seasons, the maximum active layer thickness was significantly larger at Berry Hill slopes (80 to 82 cm) than at Abernethy Flats (52 to 64 cm). We assume this differences are affected by

  2. Alkynol natural products target ALDH2 in cancer cells by irreversible binding to the active site.

    PubMed

    Heydenreuter, Wolfgang; Kunold, Elena; Sieber, Stephan A

    2015-11-11

    Falcarinol and stipudiol are natural products with potent anti-cancer activity found in several vegetables. Here, we use a chemical proteomic strategy to identify ALDH2 as a molecular target of falcarinol in cancer cells and confirm enzyme inhibition via covalent alkylation of the active site. Furthermore, the synthesis of stipudiol led to the observation that ALDH2 exhibits preference for alkynol-based binders. Inhibition of ALDH2 impairs detoxification of reactive aldehydes and limits oxidative stress response, two crucial pathways for cellular viability.

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

    SciTech Connect

    Sultatos, L.G. Kaushik, R.

    2008-08-01

    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 B{sub max} and K{sub d} 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 B{sub max} 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 B{sub max}, would accompany the decreased rigidity of bound thioflavin t molecules. The organophosphate-induced alterations in K{sub d} represented changes in binding affinity of thioflavin t, with diethylphosphorylation of Ser203 increasing K{sub d}, and dimethylphosphorylation of Ser203 decreasing K{sub d}. 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.

  4. Stochastic analysis of myoelectric temporal signatures for multifunctional single-site activation of prostheses and orthoses.

    PubMed

    Graupe, D; Salahi, J; Zhang, D S

    1985-01-01

    This paper is concerned with a stochastic time-series analysis of the temporal signatures of myoelectric (ME) signals including the determination of model order and sampling rate. The paper considers the use of time-series parameters for the activation of artificial limbs for high-level amputees, of stimulation electrodes or of powered braces for paralysed persons, in several degrees of freedom, from a single or two surface-electrode pairs at locations where considerable ME cross-talk exists. The multifunctional capability from a single site is based on the differences between the time-series (TS) parameters for different muscle activation patterns at the same ME site, these differences being thus used for limb function discrimination via easily trainable muscle activation patterns at the vicinity of the electrode site. Specifically, the analysis is in terms of identifying the AR parameters of a time-domain autoregressive (AR) signature model both for the complete ME spectrum and for parts thereof, and in terms of the autocorrelation of the signal and of the models residual. Determination of sampling rate and of model orders is discussed in detail. It is shown that, using online real-time analysis, differences in the AR time-series parameters can be observed for different trainable patterns of muscle activation, at the same electrode location, even at the same ME power levels, as long as considerable cross-talk exists at the electrode site. These parameter differences can be accentuated if one considers the AR parameters for lower-frequency spectral windows. A case is made in this paper for employing TS analysis to squeeze out information in a distinct but low-level ripple of the low frequency spectrum of the signal. This information tends to be ignored in frequency domain, but is all that the AR parameters care for in TS analysis, since they are not concerned, with a flat-average low-frequency spectrum, i.e., its white-noise-like part, which is the residual term

  5. Flexibility Matters: Cooperative Active Sites in Covalent Organic Framework and Threaded Ionic Polymer.

    PubMed

    Sun, Qi; Aguila, Briana; Perman, Jason; Nguyen, Nicholas; Ma, Shengqian

    2016-12-07

    The combination of two or more reactive centers working in concert on a substrate to facilitate the reaction is now considered state of the art in catalysis, yet there still remains a tremendous challenge. Few heterogeneous systems of this sort have been exploited, as the active sites spatially separated within the rigid framework are usually difficult to cooperate. It is now shown that this roadblock can be surpassed. The underlying principle of the strategy presented here is the integration of catalytic components with excellent flexibility and porous heterogeneous catalysts, as demonstrated by the placement of linear ionic polymers in close proximity to surface Lewis acid active sites anchored on the walls of a covalent organic framework (COF). Using the cycloaddition of the epoxides and CO2 as a model reaction, dramatic activity improvements have been achieved for the composite catalysts in relation to the individual catalytic component. Furthermore, they also clearly outperform the benchmark catalytic systems formed by the combination of the molecular organocatalysts and heterogeneous Lewis acid catalysts, while affording additional recyclability. The extraordinary flexibility and enriched concentration of the catalytically active moieties on linear polymers facilitate the concerted catalysis, thus leading to superior catalytic performance. This work therefore uncovers an entirely new strategy for designing bifunctional catalysts with double-activation behavior and opens a new avenue in the design of multicapable systems that mimic biocatalysis.

  6. Effect of prolonged exposure to organic solvents on the active site environment of subtilisin Carlsberg.

    PubMed

    Bansal, Vibha; Delgado, Yamixa; Fasoli, Ezio; Ferrer, Amaris; Griebenow, Kai; Secundo, Francesco; Barletta, Gabriel L

    2010-06-01

    The potential of enzyme catalysis as a tool for organic synthesis is nowadays indisputable, as is the fact that organic solvents affect an enzyme's activity, selectivity and stability. Moreover, it was recently realized that an enzyme's initial activity is substantially decreased after prolonged exposure to organic media, an effect that further hampers their potential as catalysts for organic synthesis. Regrettably, the mechanistic reasons for these effects are still debatable. In the present study we have made an attempt to explain the reasons behind the partial loss of enzyme activity on prolonged exposure to organic solvents. Fluorescence spectroscopic studies of the serine protease subtilisin Carlsberg chemically modified with polyethylene glycol (PEG-SC) and inhibited with a Dancyl fluorophore, and dissolved in two organic solvents (acetonitrile and 1,4-dioxane) indicate that when the enzyme is initially introduced into these solvents, the active site environment is similar to that in water; however prolonged exposure to the organic medium causes this environment to resemble that of the solvent in which the enzyme is dissolved. Furthermore, kinetic studies show a reduction on both V(max) and K(M) as a result of prolonged exposure to the solvents. One interpretation of these results is that during this prolonged exposure to organic solvents the active-site fluorescent label inhibitor adopts a different binding conformation. Extrapolating this to an enzymatic reaction we argue that substrates bind in a less catalytically favorable conformation after the enzyme has been exposed to organic media for several hours.

  7. Orthogonal electrode catheter array for mapping of endocardial focal site of ventricular activation

    SciTech Connect

    Desai, J.M.; Nyo, H.; Vera, Z.; Seibert, J.A.; Vogelsang, P.J. )

    1991-04-01

    Precise location of the endocardial site of origin of ventricular tachycardia may facilitate surgical and catheter ablation of this arrhythmia. The endocardial catheter mapping technique can locate the site of ventricular tachycardia within 4-8 cm2 of the earliest site recorded by the catheter. This report describes an orthogonal electrode catheter array (OECA) for mapping and radiofrequency ablation (RFA) of endocardial focal site of origin of a plunge electrode paced model of ventricular activation in dogs. The OECA is an 8 F five pole catheter with four peripheral electrodes and one central electrode (total surface area 0.8 cm{sup 2}). In eight mongrel dogs, mapping was performed by arbitrarily dividing the left ventricle (LV) into four segments. Each segment was mapped with OECA to find the earliest segment. Bipolar and unipolar electrograms were obtained. The plunge electrode (not visible on fluoroscopy) site was identified by the earliest wave front arrival times of -30 msec or earlier at two or more electrodes (unipolar electrograms) with reference to the earliest recorded surface ECG (I, AVF, and V1). Validation of the proximity of the five electrodes of the OECA to the plunge electrode was performed by digital radiography and RFA. Pathological examination was performed to document the proximity of the OECA to the plunge electrode and also for the width, depth, and microscopic changes of the ablation. To find the segment with the earliest LV activation a total of 10 {plus minus} 3 (mean {plus minus} SD) positions were mapped. Mean arrival times at the two earlier electrodes were -39 {plus minus} 4 msec and -35 {plus minus} 3 msec. Digital radiography showed the plunge electrode to be within the area covered by all five electrodes in all eight dogs. The plunge electrode was within 1 cm2 area of the region of RFA in all eight dogs.

  8. Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity.

    PubMed

    Mottin, Melina; Braga, Rodolpho C; da Silva, Roosevelt A; Silva, Joao H Martins da; Perryman, Alexander L; Ekins, Sean; Andrade, Carolina Horta

    2017-03-21

    America is still suffering with the outbreak of Zika virus (ZIKV) infection. Congenital ZIKV syndrome has already caused a public health emergency of international concern. However, there are still no vaccines to prevent or drugs to treat the infection caused by ZIKV. The ZIKV NS3 helicase (NS3h) protein is a promising target for drug discovery due to its essential role in viral genome replication. NS3h unwinds the viral RNA to enable the replication of the viral genome by the NS5 protein. NS3h contains two important binding sites: the NTPase binding site and the RNA binding site. Here, we used molecular dynamics (MD) simulations to study the molecular behavior of ZIKV NS3h in the presence and absence of ssRNA and the potential implications for NS3h activity and inhibition. Although there is conformational variability and poor electron densities of the RNA binding loop in various apo flaviviruses NS3h crystallographic structures, the MD trajectories of NS3h-ssRNA demonstrated that the RNA binding loop becomes more stable when NS3h is occupied by RNA. Our results suggest that the presence of RNA generates important interactions with the RNA binding loop, and these interactions stabilize the loop sufficiently that it remains in a closed conformation. This closed conformation likely keeps the ssRNA bound to the protein for a sufficient duration to enable the unwinding/replication activities of NS3h to occur. In addition, conformational changes of this RNA binding loop can change the nature and location of the optimal ligand binding site, according to ligand binding site prediction results. These are important findings to help guide the design and discovery of new inhibitors of NS3h as promising compounds to treat the ZIKV infection.

  9. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

    PubMed Central

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-01-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

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

    SciTech Connect

    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.

  11. Control of the active site structure of giant bilayer hemoglobin from the Annelid Eisenia foetida using hierarchic assemblies

    SciTech Connect

    Girasole, Marco; Arcovito, Alessandro; Marconi, Augusta; Davoli, Camilla; Congiu-Castellano, Agostina; Bellelli, Andrea; Amiconi, Gino

    2005-12-05

    The active site structure of the oxygenated derivative of the main subassemblies (whole protein, dodecamers, and trimers) of the giant haemoglobin from Eisenia foetida has been characterized by x-ray absorption near edge structure spectroscopy. The data revealed a remarkable effect of the hierarchic assemblies on the active site of the subunit. Specifically, the whole protein has the same site structure of the dodecamer, while a sharp conformational transition occurs when the dodecamer is disassembled into trimers (and monomers) revealing that constraints due to the protein matrix determine the active site geometry and, consequently, the protein function in these large complexes.

  12. Extracellular matrix-specific focal adhesions in vascular smooth muscle produce mechanically active adhesion sites

    PubMed Central

    Sun, Zhe; Martinez-Lemus, Luis A.; Hill, Michael A.; Meininger, Gerald A.

    2008-01-01

    Integrin-mediated mechanotransduction in vascular smooth muscle cells (VSMCs) plays an important role in the physiological control of tissue blood flow and vascular resistance. To test whether force applied to specific extracellular matrix (ECM)-integrin interactions could induce myogenic-like mechanical activity at focal adhesion sites, we used atomic force microscopy (AFM) to apply controlled forces to specific ECM adhesion sites on arteriolar VSMCs. The tip of AFM probes were fused with a borosilicate bead (2∼5 μm) coated with fibronectin (FN), collagen type I (CNI), laminin (LN), or vitronectin (VN). ECM-coated beads induced clustering of α5- and β3-integrins and actin filaments at sites of bead-cell contact indicative of focal adhesion formation. Step increases of an upward (z-axis) pulling force (800∼1,600 pN) applied to the bead-cell contact site for FN-specific focal adhesions induced a myogenic-like, force-generating response from the VSMC, resulting in a counteracting downward pull by the cell. This micromechanical event was blocked by cytochalasin D but was enhanced by jasplakinolide. Function-blocking antibodies to α5β1- and αvβ3-integrins also blocked the micromechanical cell event in a concentration-dependent manner. Similar pulling experiments with CNI, VN, or LN failed to induce myogenic-like micromechanical events. Collectively, these results demonstrate that mechanical force applied to integrin-FN adhesion sites induces an actin-dependent, myogenic-like, micromechanical event. Focal adhesions formed by different ECM proteins exhibit different mechanical characteristics, and FN appears of particular relevance in its ability to strongly attach to VSMCs and to induce myogenic-like, force-generating reactions from sites of focal adhesion in response to externally applied forces. PMID:18495809

  13. Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic

    PubMed Central

    Esselborn, Julian; Berggren, Gustav; Noth, Jens; Siebel, Judith; Hemschemeier, Anja; Artero, Vincent; Reijerse, Edward; Fontecave, Marc; Lubitz, Wolfgang; Happe, Thomas

    2013-01-01

    Hydrogenases catalyze the formation of hydrogen. The cofactor (H-cluster) of [FeFe]-hydrogenases consists of a [4Fe-4S]-cluster bridged to a unique [2Fe]-subcluster whose biosynthesis in vivo requires hydrogenase-specific maturases. Here we show that a chemical mimic of the [2Fe]-subcluster can reconstitute apo-hydrogenase to full activity, independent of helper proteins. The assembled H-cluster is virtually indistinguishable from the native cofactor. This procedure will be a powerful tool for developing novel artificial H2-producing catalysts. PMID:23934246

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

    PubMed Central

    Lin, Xiaofeng; Ayrapetov, Marina K; Sun, Gongqin

    2005-01-01

    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. PMID:16305747

  15. Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P.

    PubMed Central

    Kufel, J; Kirsebom, L A

    1996-01-01

    We have studied RNase P RNA (M1 RNA) cleavage of model tRNA precursors that are cleaved at two independent positions. Here we present data demonstrating that cleavage at both sites depends on the 2'-OH immediately 5' of the respective cleavage site. However, we show that the 2-amino group of a guanosine at the cleavage site plays a significant role in cleavage at one of these sites but not at the other. These data suggest that these two cleavage sites are handled differently by the ribozyme. This theory is supported by our finding that the cross-linking pattern between Ml RNA and tRNA precursors carrying 4-thioU showed distinct differences, depending on the location of the 4-thioU relative to the respective cleavage site. These findings lead us to suggest that different cleavage sites are aligned differently in the active site, possibly as a result of different binding modes of a substrate to M1 RNA. We discuss a model in which the interaction between the 3'-terminal "RCCA" motif (first three residues interact) of a tRNA precursor and M1 RNA plays a significant role in this process. Images Fig. 2 Fig. 3 Fig. 4 PMID:8650223

  16. Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism

    SciTech Connect

    Gallagher, D.T.; Robinson, H.; Kim, S.-K.; Reddy, P. T.

    2011-01-21

    Adenylyl cyclases (ACs) belonging to three nonhomologous classes (II, III, and IV) have been structurally characterized, enabling a comparison of the mechanisms of cyclic adenosine 3',5'-monophosphate biosynthesis. We report the crystal structures of three active-site complexes for Yersinia pestis class IV AC (AC-IV)-two with substrate analogs and one with product. Mn{sup 2+} binds to all three phosphates, and to Glu12 and Glu136. Electropositive residues Lys14, Arg63, Lys76, Lys111, and Arg113 also form hydrogen bonds to phosphates. The conformation of the analogs is suitable for in-line nucleophilic attack by the ribose O3' on {alpha}-phosphate (distance {approx} 4 {angstrom}). In the product complex, a second Mn ion is observed to be coordinated to both ribose 2' oxygen and ribose 3' oxygen. Observation of both metal sites, together with kinetic measurements, provides strong support for a two-cation mechanism. Eleven active-site mutants were also made and kinetically characterized. These findings and comparisons with class II and class III enzymes enable a detailed transphyletic analysis of the AC mechanism. Consistent with its lack of coordination to purine, Y. pestis AC-IV cyclizes both ATP and GTP. As in other classes of AC, the ribose is loosely bound, and as in class III, no base appears to ionize the O3' nucleophile. Different syn/anti conformations suggest that the mechanism involves a conformational transition, and further evidence suggests a role for ribosyl pseudorotation. With resolutions of 1.6-1.7 {angstrom}, these are the most detailed active-site ligand complexes for any class of this ubiquitous signaling enzyme.

  17. Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism

    SciTech Connect

    D Gallagher; S Kim; H Robinson; P Reddy

    2011-12-31

    Adenylyl cyclases (ACs) belonging to three nonhomologous classes (II, III, and IV) have been structurally characterized, enabling a comparison of the mechanisms of cyclic adenosine 3',5'-monophosphate biosynthesis. We report the crystal structures of three active-site complexes for Yersinia pestis class IV AC (AC-IV) - two with substrate analogs and one with product. Mn{sup 2+} binds to all three phosphates, and to Glu12 and Glu136. Electropositive residues Lys14, Arg63, Lys76, Lys111, and Arg113 also form hydrogen bonds to phosphates. The conformation of the analogs is suitable for in-line nucleophilic attack by the ribose O3' on {alpha}-phosphate (distance {approx} 4 {angstrom}). In the product complex, a second Mn ion is observed to be coordinated to both ribose 2' oxygen and ribose 3' oxygen. Observation of both metal sites, together with kinetic measurements, provides strong support for a two-cation mechanism. Eleven active-site mutants were also made and kinetically characterized. These findings and comparisons with class II and class III enzymes enable a detailed transphyletic analysis of the AC mechanism. Consistent with its lack of coordination to purine, Y. pestis AC-IV cyclizes both ATP and GTP. As in other classes of AC, the ribose is loosely bound, and as in class III, no base appears to ionize the O3' nucleophile. Different syn/anti conformations suggest that the mechanism involves a conformational transition, and further evidence suggests a role for ribosyl pseudorotation. With resolutions of 1.6-1.7 {angstrom}, these are the most detailed active-site ligand complexes for any class of this ubiquitous signaling enzyme.

  18. Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site.

    PubMed

    Prado, R A; Barbosa, J A; Ohmiya, Y; Viviani, V R

    2011-07-01

    The structural origin and evolution of bioluminescent activity of beetle luciferases from AMP/CoA ligases remains a mystery. Previously we cloned the luciferase-like enzyme from Zophobas morio mealworm, a reasonable protoluciferase model that could shine light on this mystery. Kinetic characterization and studies with D- and L-luciferin and their adenylates showed that stereoselectivity constitutes a critical feature for the origin of luciferase activity in AMP/CoA ligases. Comparison of the primary structures and modeling studies of this protoluciferase and the three main families of beetle luciferases showed that the carboxylic acid substrate binding site of this enzyme is smaller and more hydrophobic than the luciferin binding site of beetle luciferases, showing several substitutions of otherwise conserved residues. Thus, here we performed a site-directed mutagenesis survey of the carboxylic binding site motifs of the protoluciferase by replacing their residues by the respective conserved ones found in beetle luciferases in order to identify the structural determinants of luciferase/oxygenase activity. Although most of the substitutions had negative impact on the luminescence activity of the protoluciferase, only the substitution I327T improved the luminescence activity, resulting in a broad and 15 nm blue-shifted luminescence spectrum. Such substitution indicates the importance of the loop motif 322YGMSEI327 (341YGLTETT347 in Photinus pyralis luciferase) for luciferase activity, and indicates a possible route for the evolution of bioluminescence function of beetle luciferases.

  19. Burial diagenesis in the Upper Devonian reef complexes of the Geikie Gorge region, Canning basin, Western Australia

    SciTech Connect

    Wallace, M.W. ); Kerans, C. ); Playford, P.E. ); McManus, A. )

    1991-06-01

    The Devonian carbonates of the Geikie Gorge region, Canning basin, have undergone a long and complex diagenetic history that began in Devonian seawater with extensive marine cementation of platform-margin lithologies. Devonian-Lower Carboniferous burial diagenesis was the most important porosity occluding episode because almost all primary porosity was destroyed by equant calcite cements during this interval. Dolomitization and consequent secondary porosity development also occurred during early burial diagenesis. The distribution and geochemistry of the major calcite cements and dolomite types are consistent with these phases having been precipitated from connate marine or basinal brines. Karstification and minor calcite cementation took place during late Carboniferous subaerial exposure. Minor calcite cementation occurred during Permian-Cenozoic burial, predominantly in secondary porosity within pervasively dolomitized lithologies. Karstification, dedolomitization, and calcite recrystallization took place in association with Cenozoic meteoric diagenesis. Secondary moldic and intercrystalline porosity within the completely dolomitized lithologies were the longest lived porosity types in the carbonates. Some secondary porosity escaped both Devonian-Carboniferous and Permian-Cenozoic burial cementation, probably due to a lack of nucleation sites for calcite cements within completely dolomitized lithologies.

  20. Assessment of the impacts of land use changes on nonpoint source pollution inputs upstream of the Three Gorges Reservoir.

    PubMed

    Yang, Huicai; Wang, Guoqiang; Yang, Yan; Xue, Baolin; Wu, Binbin

    2014-01-01

    In recent years, land use upstream of the Three Gorges Reservoir (TGR) has changed significantly because of the TGR project. In this study, the Soil and Water Assessment Tool (SWAT) model was examined for its ability to assess relationships between land use changes and nonpoint pollutant indexes upstream of the TGR. Results indicated that the SWAT model, calibrated with the adjusted parameters, could successfully reproduce the nonpoint indexes at the water quality monitoring sites in the two rivers. The different land use change types were shown to be sensitive to nonpoint pollutants in the study area. The land use change type from upland to water was the strongest influence on changes in total nitrogen and total phosphorus. An empirical regression equation between nonpoint indexes and different land use change types was developed for the study area by partial least squares regression (PLSR) as follows: Y = b 0 + ∑ i=1 (m) b i X i. This regression equation was useful for evaluating the influence of land use change types on changes in nonpoint pollutants over a long time period. The results from this study may be useful for the TGR management and may help to reduce nonpoint pollutant loads into downstream water bodies.

  1. Assessing soil heavy metal pollution in the water-level-fluctuation zone of the Three Gorges Reservoir, China.

    PubMed

    Ye, Chen; Li, Siyue; Zhang, Yulong; Zhang, Quanfa

    2011-07-15

    The water-level-fluctuation zone (WLFZ) between the elevations of 145-175 m in China's Three Gorges Reservoir has experienced a novel hydrological regime with half a year (May-September) exposed in summer and another half (October-April) submerged in winter. In September 2008 (before submergence) and June 2009 (after submergence), soil samples were collected in 12 sites in the WLFZ and heavy metals (Hg, As, Cr, Cd, Pb, Cu, Zn, Fe, and Mn) were determined. Enrichment factor (EF), factor analysis (FA), and factor analysis-multiple linear regression (FA-MLR) were employed for heavy metal pollution assessment, source identification, and source apportionment, respectively. Results demonstrate spatial variability in heavy metals before and after submergence and elements of As, Cd, Pb, Cu, and Zn are higher in the upper and low reaches. FA and FA-MLR reveal that As and Cd are the primary pollutants before submergence, and over 45% of As originates from domestic sewage and 59% of Cd from industrial wastes. After submergence, the major contaminants are Hg, Cd, and Pb, and traffic exhaust contributes approximately 81% to Hg and industrial effluent accounts about 36% and 73% for Cd and Pb, respectively. Our results suggest that increased shipping and industrial wastes have deposited large amounts of heavy metals which have been accumulated in the WLFZ during submergence period.

  2. Musk Kinase Activity is Modulated By A Serine Phosphorylation Site in The Kinase Loop.

    PubMed

    Camurdanoglu, B Z; Hrovat, C; Dürnberger, G; Madalinski, M; Mechtler, K; Herbst, R

    2016-09-26

    The neuromuscular junction (NMJ) forms when a motor neuron contacts a muscle fibre. A reciprocal exchange of signals initiates a cascade of signalling events that result in pre- and postsynaptic differentiation. At the centre of these signalling events stands muscle specific kinase (MuSK). MuSK activation, kinase activity and subsequent downstream signalling are crucial for NMJ formation as well as maintenance. Therefore MuSK kinase activity is tightly regulated to ensure proper NMJ development. We have identified a novel serine phosphorylation site at position 751 in MuSK that is increasingly phosphorylated upon agrin stimulation. S751 is also phosphorylated in muscle tissue and its phosphorylation depends on MuSK kinase activity. A phosphomimetic mutant of S751 increases MuSK kinase activity in response to non-saturating agrin concentrations . In addition, basal MuSK and AChR phosphorylation as well as AChR cluster size are increased. We believe that the phosphorylation of S751 provides a novel mechanism to relief the autoinhibition of the MuSK activation loop. Such a lower autoinhibition could foster or stabilize MuSK kinase activation, especially during stages when no or low level of agrin are present. Phosphorylation of S751 might therefore represent a novel mechanism to modulate MuSK kinase activity during prepatterning or NMJ maintenance.

  3. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

    PubMed Central

    Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

    2016-01-01

    Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

  4. Bull Trout Population Assessment in the Columbia River Gorge : Annual Report 2000.

    SciTech Connect

    Byrne, Jim; McPeak, Ron

    2001-02-01

    We summarized existing knowledge regarding the known distribution of bull trout (Salvelinus confluentus) across four sub-basins in the Columbia River Gorge in Washington. The Wind River, Little White Salmon River, White Salmon River, and the Klickitat River sub-basins were analyzed. Cold water is essential to the survival, spawning, and rearing of bull trout. We analyzed existing temperature data, installed Onset temperature loggers in the areas of the four sub-basins where data was not available, and determined that mean daily water temperatures were <15 C and appropriate for spawning and rearing of bull trout. We snorkel surveyed more than 74 km (46.25 mi.) of rivers and streams in the four sub-basins (13.8 km at night and 60.2 km during the day) and found that night snorkeling was superior to day snorkeling for locating bull trout. Surveys incorporated the Draft Interim Protocol for Determining Bull Trout Presence (Peterson et al. In Press). However, due to access and safety issues, we were unable to randomly select sample sites nor use block nets as recommended. Additionally, we also implemented the Bull Trout/Dolly Varden sampling methodology described in Bonar et al. (1997). No bull trout were found in the Wind River, Little White Salmon, or White Salmon River sub-basins. We found bull trout in the West Fork Klickitat drainage of the Klickitat River Sub-basin. Bull trout averaged 6.7 fish/100m{sup 2} in Trappers Creek, 2.6 fish/100m{sup 2} on Clearwater Creek, and 0.4 fish/100m{sup 2} in Little Muddy Creek. Bull trout was the only species of salmonid encountered in Trappers Creek and dominated in Clearwater Creek. Little Muddy Creek was the only creek where bull trout and introduced brook trout occurred together. We found bull trout only at night and typically in low flow regimes. A single fish, believed to be a bull trout x brook trout hybrid, was observed in the Little Muddy Creek. Additional surveys are needed in the West Fork Klickitat and mainstem

  5. Interannual active layer thermal and dynamics evolution at the crater Lake CALM site, Deception Island (Antarctica).

    NASA Astrophysics Data System (ADS)

    Ramos, Miguel; Vieira, Gonzalo; Ángel De Pablo, Miguel; Molina, Antonio; Abramov, Andrey

    2015-04-01

    Deception Island, is an active strato-volcano on South Shetland Archipelago of Antarctica (62° 55' 0″ S, 60° 37' 0″ W), is a cold region with harsh remote and hostile environmental conditions. The permafrost and active layer existence, and the cold climate conditions together with volcanic material with height water content inside made this region of the Earth a perfect site to study the active layer and permafrost evolution involved in the Circumpolar Active Layer South (CALM-S) program. The active layer is measured in late January or firs february (during the end of the thaw period) at the "Crater Lake" CALM site (62°58'06.7''; 60°40'44.8'') on Deception Island, Antarctica, at the period 2006 to 2014 we obtained a mean annual value of 29,7±2 cm. In this paper, we describe the spatial active layer thickness distribution and report the reduction on the mean thickness between February 2006 and 2014. Below the active layer, permafrost could be also reported (with a mean thickness of 4.5± 0.5 m.) based on the temperature data acquired by sensors installed at different depth inside the soil; three different shallow boreholes was drilled (1.0 m., 1.6 m., 4.5 m. in depth) and we have been registered its temperature gradient at the 2010 to 2013 period. Here we use all those data 1) to describe the thermal behavior of the permafrost at the CALM site, and 2) to describe its evolution (aggradation/degradation) along fourteen years of continuous measurements. We develop this study, to known the thermal behavior of the permafrost and the active layer related with the air/soil interaction being one of the most important factors the snow layer that was measured by the installation of termo-snowmeters with the complement of an automatic digital camera during the 2008 to 2014 period. On the other hand, the pyroclastics soil materials has a very high values of water content then the latent heat in the freezing/thawing process controls the active layer evolution and the

  6. Active-site properties of Phrixotrix railroad worm green and red bioluminescence-eliciting luciferases.

    PubMed

    Viviani, V R; Arnoldi, F G C; Venkatesh, B; Neto, A J S; Ogawa, F G T; Oehlmeyer, A T L; Ohmiya, Y

    2006-10-01

    The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green- (PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferin-binding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Mutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the red-emitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.

  7. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions

    SciTech Connect

    Bondar, A.N.; Baudry, Jerome Y; Suhai, Sandor; Fischer, S.; Smith, Jeremy C

    2008-10-01

    The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.

  8. CO-dynamics in the active site of cytochrome c oxidase

    NASA Astrophysics Data System (ADS)

    Soloviov, Maksym; Meuwly, Markus

    2014-04-01

    The transfer of CO from heme a3 to the CuB site in Cytochrome c oxidase (CcO) after photolysis is studied using molecular dynamics simulations using an explicitly reactive, parametrized potential energy surface based on density functional theory calculations. After photodissociation from the heme-Fe, the CO ligand rebinds to the CuB site on the sub-picosecond time scale. Depending on the simulation protocol the characteristic time ranges from 260 fs to 380 fs which compares with an estimated 450 fs from experiment based on the analysis of the spectral changes as a function of time delay after the photodissociating pulse. Following photoexcitation ≈90% of the ligands are found to rebind to either the CuB (major component, 85%) or the heme-Fe (minor component, 2%) whereas about 10% remain in an unbound state. The infrared spectra of unbound CO in the active site is broad and featureless and no appreciable shift relative to gas-phase CO is found, which is in contrast to the situation in myoglobin. These observations explain why experimentally, unbound CO in the binuclear site of CcO has not been found as yet.

  9. Probing cathepsin K activity with a selective substrate spanning its active site.

    PubMed Central

    Lecaille, Fabien; Weidauer, Enrico; Juliano, Maria A; Brömme, Dieter; Lalmanach, Gilles

    2003-01-01

    The limited availability of highly selective cathepsin substrates seriously impairs studies designed to monitor individual cathepsin activities in biological samples. Among mammalian cysteine proteases, cathepsin K has a unique preference for a proline residue at P2, the primary determinant of its substrate specificity. Interestingly, congopain from Trypanosoma congolense also accommodates a proline residue in its S2 subsite. Analysis of a congopain model showed that amino acids forming its S2 subsite are identical with those of cathepsin K, except Leu67 which is replaced by a tyrosine residue in cathepsin K. Furthermore, amino acid residues of the congopain S2' binding pocket, which accepts a proline residue, are strictly identical with those of cathepsin K. Abz-HPGGPQ-EDN2ph [where Abz represents o-aminobenzoic acid and EDN2ph (=EDDnp) represents N -(2,4-dinitrophenyl)-ethylenediamine], a substrate initially developed for trypanosomal enzymes, was efficiently cleaved at the Gly-Gly bond by cathepsin K (kcat/ K(m)=426000 M(-1) x s(-1)). On the other hand, Abz-HPGGPQ-EDN2ph was resistant to hydrolysis by cathepsins B, F, H, L, S and V (20 nM enzyme concentration) and the Y67L (Tyr67-->Leu)/L205A cathepsin K mutant (20 nM), but still acted as a competitive inhibitor. Taken together, the selectivity of Abz-HPGGPQ-EDN2ph to cathepsin K primarily depends on the S2 and S2' subsite specificities of cathepsin K and the ionization state of histidine at P3. Whereas Abz-HPGGPQ-EDN2ph was hydrolysed by wild-type mouse fibroblast lysates, its hydrolysis was completely abolished in the cathepsin K-deficient samples, indicating that Abz-HPGGPQ-EDN2ph can be used to monitor selectively cathepsin K activity in physiological fluids and cell lysates. PMID:12837132

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

    NASA Astrophysics Data System (ADS)

    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.

    PubMed

    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.

  12. Hydroxynonenal inactivates cathepsin B by forming Michael adducts with active site residues.

    PubMed

    Crabb, John W; O'Neil, June; Miyagi, Masaru; West, Karen; Hoff, Henry F

    2002-04-01

    Oxidation of plasma low-density lipoprotein (oxLDL) generates the lipid peroxidation product 4-hydroxy-2 nonenal (HNE) and also reduces proteolytic degradation of oxLDL and other proteins internalized by mouse peritoneal macrophages in culture. This leads to accumulation of undegraded material in lysosomes and formation of ceroid, a component of foam cells in atherosclerotic lesions. To explore the possibility that HNE contributes directly to the inactivation of proteases, structure-function studies of the lysosomal protease cathepsin B have been pursued. We found that treatment of mouse macrophages with HNE reduces degradation of internalized maleyl bovine serine albumin and cathepsin B activity. Purified bovine cathepsin B treated briefly with 15 microM HNE lost approximately 76% of its protease activity and also developed immunoreactivity with antibodies to HNE adducts in Western blot analysis. After stabilization of the potential Michael adducts by sodium borohydride reduction, modified amino acids were localized within the bovine cathepsin B protein structure by mass spectrometric analysis of tryptic peptides. Michael adducts were identified by tandem mass spectrometry at cathepsin B active site residues Cys 29 (mature A chain) and His 150 (mature B chain). Thus, covalent interaction between HNE and critical active site residues inactivates cathepsin B. These results support the hypothesis that the accumulation of undegraded macromolecules in lysosomes after oxidative damage are caused in part by direct protease inactivation by adduct formation with lipid peroxidation products such as HNE.

  13. [Enhancing glutamate decarboxylase activity by site-directed mutagenesis: an insight from Ramachandran plot].

    PubMed

    Ke, Piyu; Huang, Jun; Hu, Sheng; Zhao, Weirui; Lü, Changjiang; Yu, Kai; Lei, Yinlin; Wang, Jinbo; Mei, Lehe

    2016-01-01

    Glutamate decarboxylase (GAD) can catalyze the decarboxylation of glutamate into γ-aminobutyrate (GABA) and is the only enzyme of GABA biosynthesis. Improving GAD activity and thermostability will be helpful for the highly efficient biosynthesis of GABA. According to the Ramachandran plot information of GAD 1407 three-dimensional structure from Lactobacillus brevis CGMCC No. 1306, we identified the unstable site K413 as the mutation target, constructed the mutant GAD by site-directed mutagenesis and measured the thermostability and activity of the wide type and mutant GAD. Mutant K413A led to a remarkably slower inactivation rate, and its half-life at 50 °C reached 105 min which was 2.1-fold higher than the wild type GAD1407. Moreover, mutant K413I exhibited 1.6-fold higher activity in comparison with the wide type GAD1407, although it had little improvement in thermostability of GAD. Ramachandran plot can be considered as a potential approach to increase GAD thermostability and activity.

  14. Single-site substitutions improve cold activity and increase thermostability of the dehairing alkaline protease (DHAP).

    PubMed

    Zhao, Hong-Yan; Wu, Li-Ying; Liu, Gang; Feng, Hong

    2016-12-01

    To engineer dehairing alkaline protease (DHAP) variants to improve cold activity and increase thermostability so these variants are suitable for the leather processing industry. Based on previous studies with bacterial alkaline proteases, double-site mutations (W106K/V149I and W106K/M124L) were introduced into the DHAP from Bacillus pumilus. Compared with the wild-type DHAP hydrolytic activity, the double-site variant W106K/V149I showed an increase in specific hydrolytic activity at 15 °C by 2.3-fold toward casein in terms of hydrolytic rate and 2.7-fold toward the synthetic peptide AAPF-pN by means of kcat/Km value. The thermostability of the variant (W106K/V149I) was improved with the half-life at 60 and 70 °C increased by 2.7- and 5.0-fold, respectively, when compared with the thermostability of the wild-type DHAP. Conclusively, an increase in the cold activity and thermostability of a bacterial alkaline protease was achieved by protein engineering.

  15. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

    PubMed

    Pujadas, G; Palau, J

    2001-08-01

    Soybean beta-amylase (EC 3.2.1.2) has been crystallized both free and complexed with a variety of ligands. Four water molecules in the free-enzyme catalytic cleft form a multihydrogen-bond network with eight strategic residues involved in enzyme-ligand hydrogen bonds. We show here that the positions of these four water molecules are coincident with the positions of four potential oxygen atoms of the ligands within the complex. Some of these waters are displaced from the active site when the ligands bind to the enzyme. How many are displaced depends on the shape of the ligand. This means that when one of the four positions is not occupied by a ligand oxygen atom, the corresponding water remains. We studied the functional/structural role of these four waters and conclude that their presence means that the conformation of the eight side chains is fixed in all situations (free or complexed enzyme) and preserved from unwanted or forbidden conformational changes that could hamper the catalytic mechanism. The water structure at the active pocket of beta-amylase is therefore essential for providing the ligand recognition process with plasticity. It does not affect the protein active-site geometry and preserves the overall hydrogen-bonding network, irrespective of which ligand is bound to the enzyme. We also investigated whether other enzymes showed a similar role for water. Finally, we discuss the potential use of these results for predicting whether water molecules can mimic ligand atoms in the active center.

  16. The Active Site of Oligogalacturonate Lyase Provides Unique Insights into Cytoplasmic Oligogalacturonate β-Elimination*

    PubMed Central

    Abbott, D. Wade; Gilbert, Harry J.; Boraston, Alisdair B.

    2010-01-01

    Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism to preferentially catalyze the conversion of saturated and unsaturated digalacturonate into monogalacturonate and the 4,5-unsaturated monogalacturonate-like molecule, 5-keto-4-deoxyuronate. To provide mechanistic insights into the specificity of this enzyme activity, we have characterized the OGL from Y. enterocolitica, YeOGL, on oligogalacturonides and determined its three-dimensional x-ray structure to 1.65 Å. The model contains a Mn2+ atom in the active site, which is coordinated by three histidines, one glutamine, and an acetate ion. The acetate mimics the binding of the uronate group of galactourono-configured substrates. These findings, in combination with enzyme kinetics and metal supplementation assays, provide a framework for modeling the active site architecture of OGL. This enzyme appears to contain a histidine for the abstraction of the α-proton in the −1 subsite, a residue that is highly conserved throughout the OGL family and represents a unique catalytic base among pectic active lyases. In addition, we present a hypothesis for an emerging relationship observed between the cellular distribution of pectate lyase folding and the distinct metal coordination chemistries of pectate lyases. PMID:20851883

  17. Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol*

    PubMed Central

    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.

    2015-01-01

    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

  18. Effect of particle surface area on ice active site densities retrieved from droplet freezing spectra

    NASA Astrophysics Data System (ADS)

    Beydoun, Hassan; Polen, Michael; Sullivan, Ryan C.

    2016-10-01

    Heterogeneous ice nucleation remains one of the outstanding problems in cloud physics and atmospheric science. Experimental challenges in properly simulating particle-induced freezing processes under atmospherically relevant conditions have largely contributed to the absence of a well-established parameterization of immersion freezing properties. Here, we formulate an ice active, surface-site-based stochastic model of heterogeneous freezing with the unique feature of invoking a continuum assumption on the ice nucleating activity (contact angle) of an aerosol particle's surface that requires no assumptions about the size or number of active sites. The result is a particle-specific property g that defines a distribution of local ice nucleation rates. Upon integration, this yields a full freezing probability function for an ice nucleating particle. Current cold plate droplet freezing measurements provide a valuable and inexpensive resource for studying the freezing properties of many atmospheric aerosol systems. We apply our g framework to explain the observed dependence of the freezing temperature of droplets in a cold plate on the concentration of the particle species investigated. Normalizing to the total particle mass or surface area present to derive the commonly used ice nuclei active surface (INAS) density (ns) often cannot account for the effects of particle concentration, yet concentration is typically varied to span a wider measurable freezing temperature range. A method based on determining what is denoted an ice nucleating species' specific critical surface area is presented and explains the concentration dependence as a result of increasing the variability in ice nucleating active sites between droplets. By applying this method to experimental droplet freezing data from four different systems, we demonstrate its ability to interpret immersion freezing temperature spectra of droplets containing variable particle concentrations. It is shown that general

  19. Lake trout consumption and recent changes in the fish assemblage of Flaming Gorge Reservoir

    SciTech Connect

    Yule, D.L. ); Luecke, C. )

    1993-11-01

    Bioenergetics modeling was used to quantify the consumption dynamics of lake trout Salvelinus namaycush in Flaming Gorge Reservoir, Utah-Wyoming. Analysis of diet and population estimates of different size-classes of lake trout indicated that kokanees Oncorhynchus nerka made up the greatest proportion of prey biomass. Examination of growth rates of forage fish and predator-prey size ratios indicated that Utah chub Gila atraria were more vulnerable than kokanees to lake trout predation. Utah chub grow slower than kokanees and thus were susceptible to piscivores over a longer age span. The authors conclude the kokanees will make up an even large proportion of the pelagic fish assemblage of Flaming Gorge Reservoir in future years. 44 refs., 5 figs., 4 tabs.

  20. [Spatial pattern of vegetation landscape diversity in longitudinal Range-Gorge Region, southwestern China].

    PubMed

    Pan, Tao; Wu, Shao-hong; Dai, Er-fu; Zhao, Dong-sheng; Yin, Yun-he

    2010-12-01

    Based on the China 1:1000000 vegetation type map, and by using GIS spatial analysis, the spatial pattern of major vegetation landscape diversity indices and its relationships with environmental factors in Longitudinal Range-Gorge Region (LRGR) were analyzed. The proper scale for studying the vegetation landscape diversity in LRGR was 2000 m. In the study region, an obvious regional difference was observed in the vegetation landscape diversity indices, exhibiting typical longitudinal "corridor" and latitudinal "barrier" characteristics. The correlations between the vegetation landscape diversity indices and environmental elements were significant, and the regional difference in the environmental elements was the main factor controlling the spatial pattern of vegetation landscape diversity indices. The "corridor-barrier" function of the longitudinal range-gorge terrain made a spatial redistribution of hydro-thermal conditions, being the main cause of the special pattern of the vegetation landscape diversity in LRGR.

  1. Compensatory signals associated with the activation of human GC 5' splice sites.

    PubMed

    Kralovicova, Jana; Hwang, Gyulin; Asplund, A Charlotta; Churbanov, Alexander; Smith, C I Edvard; Vorechovsky, Igor

    2011-09-01

    GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5'ss activated by a mutation in BTK intron 3. This GC 5'ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5'ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5'ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5'ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5'ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5'ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5'ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.

  2. Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog

    PubMed Central

    Englert, Markus; Nakamura, Akiyoshi; Wang, Yane-Shih; Eiler, Daniel; Söll, Dieter; Guo, Li-Tao

    2015-01-01

    Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins. PMID:26582921

  3. Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase

    PubMed Central

    Tran, Huyen-Thi; Lee, Seon-Hwa; Ho, Thien-Hoang; Hong, Seung-Hye; Huynh, Kim-Hung; Ahn, Yeh-Jin; Oh, Deok-Kun; Kang, Lin-Woo

    2016-01-01

    Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it. PMID:27733232

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

    NASA Astrophysics Data System (ADS)

    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

  5. Structural Characterization of Human 8-Oxoguanine DNA Glycosylase Variants Bearing Active Site Mutations

    SciTech Connect

    Radom,C.; Banerjee, A.; Verdine, G.

    2007-01-01

    The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5 to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is 'hardwired'. Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F{sup *149}) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F{sup *292}) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.

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

    SciTech Connect

    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.

  7. Identification of an activation site in Bak and mitochondrial Bax triggered by antibodies

    PubMed Central

    Iyer, Sweta; Anwari, Khatira; Alsop, Amber E.; Yuen, Wai Shan; Huang, David C. S.; Carroll, John; Smith, Nicholas A.; Smith, Brian J.; Dewson, Grant; Kluck, Ruth M.

    2016-01-01

    During apoptosis, Bak and Bax are activated by BH3-only proteins binding to the α2–α5 hydrophobic groove; Bax is also activated via a rear pocket. Here we report that antibodies can directly activate Bak and mitochondrial Bax by binding to the α1–α2 loop. A monoclonal antibody (clone 7D10) binds close to α1 in non-activated Bak to induce conformational change, oligomerization, and cytochrome c release. Anti-FLAG antibodies also activate Bak containing a FLAG epitope close to α1. An antibody (clone 3C10) to the Bax α1–α2 loop activates mitochondrial Bax, but blocks translocation of cytosolic Bax. Tethers within Bak show that 7D10 binding directly extricates α1; a structural model of the 7D10 Fab bound to Bak reveals the formation of a cavity under α1. Our identification of the α1–α2 loop as an activation site in Bak paves the way to develop intrabodies or small molecules that directly and selectively regulate these proteins. PMID:27217060

  8. The Dry Season Shuffle: Gorges Provide Refugia for Animal Communities in Tropical Savannah Ecosystems.

    PubMed

    Doody, J Sean; Clulow, Simon; Kay, Geoff; D'Amore, Domenic; Rhind, David; Wilson, Steve; Ellis, Ryan; Castellano, Christina; McHenry, Colin; Quayle, Michelle; Hands, Kim; Sawyer, Graeme; Bass, Michael

    2015-01-01

    In the wet-dry tropics, animal species face the major challenges of acquiring food, water or shelter during an extended dry season. Although large and conspicuous animals such as ungulates and waterfowl migrate to wetter areas during this time, little is known of how smaller and more cryptic animal species with less mobility meet these challenges. We fenced off the entire entrance of a gorge in the Australian tropical savanna, offering the unique opportunity to determine the composition and seasonal movement patterns of the small vertebrate community. The 1.7 km-long fence was converted to a trapline that was deployed for 18-21 days during the early dry season in each of two years, and paired traps on both sides of the fence allowed us to detect the direction of animal movements. We predicted that semi-aquatic species (e.g., frogs and turtles) would move upstream into the wetter gorge during the dry season, while more terrestrial species (e.g., lizards, snakes, mammals) would not. The trapline captured 1590 individual vertebrates comprising 60 species. There was a significant bias for captures on the outside of the fence compared to the inside for all species combined (outside/inside = 5.2, CI = 3.7-7.2), for all vertebrate classes, and for specific taxonomic groups. The opposite bias (inside/outside = 7.3, N= 25) for turtles during the early wet season suggested return migration heading into the wet season. Our study revealed that the small vertebrate community uses the gorge as a dry season refuge. The generality of this unreplicated finding could be tested by extending this type of survey to tropical savannahs worldwide. A better understanding of how small animals use the landscape is needed to reveal the size of buffer zones around wetlands required to protect both semi-aquatic and terrestrial fauna in gorges in tropical savannah woodland, and thus in ecosystems in general.

  9. The Empirical Study on the Labor Export of Three Gorges Reservoir Area in China

    NASA Astrophysics Data System (ADS)

    Hu, Bangyong

    There are many large surplus labor force in the three gorges reservoir area, export of labor services is one way to tackle the problem of employment of the surplus-labor and increase farmers income, export of labor is also a effective way to solve three rural issues. This paper analyzes the need for the development of service economy, study the problems of export of labor services, at last the author give some suggestion to develop labor economy.

  10. The Dry Season Shuffle: Gorges Provide Refugia for Animal Communities in Tropical Savannah Ecosystems

    PubMed Central

    Doody, J. Sean; Clulow, Simon; Kay, Geoff; D’Amore, Domenic; Rhind, David; Wilson, Steve; Ellis, Ryan; Castellano, Christina; McHenry, Colin; Quayle, Michelle; Hands, Kim; Sawyer, Graeme; Bass, Michael

    2015-01-01

    In the wet-dry tropics, animal species face the major challenges of acquiring food, water o