High Plains Regional Ground-water Study web site

USGS Publications Warehouse

Qi, Sharon L.

2000-01-01

Now available on the Internet is a web site for the U.S. Geological Survey's (USGS) National Water-Quality Assessment (NAWQA) Program-High Plains Regional Ground-Water Study. The purpose of the web site is to provide public access to a wide variety of information on the USGS investigation of the ground-water resources within the High Plains aquifer system. Typical pages on the web site include the following: descriptions of the High Plains NAWQA, the National NAWQA Program, the study-area setting, current and past activities, significant findings, chemical and ancillary data (which can be downloaded), listing and access to publications, links to other sites about the High Plains area, and links to other web sites studying High Plains ground-water resources. The High Plains aquifer is a regional aquifer system that underlies 174,000 square miles in parts of eight States (Colorado, Kansas, Nebraska, New Mexico, Oklahoma, South Dakota, Texas, and Wyoming). Because the study area is so large, the Internet is an ideal way to provide project data and information on a near real-time basis. The web site will be a collection of living documents where project data and information are updated as it becomes available throughout the life of the project. If you have an interest in the High Plains area, you can check this site periodically to learn how the High Plains NAWQA activities are progressing over time and access new data and publications as they become available.

Active microwave water equivalence

NASA Technical Reports Server (NTRS)

Boyne, H. S.; Ellerbruch, D. A.

1980-01-01

Measurements of water equivalence using an active FM-CW microwave system were conducted over the past three years at various sites in Colorado, Wyoming, and California. The measurement method is described. Measurements of water equivalence and stratigraphy are compared with ground truth. A comparison of microwave, federal sampler, and snow pillow measurements at three sites in Colorado is described.

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

PubMed

Kim, Jin Kyun; Lomelino, Carrie L; Avvaru, Balendu Sankara; Mahon, Brian P; McKenna, Robert; Park, SangYoun; Kim, Chae Un

2018-01-01

Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

PubMed

Graham, Sarah E; Smith, Richard D; Carlson, Heather A

2018-02-26

Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between the protein and ligand. Depending on the specific interactions made by the ligand, displacing waters can yield a gain in binding affinity. The extent to which binding affinity may increase is difficult to predict, as the favorable displacement of a water molecule is dependent on the site-specific interactions made by the water and the potential ligand. Several methods have been developed to predict the location of water sites on a protein's surface, but the majority of methods are not able to take into account both protein dynamics and the interactions made by specific functional groups. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that explicitly accounts for the interaction of both water and small molecule probes with a protein's surface, allowing for their direct competition. This method has previously been shown to identify both active and allosteric sites on a protein's surface. Using a test set of eight systems, we have developed a method using MixMD to identify conserved and displaceable water sites. Conserved sites can be determined by an occupancy-based metric to identify sites which are consistently occupied by water even in the presence of probe molecules. Conversely, displaceable water sites can be found by considering the sites which preferentially bind probe molecules. Furthermore, the inclusion of six probe types allows the MixMD method to predict which functional groups are capable of displacing which water sites. The MixMD method consistently identifies sites which are likely to be nondisplaceable and predicts the favorable displacement of water sites that are known to be displaced upon ligand binding.

Hydrogen production by the naked active site of the di-iron hydrogenases in water.

PubMed

Zipoli, Federico; Car, Roberto; Cohen, Morrel H; Selloni, Annabella

2009-10-01

We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car-Parrinello molecular-dynamics simulations. We focused on the identification of the structures that are stable and metastable in acidified water and on their activity for hydrogen production. Our calculations revealed that the naked active center could be an efficient catalyst provided that electrons are transferred to the cluster. We found that both bridging and terminal isomers are present at equilibrium and that the bridging configuration is essential for efficient hydrogen production. The formation of the hydrogen molecule occurs via sequential protonations of the distal iron and of the N-atom of the S-CH(2)-NH-CH(2)-S chelating group. H(2) desorption does not involve a significant energy barrier, making the process very efficient at room temperature. We established that the bottleneck in the reaction is the direct proton transfer from water to the vacant site of the distal iron. Moreover, we found that even if the terminal isomer is present at the equilibrium, its strong local hydrophobicity prevents poisoning of the cluster.

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

PubMed

Hylsová, Michaela; Carbain, Benoit; Fanfrlík, Jindřich; Musilová, Lenka; Haldar, Susanta; Köprülüoğlu, Cemal; Ajani, Haresh; Brahmkshatriya, Pathik S; Jorda, Radek; Kryštof, Vladimír; Hobza, Pavel; Echalier, Aude; Paruch, Kamil; Lepšík, Martin

2017-01-27

We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R 2  = 0.49). However, the addition of the active-site waters resulted in significant improvement (R 2  = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Dissecting the active site of a photoreceptor protein

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

Applicability of rapid and on-site measured enzyme activity for surface water quality monitoring in an agricultural catchment

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Farnleitner, Andreas H.; Sommer, Regina; Kumpan, Monika; Zessner, Matthias

2014-05-01

For the near real time and on-site detection of microbiological fecal pollution of water, the measurement of beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter and has been already successfully operated for water quality monitoring of ground water resources (Ryzinska-Paier et al. 2014). Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the fecal indication capacity of GLUC (specificity, sensitivity, persistence, etc.) in relation to potential pollution sources and catchment conditions (Cabral 2010, Ryzinska-Paier et al. 2014). Furthermore surface waters are a big challenge for automated detection devices in a technical point of view due to the high sediment load during event conditions. This presentation shows results gained form two years of monitoring in an experimental catchment (HOAL) dominated by agricultural land use. Two enzymatic measurement devices are operated parallel at the catchment outlet to test the reproducibility and precision of the method. Data from continuous GLUC monitoring under both base flow and event conditions is compared with reference samples analyzed by standardized laboratory methods for fecal pollution detection (e.g. ISO 16649-1, Colilert18). It is shown that rapid enzymatic on-site GLUC determination can successfully be operated from a technical point of view for surface water quality monitoring under the observed catchment conditions. The comparison of enzyme activity with microbiological standard analytics reveals distinct differences in the dynamic of the signals during event conditions. Cabral J. P. S. (2010) "Water Microbiology. Bacterial Pathogens and Water" International Journal of

Interaction of on-site and near real time measured turbidity and enzyme activity in stream water.

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Farnleitner, Andreas H.; Zessner, Matthias

2013-04-01

On-site and on-line systems that provide an integrated surveillance of physicochemical and microbiological parameters gain significance in water quality monitoring. Particular relating to diffuse pollution from agricultural areas and use-orientated protection of waters the detection of faecal pollution is a fundamental part. For the near real time and on-site detection of microbiological faecal pollution of water, the beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter. Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the sensitivity and specificity concerning the faecal indication capacity of GLUC in relation to standard assays (Cabral 2010). Interference effects of physicochemical parameters on the enzymatic activity respectively fluorescence have been discussed (Molina-Munoz et al. 2007; Tryland and Fiksdal 1998, Biswal et al. 2003). Results from a monitoring of a rivulet in an agricultural catchment in Lower Austria (HOAL - Hydrological Open Air Laboratory) are presented here. The HOAL offers technical resources that allow measurements at high temporal and spatial resolution and to apply various hydrological methods in one catchment. Two automated enzymatic measuring devices (Coliguard, mbOnline, Austria) and physicochemical in-stream measurements are used, as well as in-stream spectroscopy (spectrolyser, s::can, Austria). Accuracy of both enzymatic measuring devices is compared through diverse hydrological and seasonal conditions. Reference analyses by cultivation based determination were performed. Data from Coliguard devices is combined with physicochemical and spectroscopy data to gain information about the

LLNL Experimental Test Site (Site 300) Potable Water System Operations Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ocampo, R. P.; Bellah, W.

The existing Lawrence Livermore National Laboratory (LLNL) Site 300 drinking water system operation schematic is shown in Figures 1 and 2 below. The sources of water are from two Site 300 wells (Well #18 and Well #20) and San Francisco Public Utilities Commission (SFPUC) Hetch-Hetchy water through the Thomas shaft pumping station. Currently, Well #20 with 300 gallons per minute (gpm) pump capacity is the primary source of well water used during the months of September through July, while Well #18 with 225 gpm pump capacity is the source of well water for the month of August. The well watermore » is chlorinated using sodium hypochlorite to provide required residual chlorine throughout Site 300. Well water chlorination is covered in the Lawrence Livermore National Laboratory Experimental Test Site (Site 300) Chlorination Plan (“the Chlorination Plan”; LLNL-TR-642903; current version dated August 2013). The third source of water is the SFPUC Hetch-Hetchy Water System through the Thomas shaft facility with a 150 gpm pump capacity. At the Thomas shaft station the pumped water is treated through SFPUC-owned and operated ultraviolet (UV) reactor disinfection units on its way to Site 300. The Thomas Shaft Hetch- Hetchy water line is connected to the Site 300 water system through the line common to Well pumps #18 and #20 at valve box #1.« less

Site 300 City Water Master Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaw, Jeff

Lawrence Livermore National Laboratory (LLNL), a scientific research facility, operates an experimental test site known as Site 300. The site is located in a remote area of southeastern Alameda County, California, and consists of about 100 facilities spread across 7,000-acres. The Site 300 water system includes groundwater wells and a system of storage tanks, booster pumps, and underground piping to distribute water to buildings and significant areas throughout the site. Site 300, which is classified as a non-transient non-community (NTNC) water system, serves approximately 110 employees through 109 service connections. The distribution system includes approximately 76,500-feet of water mains varyingmore » from 4- to 10-inches in diameter, mostly asbestos cement (AC) pipe, and eleven water storage tanks. The water system is divided into four pressure zones fed by three booster pump stations to tanks in each zone.« less

Redefinition of rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues.

PubMed

Kannappan, Babu; Gready, Jill E

2008-11-12

Crystallographic, mutagenesis, kinetic, and computational studies on Rubisco over three decades have revealed much about its catalytic mechanism and the role played by several active-site residues. However, key questions remain unanswered. Specific details of the carboxylase and oxygenase mechanisms, required to underpin the rational re-engineering of Rubisco, are still speculative. Here we address critical gaps in knowledge with a definitive comprehensive computational investigation of the mechanism of carboxylase activity at the Rubisco active site. Density functional theory calculations (B3LYP/6-31G(d,p)) were performed on active-site fragment models of a size up to 77 atoms, not previously possible computationally. All amino acid residues suspected to play roles in the acid-base chemistry in the multistep reaction, and interacting directly with the central Mg (2+) atom and the reactive moiety of substrate and intermediates, were included. The results provide a firm basis for us to propose a novel mechanism for the entire sequence of reactions in the carboxylase catalysis and to define precise roles for the active-site residues, singly and in concert. In this mechanism, the carbamylated LYS201 plays a more limited role than previously proposed but is crucial for initiating the reaction by acting as a base in the enolization. We suggest a wider role for HIS294, with involvement in the carboxylation, hydration, and C2-C3 bond-scission steps, consistent with the suggestion of Harpel et al. (1998) but contrary to the consensus view of Cleland et al. (1998). In contrast to the common assumption that the water molecule for the hydration step comes from within the active site, we propose that the Mg-coordinated water is not dissociated at the start of the gas-addition reaction but rather remains coordinated and is used for the hydration of the C3 carbon atom. New roles are also proposed for LYS175, GLU204, and HIS294. The mechanism suggests roles in the gas

The influence of small mammal burrowing activity on water storage at the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Landeen, D.S.

The amount and rate at which water may penetrate a protective barrier and come into contact with buried radioactive waste is a major concern. Because burrowing animals eventually will reside on the surface of any protective barrier, the effect these burrow systems may have on the loss or retention of water needs to be determined. The first section of this document summarizes the known literature relative to small mammals and the effects that burrowing activities have on water distribution, infiltration, and the overall impact of burrows on the ecosystem. Topics that are summarized include burrow air pressures, airflow, burrow humidity,more » microtopography, mounding, infiltration, climate, soil evaporation, and discussions of large pores relative to water distribution. The second section of this document provides the results of the study that was conducted at the Hanford Site to determine what effect small mammal burrows have on water storage. This Biointrusion task is identified in the Permanent Isolation Surface Barrier Development Plan in support of protective barriers. This particular animal intrusion task is one part of the overall animal intrusion task identified in Animal Intrusion Test Plan.« less

Site-Specific Measurement of Water Dynamics in the Substrate Pocket of Ketosteroid Isomerase Using Time-Resolved Vibrational Spectroscopy

PubMed Central

Jha, Santosh Kumar; Ji, Minbiao; Gaffney, Kelly J.; Boxer, Steven G.

2012-01-01

Little is known about the reorganization capacity of water molecules at the active sites of enzymes and how this couples to the catalytic reaction. Here, we study the dynamics of water molecules at the active site of a highly proficient enzyme, Δ5-3-ketosteroid isomerase (KSI), during a light-activated mimic of its catalytic cycle. Photo-excitation of a nitrile containing photo-acid, coumarin183 (C183), mimics the change in charge density that occurs at the active site of KSI during the first step of the catalytic reaction. The nitrile of C183 is exposed to water when bound to the KSI active site, and we used time-resolved vibrational spectroscopy as a site-specific probe to study the solvation dynamics of water molecules in the vicinity of the nitrile. We observed that water molecules at the active site of KSI are highly rigid, during the light-activated catalytic cycle, compared to the solvation dynamics observed in bulk water. Based upon this result we hypothesize that rigid water dipoles at the active site might help in the maintenance of the pre-organized electrostatic environment required for efficient catalysis. The results also demonstrate the utility of nitrile probes in measuring the dynamics of local (H-bonded) water molecules in contrast to the commonly used fluorescence methods which measure the average behavior of primary and subsequent spheres of solvation. PMID:22931297

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

PubMed Central

Dodson, M. L.; Walker, Ross C.; Lloyd, R. Stephen

2012-01-01

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site

Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules

PubMed Central

Davidge, Kelly S; Singh, Sandip; Bowman, Lesley AH; Tinajero-Trejo, Mariana; Carballal, Sebastián; Radi, Rafael; Poole, Robert K; Dikshit, Kanak; Estrin, Dario A; Marti, Marcelo A; Boechi, Leonardo

2015-01-01

Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and •NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify •NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, •NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site. PMID:26478812

Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules.

PubMed

Boron, Ignacio; Bustamante, Juan Pablo; Davidge, Kelly S; Singh, Sandip; Bowman, Lesley Ah; Tinajero-Trejo, Mariana; Carballal, Sebastián; Radi, Rafael; Poole, Robert K; Dikshit, Kanak; Estrin, Dario A; Marti, Marcelo A; Boechi, Leonardo

2015-01-01

Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and • NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify • NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, • NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

Remedial action plan and site design for stabilization of the inactive Uranium Mill Tailing site Maybell, Colorado. Attachment 3, ground water hydrology report, Attachment 4, water resources protection strategy. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-06-01

The U.S. Environmental Protection Agency (EPA) has established health and environmental regulations to correct and prevent ground water contamination resulting from former uranium processing activities at inactive uranium processing sites (40 CFR Part 192 (1993)) (52 FR 36000 (1978)). According to the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978 (42 USC {section} 7901 et seq.), the U.S. Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has decided that each assessment will include information on hydrogeologic site characterization. The water resources protection strategy that describes the proposed action compliance with the EPAmore » ground water protection standards is presented in Attachment 4, Water Resources Protection Strategy. Site characterization activities discussed in this section include the following: (1) Definition of the hydrogeologic characteristics of the environment, including hydrostratigraphy, aquifer parameters, areas of aquifer recharge and discharge, potentiometric surfaces, and ground water velocities. (2) Definition of background ground water quality and comparison with proposed EPA ground water protection standards. (3) Evaluation of the physical and chemical characteristics of the contaminant source and/or residual radioactive materials. (4) Definition of existing ground water contamination by comparison with the EPA ground water protection standards. (5) Description of the geochemical processes that affect the migration of the source contaminants at the processing site. (6) Description of water resource use, including availability, current and future use and value, and alternate water supplies.« less

Hanford Site ground-water monitoring for 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dresel, P.E.; Luttrell, S.P.; Evans, J.C.

This report presents the results of the Ground-Water Surveillance Project monitoring for calendar year 1993 on the Hanford Site, Washington. Hanford Site operations from 1943 onward produced large quantities of radiological and chemical waste that have impacted ground-water quality on the Site. Monitoring of water levels and ground-water chemistry is performed to track the extent of contamination and trends in contaminant concentrations. The 1993 monitoring was also designed to identify emerging ground-water quality problems. The information obtained is used to verify compliance with applicable environmental regulations and to evaluate remedial actions. Data from other monitoring and characterization programs were incorporatedmore » to provide an integrated assessment of Site ground-water quality. Additional characterization of the Site`s geologic setting and hydrology was performed to support the interpretation of contaminant distributions. Numerical modeling of sitewide ground-water flow also supported the overall project goals. Water-level monitoring was performed to evaluate ground-water flow directions, to track changes in water levels, and to relate such changes to changes in site disposal practices. Water levels over most of the Hanford Site continued to decline between June 1992 and June 1993. The greatest declines occurred in the 200-West Area. These declines are part of the continued response to the cessation of discharge to U Pond and other disposal facilities. The low permeability in this area which enhanced mounding of waste-water discharge has also slowed the response to the reduction of disposal. Water levels remained nearly constant in the vicinity of B Pond, as a result of continued disposal to the pond. Water levels measured from wells in the unconfined aquifer north and east of the Columbia River indicate that the primary source of recharge is irrigation practices.« less

A role for catalase-peroxidase large loop 2 revealed by deletion mutagenesis: control of active site water and ferric enzyme reactivity.

PubMed

Kudalkar, Shalley N; Njuma, Olive J; Li, Yongjiang; Muldowney, Michelle; Fuanta, N Rene; Goodwin, Douglas C

2015-03-03

Catalase-peroxidases (KatGs), the only catalase-active members of their superfamily, all possess a 35-residue interhelical loop called large loop 2 (LL2). It is essential for catalase activity, but little is known about its contribution to KatG function. LL2 shows weak sequence conservation; however, its length is nearly identical across KatGs, and its apex invariably makes contact with the KatG-unique C-terminal domain. We used site-directed and deletion mutagenesis to interrogate the role of LL2 and its interaction with the C-terminal domain in KatG structure and catalysis. Single and double substitutions of the LL2 apex had little impact on the active site heme [by magnetic circular dichroism or electron paramagnetic resonance (EPR)] and activity (catalase or peroxidase). Conversely, deletion of a single amino acid from the LL2 apex reduced catalase activity by 80%. Deletion of two or more apex amino acids or all of LL2 diminished catalase activity by 300-fold. Peroxide-dependent but not electron donor-dependent kcat/KM values for deletion variant peroxidase activity were reduced 20-200-fold, and kon for cyanide binding diminished by 3 orders of magnitude. EPR spectra for deletion variants were all consistent with an increase in the level of pentacoordinate high-spin heme at the expense of hexacoordinate high-spin states. Together, these data suggest a shift in the distribution of active site waters, altering the reactivity of the ferric state, toward, among other things, compound I formation. These results identify the importance of LL2 length conservation for maintaining an intersubunit interaction that is essential for an active site water distribution that facilitates KatG catalytic activity.

Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study.

PubMed

Wang, Lingyun; Yan, Feng

2017-10-01

Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn 2+ ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn 2+ ions and the other terminally coordinated with one of the Mn 2+ ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn 2+ ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II.

PubMed

Bairagya, Hridoy R; Mukhopadhyay, Bishnu P; Bera, Asim K

2011-01-01

Inosine monophosphate dehydrogenase (IMPDH) of human is involved in GMP biosynthesis pathway, increased level of IMPDH-II (an isoform of enzyme) activity have found in leukemic and sarcoma cells. Modeling and extensive molecular dynamics simulation (15 ns) studies of IMPDH-II (1B3O PDB structure) have indicated the intricate involvement of four conserved water molecules (W 1, W 2, W 3, and W 4) in the conformational transition or the mobilities of "flap" (residues 400-450) and "loop" (residues 325-342) regions in enzyme. The stabilization of active site residues Asn 303, Gly 324, Ser 329, Cys 331, Asp 364, and Tyr 411 through variable H-bonding coordination from the conserved water molecular center seems interesting in the uninhibited hydrated form of human IMPDH-II structures. This conformational transition or the flexibility of mobile regions, water molecular recognition to active site residues Cys 331 and Tyr 411, and the presence of a hydrophilic cavity approximately 540 Å(3) (enclaved by the loop and flap region) near the C-terminal surface of this enzyme may explore a rational hope toward the water mimic inhibitor or anticancer agent design for human. 2010 John Wiley & Sons, Ltd.

Protecting Surface Water Systems on Forest Sites Through Herbicide Use

Treesearch

J.L. Michael; H.L. Gibbs; J.B. Fischer; E.C. Webber

2000-01-01

Sediment, nutrients, and pesticides are universally accepted as the greatest threats to surface water quality world-wide. Sedimentation in surface waters is a natural phenomenon, but is magnified by human activities. Intensive forest management practices, particularly road building, harvesting and planting site preparation, result in the greatest increases in erosion...

Quantum mechanical design of enzyme active sites.

PubMed

Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

2008-02-01

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Radioactive Water Treatment at a United States Environmental Protection Agency Superfund Site - 12322

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beckman, John C.

2012-07-01

A water treatment system at a United States Environmental Protection Agency (USEPA) Superfund site impacted by radiological contaminants is used to treat water entering the site. The United States Army Corps of Engineers (USACE) is actively managing the remedial action for the USEPA using contracts to support the multiple activities on site. The site is where former gas mantle production facilities operated around the turn of the century. The manufacturing facilities used thorium ores to develop the mantles and disposed of off-specification mantles and ore residuals in the surrounding areas. During Site remedial actions, both groundwater and surface water comesmore » into contact with contaminated soils and must be collected and treated at an on-site treatment facility. The radionuclides thorium and radium with associated progeny are the main concern for treatment. Suspended solids, volatile organic compounds, and select metals are also monitored during water treatment. The water treatment process begins were water is pumped to a collection tank where debris and grit settle out. Stored water is pumped to a coagulant tank containing poly-aluminum chloride to collect dissolved solids. The water passes into a reaction tube where aspirated air is added or reagent added to remove Volatile Organic Compounds (VOC'S) by mass transfer and convert dissolved iron to a solid. The water enters the flocculent polymer tank to drop solids out. The flocculated water overflows to a fluidized bed contact chamber to increase precipitation. Flocculation is where colloids of material drop out of suspension and settle. The settled solids are periodically removed and disposed of as radioactive waste. The water is passed through filters and an ion exchange process to extract the radionuclides. Several million liters of water are processed each year from two water treatment plants servicing different areas of the remediation site. Ion exchange resin and filter material are periodically

Geochemical Data from Produced Water Contamination Investigations: Osage-Skiatook Petroleum Environmental Research (OSPER) Sites, Osage County, Oklahoma

USGS Publications Warehouse

Thordsen, James J.; Kharaka, Yousif K.; Ambats, Gil; Kakouros, Evangelos; Abbott, Marvin M.

2007-01-01

We report chemical and isotopic analyses of 345 water samples collected from the Osage-Skiatook Petroleum Environmental Research (OSPER) project. Water samples were collected as part of an ongoing multi-year USGS investigation to study the transport, fate, natural attenuation, and ecosystem impacts of inorganic salts and organic compounds present in produced water releases at two oil and gas production sites from an aging petroleum field located in Osage County, in northeast Oklahoma. The water samples were collected primarily from monitoring wells and surface waters at the two research sites, OSPER A (legacy site) and OSPER B (active site), during the period March, 2001 to February, 2005. The data include produced water samples taken from seven active oil wells, one coal-bed methane well and two domestic groundwater wells in the vicinity of the OSPER sites.

Lawrence Livermore National Laboratory Experimental Test Site (Site 300) Potable Water System Operations Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ocampo, Ruben P.; Bellah, Wendy

The existing Lawrence Livermore National Laboratory (LLNL) Site 300 drinking water system operation schematic is shown in Figures 1 and 2 below. The sources of water are from two Site 300 wells (Well #18 and Well #20) and San Francisco Public Utilities Commission (SFPUC) Hetch-Hetchy water through the Thomas shaft pumping station. Currently, Well #20 with 300 gallons per minute (gpm) pump capacity is the primary source of well water used during the months of September through July, while Well #18 with 225 gpm pump capacity is the source of well water for the month of August. The well watermore » is chlorinated using sodium hypochlorite to provide required residual chlorine throughout Site 300. Well water chlorination is covered in the Lawrence Livermore National Laboratory Experimental Test Site (Site 300) Chlorination Plan (“the Chlorination Plan”; LLNL-TR-642903; current version dated August 2013). The third source of water is the SFPUC Hetch-Hetchy Water System through the Thomas shaft facility with a 150 gpm pump capacity. At the Thomas shaft station the pumped water is treated through SFPUC-owned and operated ultraviolet (UV) reactor disinfection units on its way to Site 300. The Thomas Shaft Hetch- Hetchy water line is connected to the Site 300 water system through the line common to Well pumps #18 and #20 at valve box #1.« less

DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

PubMed

Kearney, Bradley M; Johnson, Christian W; Roberts, Daniel M; Swartz, Paul; Mattos, Carla

2014-02-06

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. Copyright © 2013 Elsevier Ltd. All rights reserved.

MX Siting Investigation. Water Resources Program Industry Activity Inventory, Nevada-Utah.

DTIC Science & Technology

1980-09-02

sites. New and revived mining activities and the cooling needs of possible new coal -fired electric power plants represent the chief competitors with MX...34 !- ---- ON CO. Figure .-. Ma showing araipce yUaIoto f𔃻XMsieCmlx 1 3 include new mining activity and coal -fired, geothermal, and hydroelectric j energy...in northeastern Juab County. The Soil Conservation Service has been actively pushing land treatment programs to increase the productivity of irrigated

National water-information clearinghouse activities; ground-water perspective

USGS Publications Warehouse

Haupt, C.A.; Jensen, R.A.

1988-01-01

The US Geological Survey (USGS) has functioned for many years as an informal clearinghouse for water resources information, enabling users to access groundwater information effectively. Water resources clearinghouse activities of the USGS are conducted through several separate computerized water information programs that are involved in the collection, storage, retrieval, and distribution of different types of water information. The following USGS programs perform water information clearinghouse functions and provide the framework for a formalized National Water-Information Clearinghouse: (1) The National Water Data Exchange--a nationwide confederation of more than 300 Federal, State, local, government, academic, and private water-oriented organizations that work together to improve access to water data; (2) the Water Resources Scientific Information Center--acquires, abstracts, and indexes the major water-resources-related literature of the world, and provides this information to the water resources community; (3) the Information Transfer Program--develops innovative approaches to transfer information and technology developed within the USGS to audiences in the public and private sectors; (4) the Hydrologic Information Unit--provides responses to a variety of requests, both technical and lay-oriented, for water resources information , and helps efforts to conduct water resources research; (5) the Water Data Storage and Retrieval System--maintains accessible computerized files of hydrologic data collected nationwide, by the USGS and other governmental agencies, from stream gaging stations, groundwater observation wells, and surface- and groundwater quality sampling sites; (6) the Office of Water Data Coordination--coordinate the water data acquisition activities of all agencies of the Federal Government, and is responsible for the planning, design, and inter-agency coordination of a national water data and information network; and (7) the Water Resources Research

Revised description of index of Florida water data collection active stations and a user's guide for station or site information retrieval computer program FINDEX H578

USGS Publications Warehouse

Geiger, Linda H.

1983-01-01

The report is an update of U.S. Geological Survey Open-File Report 77-703, which described a retrieval program for administrative index of active data-collection sites in Florida. Extensive changes to the Findex system have been made since 1977 , making the previous report obsolete. A description of the data base and computer programs that are available in the Findex system are documented in this report. This system serves a vital need in the administration of the many and diverse water-data collection activities. District offices with extensive data-collection activities will benefit from the documentation of the system. Largely descriptive, the report tells how a file of computer card images has been established which contains entries for all sites in Florida at which there is currently a water-data collection activity. Entries include information such as identification number, station name, location, type of site, county, frequency of data collection, funding, and other pertinent details. The computer program FINDEX selectively retrieves entries and lists them in a format suitable for publication. The index is updated routinely. (USGS)

Martian Magmatic-Driven Hydrothermal Sites: Potential Sources of Energy, Water, and Life

NASA Technical Reports Server (NTRS)

Anderson, R. C.; Dohm, J. M.; Baker, V. R.; Ferris, J. C.; Hare, T. M.; Tanaka, K. L.; Klemaszewski, J. E.; Skinner, J. A.; Scott, D. H.

2000-01-01

Magmatic-driven processes and impact events dominate the geologic record of Mars. Such recorded geologic activity coupled with significant evidence of past and present-day water/ice, above and below the martian surface, indicate that hydrothermal environments certainly existed in the past and may exist today. The identification of such environments, especially long-lived magmatic-driven hydrothermal environments, provides NASA with significant target sites for future sample return missions, since they (1) could favor the development and sustenance of life, (2) may comprise a large variety of exotic mineral assemblages, and (3) could potentially contain water/ice reservoirs for future Mars-related human activities. If life developed on Mars, the fossil record would presumably be at its greatest concentration and diversity in environments where long-term energy sources and water coexisted such as at sites where long-lived, magmatic-driven hydrothermal activity occurred. These assertions are supported by terrestrial analogs. Small, single-celled creatures (prokaryotes) are vitally important in the evolution of the Earth; these prokaryotes are environmentally tough and tolerant of environmental extremes of pH, temperature, salinity, and anoxic conditions found around hydrothermal vents. In addition, there is a great ability for bacteria to survive long periods of geologic time in extreme conditions, including high temperature hydrogen sulfide and sulfur erupted from Mount St. Helens volcano. Our team of investigators is conducting a geological investigation using multiple mission-derived datasets (e.g., existing geologic map data, MOC imagery, MOLA, TES image data, geophysical data, etc.) to identify prime target sites of hydrothermal activity for future hydrological, mineralogical, and biological investigations. The identification of these sites will enhance the probability of success for future missions to Mars.

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

PubMed

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

2013-09-03

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

A description of the index of active Florida water data collection stations and a user's guide for station or site information retrieval using computer program Findex H578

USGS Publications Warehouse

Merritt, M.L.

1977-01-01

A computerized index of water-data collection activities and retrieval software to generate publication list of this information was developed for Florida. This system serves a vital need in the administration of the many and diverse water-data collection activities. Previously, needed data was very difficult to assemble for use in program planning or project implementation. Largely descriptive, the report tells how a file of computer card images has been established which contains entries for all sites in Florida at which there is currently a water-data-collection activity. Entries include information such as identification number, station name, location, type of site, county, information about data collection, funding, and other pertinent details. The computer program FINDEX selectively retrieves entries and lists them in a format suitable for publication. Updating the index is done routinely. (Woodard-USGS)

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

PubMed

Spyrakis, Francesca; Cavasotto, Claudio N

2015-10-01

Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. Copyright © 2015 Elsevier Inc. All rights reserved.

Give Water a Hand. School Site Action Guide. Organizing Water Conservation and Pollution Prevention Service Projects in Your Community.

ERIC Educational Resources Information Center

Wisconsin Univ., Madison. Coll. of Agricultural and Life Sciences.

Students grades 4-8 can use this guide to explore the topics of water, and water conservation at a school site, while conducting an environmental community service project. Youth groups, led by a group leader, work with local experts from business, government, or environmental organizations to complete the project. Nine activity sections involve…

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.

Fate and groundwater impacts of produced water releases at OSPER "B" site, Osage County, Oklahoma

USGS Publications Warehouse

Kharaka, Y.K.; Kakouros, E.; Thordsen, J.J.; Ambats, G.; Abbott, M.M.

2007-01-01

For the last 5 a, the authors have been investigating the transport, fate, natural attenuation and ecosystem impacts of inorganic and organic compounds in releases of produced water and associated hydrocarbons at the Osage-Skiatook Petroleum Environmental Research (OSPER) "A" and "B" sites, located in NE Oklahoma. Approximately 1.0 ha of land at OSPER "B", located within the active Branstetter lease, is visibly affected by salt scarring, tree kills, soil salinization, and brine and petroleum contamination. Site "B" includes an active production tank battery and adjacent large brine pit, two injection well sites, one with an adjacent small pit, and an abandoned brine pit and tank battery site. Oil production in this lease started in 1938, and currently there are 10 wells that produce 0.2-0.5 m3/d (1-3 bbl/d) oil, and 8-16 m3/d (50-100 bbl/d) brine. Geochemical data from nearby oil wells show that the produced water source is a Na-Ca-Cl brine (???150,000 mg/L TDS), with high Mg, but low SO4 and dissolved organic concentrations. Groundwater impacts are being investigated by detailed chemical analyses of water from repeated sampling of 41 boreholes, 1-71 m deep. The most important results at OSPER "B" are: (1) significant amounts of produced water from the two active brine pits percolate into the surficial rocks and flow towards the adjacent Skiatook reservoir, but only minor amounts of liquid petroleum leave the brine pits; (2) produced-water brine and minor dissolved organics have penetrated the thick (3-7 m) shale and siltstone units resulting in the formation of three interconnected plumes of high-salinity water (5000-30,000 mg/L TDS) that extend towards the Skiatook reservoir from the two active and one abandoned brine pits; and (3) groundwater from the deep section of only one well, BR-01 located 330 m upslope and west of the site, appear not to be impacted by petroleum operations. ?? 2007.

Water resources activities in Kentucky, 1986

USGS Publications Warehouse

Faust, R. J.

1986-01-01

The U.S. Geological Survey, Water Resources Division, conducts three major types of activities in Kentucky in order to provide hydrologic information and understanding needed for the best management of Kentucky 's and the Nation 's water resources. These activities are: (1) Data collection and dissemination; (2) Water-resources appraisals (interpretive studies); and (3) Research. Activities described in some detail following: (1) collection of surface - and groundwater data; (2) operation of stations to collect data on water quality, atmospheric deposition, and sedimentation; (3) flood investigations; (4) water use; (5) small area flood hydrology; (6) feasibility of disposal of radioactive disposal in deep crystalline rocks; (7) development of a groundwater model for the Louisville area; (8) travel times for streams in the Kentucky River Basin; (9) the impact of sinkholes and streams on groundwater flow in a carbonate aquifer system; (10) sedimentation and erosion rates at the Maxey Flats Radioactive Waste Burial site; and (11) evaluation of techniques for evaluating the cumulative impacts of mining as applied to coal fields in Kentucky. (Lantz-PTT)

Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase - The importance of accommodating the active site water.

PubMed

Heyes, Logan C; Reichau, Sebastian; Cross, Penelope J; Jameson, Geoffrey B; Parker, Emily J

2014-12-01

3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, which produces the aromatic amino acids as well as many other aromatic metabolites. DAH7PS catalyses an aldol-like reaction between phosphoenolpyruvate and erythrose 4-phosphate. Three phosphoenolpyruvate mimics, (R)-phospholactate, (S)-phospholactate and vinyl phosphonate [(E)-2-methyl-3-phosphonoacrylate], were found to competitively inhibit DAH7PS from Neisseria meningitidis, which is the pathogen responsible for bacterial meningitis. The most potent inhibitor was the vinyl phosphonate with a Ki value of 3.9±0.4μM. We report for the first time crystal structures of these compounds bound in the active site of a DAH7PS enzyme which reveals that the inhibitors bind to the active site of the enzyme in binding modes that mimic those of the predicted oxocarbenium and tetrahedral intermediates of the enzyme-catalysed reaction. Furthermore, the inhibitors accommodate the binding of a key active site water molecule. Together, these observations provide strong evidence that this active site water participates directly in the DAH7PS reaction, enabling the facial selectivity of the enzyme-catalysed reaction sequence to be delineated. Copyright © 2014 Elsevier Inc. All rights reserved.

Diffusive flux of PAHs across sediment-water and water-air interfaces at urban superfund sites.

PubMed

Minick, D James; Anderson, Kim A

2017-09-01

Superfund sites may be a source of polycyclic aromatic hydrocarbons (PAHs) to the surrounding environment. These sites can also act as PAH sinks from present-day anthropogenic activities, especially in urban locations. Understanding PAH transport across environmental compartments helps to define the relative contributions of these sources and is therefore important for informing remedial and management decisions. In the present study, paired passive samplers were co-deployed at sediment-water and water-air interfaces within the Portland Harbor Superfund Site and the McCormick and Baxter Superfund Site. These sites, located along the Willamette River (Portland, OR, USA), have PAH contamination from both legacy and modern sources. Diffusive flux calculations indicate that the Willamette River acts predominantly as a sink for low molecular weight PAHs from both the sediment and the air. The sediment was also predominantly a source of 4- and 5-ring PAHs to the river, and the river was a source of these same PAHs to the air, indicating that legacy pollution may be contributing to PAH exposure for residents of the Portland urban center. At the remediated McCormick and Baxter Superfund Site, flux measurements highlight locations within the sand and rock sediment cap where contaminant breakthrough is occurring. Environ Toxicol Chem 2017;36:2281-2289. © 2017 SETAC. © 2017 SETAC.

Optimization Review: French Gulch/Wellington-Oro Mine Site Water Treatment Plant, Breckenridge, Summit County, Colorado

EPA Pesticide Factsheets

The French Gulch/Wellington-Oro Mine Site is located near the town of Breckenridge in Summit County, Colorado. Environmental contamination of surface water, groundwater, soil and sediment at the site resulted from mining activities dating to the 1880s.

Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination

PubMed Central

Ma, Chien-Hui; Rowley, Paul A; Macieszak, Anna; Guga, Piotr; Jayaram, Makkuni

2009-01-01

Water, acting as a rogue nucleophile, can disrupt transesterification steps of important phosphoryl transfer reactions in DNA and RNA. We have unveiled this risk, and identified safeguards instituted against it, during strand cleavage and joining by the tyrosine site-specific recombinase Flp. Strand joining is threatened by a latent Flp endonuclease activity (type I) towards the 3′-phosphotyrosyl intermediate resulting from strand cleavage. This risk is not alleviated by phosphate electrostatics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) substitution does not stimulate type I endonuclease. Rather, protection derives from the architecture of the recombination synapse and conformational dynamics within it. Strand cleavage is protected against water by active site electrostatics. Replacement of the catalytic Arg-308 of Flp by alanine, along with MeP substitution, elicits a second Flp endonuclease activity (type II) that directly targets the scissile phosphodiester bond in DNA. MeP substitution, combined with appropriate active site mutations, will be useful in revealing anti-hydrolytic mechanisms engendered by systems that mediate DNA relaxation, DNA transposition, site-specific recombination, telomere resolution, RNA splicing and retrohoming of mobile introns. PMID:19440204

Idaho's surface-water-quality monitoring program: results from five sites sampled during water years 1990-93

USGS Publications Warehouse

,

1994-01-01

In 1990, the U.S. Geological Survey (USGS), in cooperation with the Idaho Department of Health and Welfare, Division of Environmental Quality, implemented a statewide water-quality monitoring program in response to Idaho's antidegradation policy as required by the Clean Water Act. The program objective is to provide water-quality managers with a coordinated statewide network to detect trends in surface-water quality. The monitoring program includes the collection and analysis of samples from 56 sites on the Bear, Clearwater, Kootenai, Pend Oreille, Salmon, Snake, and Spokane Rivers and their tributaries (fig. 1). Samples are collected every year at 5 sites (annual sites) in drainage basins where long-term water-quality management is practiced, every other year at 19 sites (biennial sites) in basins where land and water uses change slowly, and every third year at 32 sites (triennial sites) where future development may affect water quality. Each year, 25 of the 56 sites are sampled. This report discusses results of sampling at five annual sites. During water years 1990-93 (October 1, 1989, through September 30, 1993), samples were collected six times per year at the five annual sites (fig. 1). Onsite analyses were made for discharge, specific conductance, pH, temperature, dissolved oxygen, bacteria (fecal coliform and fecal streptococci), and alkalinity. Laboratory analyses were made for major ions, nutrients, trace elements, and suspended sediment. Suspended sediment, nitrate, fecal coliform, trace elements, and specific conductance were used to characterize surface-water quality. Because concentrations of all trace elements except zinc were near detection limits, only zinc is discussed.

Hydrologic Instrumentation of Field Sites to Understand Short Term Changes in Water Quality

NASA Astrophysics Data System (ADS)

Iqbal, M. Z.; Clayton, M.

2011-12-01

This project is funded by a successful NSF-CCLI grant currently in effect. The objective of this project is to build a real time water quality monitoring facility by the Dry Run Creek on the University of Northern Iowa campus. The long term goal is to turn this site into a model outdoor educational resource for students to study the critical elements of the hydrologic environment. Weekly class sessions otherwise make it difficult for students to deal with the daily changes is water chemistry. Upon completion of the project, students will be able to look at the diurnal variations in the water quality through a website available for public viewing. Besides, they will have the opportunity to participate in a variety of research and learning activities directly at the site. Four (4) pieces of instruments are in the process of being installed at the experimental site. The instruments are 1) YSI 6600 V2 extended deployment probe to measure water quality parameters in the Dry Run Creek (i.e., pH, Total Dissolved Solids, conductivity, Dissolved Oxygen, temperature, turbidity, chlorophyll, etc.); 2) OTT RLS Radar to measure water level fluctuations in the creek; 3) Hydrolab MS5 mini-sonde to continuously measure pH, TDS, conductivity, DO, temperature, turbidity, and nitrate in a 70 ft deep ground water well on the site; and 4) DL 3000 data logger to receive all data from the above 3 pieces of equipment and automatically upload them to a website. Site preparation, including digging trenches for data cable and electric wires has been completed. Instrumental calibration is in progress and the site is expected to be up and running soon. We expect that this well site expansion plan will considerably strengthen our hydrology curriculum and facilitate more effective dissemination of the project outcome.

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

PubMed

Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

2016-04-15

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.

Clean Water State Revolving Fund (CWSRF): Contaminated Sites

EPA Pesticide Factsheets

Communities can use the CWSRF to address the water quality aspects of site assessment and cleanup of brownfields, Superfund sites, and sites of current or former aboveground or underground storage tanks.

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

DOE PAGES

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.; ...

2018-02-05

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

THE WATER-WATER CYCLE IN CHLOROPLASTS: Scavenging of Active Oxygens and Dissipation of Excess Photons.

PubMed

Asada, Kozi

1999-06-01

Photoreduction of dioxygen in photosystem I (PSI) of chloroplasts generates superoxide radicals as the primary product. In intact chloroplasts, the superoxide and the hydrogen peroxide produced via the disproportionation of superoxide are so rapidly scavenged at the site of their generation that the active oxygens do not inactivate the PSI complex, the stromal enzymes, or the scavenging system itself. The overall reaction for scavenging of active oxygens is the photoreduction of dioxygen to water via superoxide and hydrogen peroxide in PSI by the electrons derived from water in PSII, and the water-water cycle is proposed for these sequences. An overview is given of the molecular mechanism of the water-water cycle and microcompartmentalization of the enzymes participating in it. Whenever the water-water cycle operates properly for scavenging of active oxygens in chloroplasts, it also effectively dissipates excess excitation energy under environmental stress. The dual functions of the water-water cycle for protection from photoinihibition are discussed.

Determination of the Bridging Ligand in the Active Site of Tyrosinase.

PubMed

Zou, Congming; Huang, Wei; Zhao, Gaokun; Wan, Xiao; Hu, Xiaodong; Jin, Yan; Li, Junying; Liu, Junjun

2017-10-28

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.

Coarse-Grained Model for Water Involving a Virtual Site.

PubMed

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.

Overview of ground-water recharge study sites

USGS Publications Warehouse

Constantz, Jim; Adams, Kelsey S.; Stonestrom, David A.; Stonestrom, David A.; Constantz, Jim; Ferré, Ty P.A.; Leake, Stanley A.

2007-01-01

Multiyear studies were done to examine meteorologic and hydrogeologic controls on ephemeral streamflow and focused ground-water recharge at eight sites across the arid and semiarid southwestern United States. Campaigns of intensive data collection were conducted in the Great Basin, Mojave Desert, Sonoran Desert, Rio Grande Rift, and Colorado Plateau physiographic areas. During the study period (1997 to 2002), the southwestern region went from wetter than normal conditions associated with a strong El Niño climatic pattern (1997–1998) to drier than normal conditions associated with a La Niña climatic pattern marked by unprecedented warmth in the western tropical Pacific and Indian Oceans (1998–2002). The strong El Niño conditions roughly doubled precipitation at the Great Basin, Mojave Desert, and Colorado Plateau study sites. Precipitation at all sites trended generally lower, producing moderate- to severe-drought conditions by the end of the study. Streamflow in regional rivers indicated diminishing ground-water recharge conditions, with annual-flow volumes declining to 10–46 percent of their respective long-term averages by 2002. Local streamflows showed higher variability, reflecting smaller scales of integration (in time and space) of the study-site watersheds. By the end of the study, extended periods (9–15 months) of zero or negligible flow were observed at half the sites. Summer monsoonal rains generated the majority of streamflow and associated recharge in the Sonoran Desert sites and the more southerly Rio Grande Rift site, whereas winter storms and spring snowmelt dominated the northern and westernmost sites. Proximity to moisture sources (primarily the Pacific Ocean and Gulf of California) and meteorologic fluctuations, in concert with orography, largely control the generation of focused ground-water recharge from ephemeral streamflow, although other factors (geology, soil, and vegetation) also are important. Watershed area correlated weakly

Ground-water quality beneath solid-waste disposal sites at anchorage, Alaska

USGS Publications Warehouse

Zenone, Chester; Donaldson, D.E.; Grunwaldt, J.J.

1975-01-01

Studies at three solid-waste disposal sites in the Anchorage area suggest that differences in local geohydrologic conditions influence ground-water quality. A leachate was detected in ground water within and beneath two sites where the water table is very near land surface and refuse is deposited either at or below the water table in some parts of the filled areas. No leachate was detected in ground water beneath a third site where waste disposal is well above the local water table.

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A

PubMed Central

Maurer, Manuela; de Beer, Stephanie B. A.; Oostenbrink, Chris

2018-01-01

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data. PMID:27092480

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.

Method of draining water through a solid waste site without leaching

DOEpatents

Treat, Russell L.; Gee, Glendon W.; Whyatt, Greg A.

1993-01-01

The present invention is a method of preventing water from leaching solid waste sites by preventing atmospheric precipitation from contacting waste as the water flows through a solid waste site. The method comprises placing at least one drain hole through the solid waste site. The drain hole is seated to prevent waste material from entering the drain hole, and the solid waste site cover material is layered and graded to direct water to flow toward the drain hole and to soil beneath the waste site.

Method of draining water through a solid waste site without leaching

DOEpatents

Treat, R.L.; Gee, G.W.; Whyatt, G.A.

1993-02-02

The present invention is a method of preventing water from leaching solid waste sites by preventing atmospheric precipitation from contacting waste as the water flows through a solid waste site. The method comprises placing at least one drain hole through the solid waste site. The drain hole is seated to prevent waste material from entering the drain hole, and the solid waste site cover material is layered and graded to direct water to flow toward the drain hole and to soil beneath the waste site.

Dynamic asymmetry and the role of the conserved active-site thiol in rabbit muscle creatine kinase.

PubMed

Londergan, Casey H; Baskin, Rachel; Bischak, Connor G; Hoffman, Kevin W; Snead, David M; Reynoso, Christopher

2015-01-13

Symmetric and asymmetric crystal structures of the apo and transition state analogue forms, respectively, of the dimeric rabbit muscle creatine kinase have invoked an "induced fit" explanation for asymmetry between the two subunits and their active sites. However, previously reported thiol reactivity studies at the dual active-site cysteine 283 residues suggest a more latent asymmetry between the two subunits. The role of that highly conserved active-site cysteine has also not been clearly determined. In this work, the S-H vibrations of Cys283 were observed in the unmodified MM isoform enzyme via Raman scattering, and then one and both Cys283 residues in the same dimeric enzyme were modified to covalently attach a cyano group that reports on the active-site environment via its infrared CN stretching absorption band while maintaining the catalytic activity of the enzyme. Unmodified and Cys283-modified enzymes were investigated in the apo and transition state analogue forms of the enzyme. The narrow and invariant S-H vibrational bands report a homogeneous environment for the unmodified active-site cysteines, indicating that their thiols are hydrogen bonded to the same H-bond acceptor in the presence and absence of the substrate. The S-H peak persists at all physiologically relevant pH's, indicating that Cys283 is protonated at all pH's relevant to enzymatic activity. Molecular dynamics simulations identify the S-H hydrogen bond acceptor as a single, long-resident water molecule and suggest that the role of the conserved yet catalytically unnecessary thiol may be to dynamically rigidify that part of the active site through specific H-bonding to water. The asymmetric and broad CN stretching bands from the CN-modified Cys283 suggest an asymmetric structure in the apo form of the enzyme in which there is a dynamic exchange between spectral subpopulations associated with water-exposed and water-excluded probe environments. Molecular dynamics simulations indicate a

Water-Surface Elevations, Discharge, and Water-Quality Data for Selected Sites in the Warm Springs Area near Moapa, Nevada

USGS Publications Warehouse

Beck, David A.; Ryan, Roslyn; Veley, Ronald J.; Harper, Donald P.; Tanko, Daron J.

2006-01-01

The U.S. Geological Survey, in cooperation with Southern Nevada Water Authority and the Nevada Division of Water Resources, operates and maintains a surface-water monitoring network of 6 continuous-record stream-flow gaging stations and 11 partial-record stations in the Warm Springs area near Moapa, Nevada. Permanent land-surface bench marks were installed within the Warm Springs area by the Las Vegas Valley Water District, the Southern Nevada Water Authority, and the U.S. Geological Survey to determine water-surface elevations at all network monitoring sites. Vertical datum elevation and horizontal coordinates were established for all bench marks through a series of Differential Global Positioning System surveys. Optical theodolite surveys were made to transfer Differential Global Positioning System vertical datums to reference marks installed at each monitoring site. The surveys were completed in June 2004 and water-surface elevations were measured on August 17, 2004. Water-surface elevations ranged from 1,810.33 feet above North American Vertical Datum of 1988 at a stream-gaging station in the Pederson Springs area to 1,706.31 feet at a station on the Muddy River near Moapa. Discharge and water-quality data were compiled for the Warm Springs area and include data provided by the U.S. Geological Survey, Nevada Division of Water Resources, U.S. Fish and Wildlife Service, Moapa Valley Water District, Desert Research Institute, and Converse Consultants. Historical and current hydrologic data-collection networks primarily are related to changes in land- and water-use activities in the Warm Springs area. These changes include declines in ranching and agricultural use, the exportation of water to other areas of Moapa Valley, and the creation of a national wildlife refuge. Water-surface elevations, discharge, and water-quality data compiled for the Warm Springs area will help identify (1) effects of changing vegetation within the former agricultural lands, (2) effects

Comparative analysis of effluent water quality from a municipal treatment plant and two on-site wastewater treatment systems.

PubMed

Garcia, Santos N; Clubbs, Rebekah L; Stanley, Jacob K; Scheffe, Brian; Yelderman, Joe C; Brooks, Bryan W

2013-06-01

Though decentralized on-site technologies are extensively employed for wastewater treatment around the globe, an understanding of effluent water quality impairments associated with these systems remain less understood than effluent discharges from centralized municipal wastewater treatment facilities. Using a unique experimental facility, a novel comparative analysis of effluent water quality was performed from model decentralized aerobic (ATS) and septic (STS) on-site wastewater treatment systems and a centralized municipal wastewater treatment plant (MTP). The ATS and STS units did not benefit from further soil treatment. Each system received common influent wastewater from the Waco, Texas, USA Metropolitan Area Regional Sewerage System. We tested the hypothesis that MTP effluent would exhibit higher water quality than on-site effluents, based on parameters selected for study. A tiered testing approach was employed to assess the three effluent discharges: select routine water quality parameters (Tier I), whole effluent toxicity (Tier II), and select endocrine-active compounds (Tier III). Contrary to our hypothesis, ATS effluent was not statistically different from MTP effluents, based on Tier I and III parameters, but reproductive responses of Daphnia magna were slightly more sensitive to ATS than MTP effluents. STS effluent water quality was identified as most degraded of the three wastewater treatment systems. Parameters used to assess centralized wastewater treatment plant effluent water quality such as whole effluent toxicity and endocrine active substances appear useful for water quality assessments of decentralized discharges. Aerobic on-site wastewater treatment systems may represent more robust options than traditional septic systems for on-site wastewater treatment in watersheds with appreciable groundwater - surface water exchange. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mechanistic Effects of Water on the Fe-Catalyzed Hydrodeoxygenation of Phenol. The Role of Brønsted Acid Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hensley, Alyssa J. R.; Wang, Yong; Mei, Donghai

A mechanistic understanding of the roles of water is essential for developing highly active and selective catalysts for hydrodeoxygenation (HDO) reactions since water is ubiquitous in such reaction systems. Here, we present a study for phenol HDO on Fe catalysts using density functional theory which examines the effect of water on three elementary pathways for phenol HDO using an explicit solvation model. The presence of water is found to significantly decrease activation barriers required by hydrogenation reactions via two pathways. First, the proton transfer in the hydrogen bonding network of the liquid water phase is nearly barrierless, which significantly promotesmore » the direct through space tautomerization of phenol. Second, due to the high degree of oxophilicity on Fe, liquid water molecules are found to be easily dissociated into surface hydroxyl groups that can act as Brønsted acid sites. These sites dramatically promote hydrogenation reactions on the Fe surface. As a result, the hydrogen assisted dehydroxylation becomes the dominant phenol HDO pathway. This work provides new fundamental insights into aqueous phase HDO of biomass-derived oxygenates over Fe-based catalysts; e.g., the activity of Fe-based catalysts can be optimized by tuning the surface coverage of Brønsted acid sites via surface doping.« less

Identification of Conserved Water Sites in Protein Structures for Drug Design.

PubMed

Jukič, Marko; Konc, Janez; Gobec, Stanislav; Janežič, Dušanka

2017-12-26

Identification of conserved waters in protein structures is a challenging task with applications in molecular docking and protein stability prediction. As an alternative to computationally demanding simulations of proteins in water, experimental cocrystallized waters in the Protein Data Bank (PDB) in combination with a local structure alignment algorithm can be used for reliable prediction of conserved water sites. We developed the ProBiS H2O approach based on the previously developed ProBiS algorithm, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user. With a protein structure, a binding site, or an individual water molecule as a query, ProBiS H2O collects similar proteins from the PDB and performs local or binding site-specific superimpositions of the query structure with similar proteins using the ProBiS algorithm. It collects the experimental water molecules from the similar proteins and transposes them to the query protein. Transposed waters are clustered by their mutual proximity, which enables identification of discrete sites in the query protein with high water conservation. ProBiS H2O is a robust and fast new approach that uses existing experimental structural data to identify conserved water sites on the interfaces of protein complexes, for example protein-small molecule interfaces, and elsewhere on the protein structures. It has been successfully validated in several reported proteins in which conserved water molecules were found to play an important role in ligand binding with applications in drug design.

Water-quality trends and constituent-transport analysis for selected sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site in the upper Clark Fork Basin, Montana, water years 1996–2015

USGS Publications Warehouse

Sando, Steven K.; Vecchia, Aldo V.

2016-07-20

During the extended history of mining in the upper Clark Fork Basin in Montana, large amounts of waste materials enriched with metallic contaminants (cadmium, copper, lead, and zinc) and the metalloid trace element arsenic were generated from mining operations near Butte and milling and smelting operations near Anaconda. Extensive deposition of mining wastes in the Silver Bow Creek and Clark Fork channels and flood plains had substantial effects on water quality. Federal Superfund remediation activities in the upper Clark Fork Basin began in 1983 and have included substantial remediation near Butte and removal of the former Milltown Dam near Missoula. To aid in evaluating the effects of remediation activities on water quality, the U.S. Geological Survey began collecting streamflow and water-quality data in the upper Clark Fork Basin in the 1980s.Trend analysis was done on specific conductance, selected trace elements (arsenic, copper, and zinc), and suspended sediment for seven sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site for water years 1996–2015. The most upstream site included in trend analysis is Silver Bow Creek at Warm Springs, Montana (sampling site 8), and the most downstream site is Clark Fork above Missoula, Montana (sampling site 22), which is just downstream from the former Milltown Dam. Water year is the 12-month period from October 1 through September 30 and is designated by the year in which it ends. Trend analysis was done by using a joint time-series model for concentration and streamflow. To provide temporal resolution of changes in water quality, trend analysis was conducted for four sequential 5-year periods: period 1 (water years 1996–2000), period 2 (water years 2001–5), period 3 (water years 2006–10), and period 4 (water years 2011–15). Because of the substantial effect of the intentional breach of Milltown Dam on March 28, 2008, period 3 was subdivided into period 3A (October 1, 2005–March 27, 2008

Bacterial Abundance and Activity across Sites within Two Northern Wisconsin Sphagnum Bogs.

PubMed

Fisher; Graham; Graham

1998-11-01

Abstract Bacterial abundance, temperature, pH, and dissolved organic carbon (DOC) concentration were compared across surface sites within and between two northern Wisconsin Sphagnum peatlands over the summer seasons in 1995 and 1996. Sites of interest were the Sphagnum mat surface, the water-filled moat (lagg) at the bog margin, and the bog lake littoral zone. Significant differences in both bacterial populations and water chemistry were observed between sites. pH was highest in the lake and lowest in the mat at both bogs; the opposite was true for DOC. Large populations of bacteria were present in surface interstitial water from the mat; abundance in this site was consistently higher than in the moat or lake. Bacterial abundance also increased across sites of increasing DOC concentration and declining pH. Bacterial activities (rates of [3H]leucine incorporation) and growth in dilution cultures (with grazers removed) were also assessed in lake, moat, and mat sites. Results using these measures generally supported the trends observed in abundance, although high rates of [3H]leucine incorporation were recorded in the moat at one of the bogs. Our results indicate that bacterial populations in Sphagnum peatlands are not adversely affected by acidity, and that DOC may be more important than pH in determining bacterial abundance in these environments.

Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.

PubMed

Caratelli, Chiara; Hajek, Julianna; Rogge, Sven M J; Vandenbrande, Steven; Meijer, Evert Jan; Waroquier, Michel; Van Speybroeck, Veronique

2018-02-19

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Eurasian beaver activity increases water storage, attenuates flow and mitigates diffuse pollution from intensively-managed grasslands.

PubMed

Puttock, Alan; Graham, Hugh A; Cunliffe, Andrew M; Elliott, Mark; Brazier, Richard E

2017-01-15

Beavers are the archetypal keystone species, which can profoundly alter ecosystem structure and function through their ecosystem engineering activity, most notably the building of dams. This can have a major impact upon water resource management, flow regimes and water quality. Previous research has predominantly focused on the activities of North American beaver (Castor canadensis) located in very different environments, to the intensive lowland agricultural landscapes of the United Kingdom and elsewhere in Europe. Two Eurasian beavers (Castor fiber) were introduced to a wooded site, situated on a first order tributary, draining from intensively managed grassland. The site was monitored to understand impacts upon water storage, flow regimes and water quality. Results indicated that beaver activity, primarily via the creation of 13 dams, has increased water storage within the site (holding ca. 1000m 3 in beaver ponds) and beavers were likely to have had a significant flow attenuation impact, as determined from peak discharges (mean 30±19% reduction), total discharges (mean 34±9% reduction) and peak rainfall to peak discharge lag times (mean 29±21% increase) during storm events. Event monitoring of water entering and leaving the site showed lower concentrations of suspended sediment, nitrogen and phosphate leaving the site (e.g. for suspended sediment; average entering site: 112±72mgl -1 , average leaving site: 39±37mgl -1 ). Combined with attenuated flows, this resulted in lower diffuse pollutant loads in water downstream. Conversely, dissolved organic carbon concentrations and loads downstream were higher. These observed changes are argued to be directly attributable to beaver activity at the site which has created a diverse wetland environment, reducing downstream hydrological connectivity. Results have important implications for beaver reintroduction programs which may provide nature based solutions to the catchment-scale water resource management issues

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

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.

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

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.

Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir, Eastern China

PubMed Central

Zhang, Haihan; Huang, Tinglin; Liu, Tingting

2013-01-01

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH3-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir. PMID:24205265

Finding New Water: Development of On-Site Non-Potable Water Reuse Systems

EPA Science Inventory

By designing our buildings to collect and treat water generated on-site, can be and reused for flushing our toilets and irrigating our landscaping. Several water sources are generated with-in a building including: rainwater, stormwater, graywater, blackwater and foundation drain...

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 [Cu IIOH] + 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 [Cu IIOH] + active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu] 2+ and Cu 3O 3 motifs.« less

A comparative study of surface energies and water adsorption on Ce-bastnäsite, La-bastnäsite, and calcite via density functional theory and water adsorption calorimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goverapet Srinivasan, Sriram; Shivaramaiah, Radha; Kent, Paul R. C.

Bastnäsite, a fluoro-carbonate mineral, is the single largest mineral source of light rare earth elements (REE), La, Ce and Nd. Enhancing the efficiency of separation of the mineral from gangue through froth flotation is the first step towards meeting an ever increasing demand for REE. To design and evaluate collector molecules that selectively bind to bastnäsite, a fundamental understanding of the structure and surface properties of bastnäsite is essential. In our earlier work (J Phys Chem C, 2016, 120, 16767), we carried out an extensive study of the structure, surface stability and water adsorption energies of La-bastnäsite. Here in thismore » work, we make a comparative study of the surface properties of Ce-bastnäsite, La-bastnäsite, and calcite using a combination of density functional theory (DFT) and water adsorption calorimetry. Spin polarized DFT+U calculations show that the exchange interaction between the electrons in Ce 4f orbitals is negligible and that these orbitals do not participate in bonding with the oxygen atom of the adsorbed water molecule. In agreement with calorimetry, DFT calculations predict larger surface energies and stronger water adsorption energies on Ce-bastnäsite than on La-bastnäsite. The order of stabilities for stoichiometric surfaces is as follows: [100] > [101] > [102] > [0001] > [112] > [104] and the most favorable adsorption sites for water molecules are the same as for La-bastnäsite. In agreement with water adsorption calorimetry, at low coverage water molecules are strongly stabilized via coordination to the surface Ce3+ ions, whereas at higher coverage they are adsorbed less strongly via hydrogen bonding interaction with the surface anions. Lastly, due to similar water adsorption energies on bastnäsite [101] and calcite [104] surfaces, the design of collector molecules that selectively bind to bastnäsite over calcite must exploit the structural differences in the predominantly exposed facets of these minerals.« less

A comparative study of surface energies and water adsorption on Ce-bastnäsite, La-bastnäsite, and calcite via density functional theory and water adsorption calorimetry

DOE PAGES

Goverapet Srinivasan, Sriram; Shivaramaiah, Radha; Kent, Paul R. C.; ...

2017-02-24

Bastnäsite, a fluoro-carbonate mineral, is the single largest mineral source of light rare earth elements (REE), La, Ce and Nd. Enhancing the efficiency of separation of the mineral from gangue through froth flotation is the first step towards meeting an ever increasing demand for REE. To design and evaluate collector molecules that selectively bind to bastnäsite, a fundamental understanding of the structure and surface properties of bastnäsite is essential. In our earlier work (J Phys Chem C, 2016, 120, 16767), we carried out an extensive study of the structure, surface stability and water adsorption energies of La-bastnäsite. Here in thismore » work, we make a comparative study of the surface properties of Ce-bastnäsite, La-bastnäsite, and calcite using a combination of density functional theory (DFT) and water adsorption calorimetry. Spin polarized DFT+U calculations show that the exchange interaction between the electrons in Ce 4f orbitals is negligible and that these orbitals do not participate in bonding with the oxygen atom of the adsorbed water molecule. In agreement with calorimetry, DFT calculations predict larger surface energies and stronger water adsorption energies on Ce-bastnäsite than on La-bastnäsite. The order of stabilities for stoichiometric surfaces is as follows: [100] > [101] > [102] > [0001] > [112] > [104] and the most favorable adsorption sites for water molecules are the same as for La-bastnäsite. In agreement with water adsorption calorimetry, at low coverage water molecules are strongly stabilized via coordination to the surface Ce3+ ions, whereas at higher coverage they are adsorbed less strongly via hydrogen bonding interaction with the surface anions. Lastly, due to similar water adsorption energies on bastnäsite [101] and calcite [104] surfaces, the design of collector molecules that selectively bind to bastnäsite over calcite must exploit the structural differences in the predominantly exposed facets of these minerals.« less

A comparative study of surface energies and water adsorption on Ce-bastnäsite, La-bastnäsite, and calcite via density functional theory and water adsorption calorimetry.

PubMed

Goverapet Srinivasan, Sriram; Shivaramaiah, Radha; Kent, Paul R C; Stack, Andrew G; Riman, Richard; Anderko, Andre; Navrotsky, Alexandra; Bryantsev, Vyacheslav S

2017-03-15

Bastnäsite, a fluoro-carbonate mineral, is the single largest mineral source of light rare earth elements (REE), La, Ce and Nd. Enhancing the efficiency of separation of the mineral from gangue through froth flotation is the first step towards meeting an ever increasing demand for REE. To design and evaluate collector molecules that selectively bind to bastnäsite, a fundamental understanding of the structure and surface properties of bastnäsite is essential. In our earlier work (J. Phys. Chem. C, 2016, 120, 16767), we carried out an extensive study of the structure, surface stability and water adsorption energies of La-bastnäsite. In this work, we make a comparative study of the surface properties of Ce-bastnäsite, La-bastnäsite, and calcite using a combination of density functional theory (DFT) and water adsorption calorimetry. Spin polarized DFT+U calculations show that the exchange interaction between the electrons in Ce 4f orbitals is negligible and that these orbitals do not participate in bonding with the oxygen atom of the adsorbed water molecule. In agreement with calorimetry, DFT calculations predict larger surface energies and stronger water adsorption energies on Ce-bastnäsite than on La-bastnäsite. The order of stabilities for stoichiometric surfaces is as follows: [101[combining macron]0] > [101[combining macron]1] > [101[combining macron]2] > [0001] > [112[combining macron]2] > [101[combining macron]4] and the most favorable adsorption sites for water molecules are the same as for La-bastnäsite. In agreement with water adsorption calorimetry, at low coverage water molecules are strongly stabilized via coordination to the surface Ce 3+ ions, whereas at higher coverage they are adsorbed less strongly via hydrogen bonding interaction with the surface anions. Due to similar water adsorption energies on bastnäsite [101[combining macron]1] and calcite [101[combining macron]4] surfaces, the design of collector molecules that selectively bind to

An assessment of drinking-water supplies on the Hanford site: an evaluation conducted at a federal nuclear facility in southeastern Washington state.

PubMed

Hanf, R William; Kelly, Lynn M

2005-03-01

Drinking water is supplied to most U.S. Department of Energy (DOE) facilities on the Hanford Site by DOE-owned, contractor-operated pumping and distribution systems. Water is primarily obtained from the Columbia River, but some facilities use water from on-site groundwater wells. Because of the large amount of radioactive and chemical waste produced, stored, and disposed of at Hanford, some people are concerned that waste materials are contaminating on-site drinking-water supplies. This paper describes the drinking-water facilities and treatment requirements on the Hanford Site and summarizes radiological and non-radiological water quality data obtained from water samples collected from each drinking-water system in use during 2001 and 2002. Monitoring data show that Hanford-produced radionuclides are measurable in some drinking-water samples. The only non-radiological contaminants detected either were by-products of the chlorination process or came from off-site agricultural activities. Contaminant level values were, in all cases, below state and federal drinking-water limits. This information will provide assurance to current employees and future site developers that drinking water on the Hanford Site is safe for public consumption.

Ground Water Issue: Phytoremediation of Contaminated Soil and Ground Water at Hazardous Waste Sites

DTIC Science & Technology

2001-02-01

Development Ground Water Issue Phytoremediation of Contaminated Soil and Ground Water at Hazardous Waste Sites National Risk Management Research... Phytoremediation , the use of plants in remediation, is one such technology. This issue paper focuses on the processes and applications of phytoremediation ...of phytoremediation as a cleanup or containment technique for remediation of hazardous waste sites. Introductory material on plant processes is

Fate of 137Cs, 90Sr and 239+240Pu in soil profiles at a water recharge site in Basel, Switzerland.

PubMed

Abraham, Johannes; Meusburger, Katrin; Waldis, Judith Kobler; Ketterer, Michael E; Zehringer, Markus

2018-02-01

An important process in the production of drinking water is the recharge of the withdrawn ground water with river water at protected recharge fields. While it is well known that undisturbed soils are efficiently filtering and adsorbing radionuclides, the goal of this study was to investigate their behaviour in an artificial recharge site that may receive rapid and additional input of radionuclides by river water (particularly when draining a catchment including nuclear power plants (NPP)). Soil profiles of recharge sites were drilled and analysed for radionuclides, specifically radiocesium ( 137 Cs), radiostrontium ( 90 Sr) and plutonium ( 239+240 Pu). The distribution of the analysed radionuclides were compared with an uncultivated reference soil outside the recharge site. The main activity of 137 Cs was located in the top soil (4.5-7.5 cm) and reached down to a depth of 84 cm and 48 cm for the recharge and the reference site, respectively. The found activities of 239+240 Pu originate from the global fallout after 1950. 239+240 Pu appeared to be strongly adsorbed onto soil particles. The shape of the depth profile was similar to 137 Cs, but also similar between the recharge and the reference site. In contrast, 90 Sr showed a uniform distribution over the entire depth of the recharge and reference profiles indicating that 90 Sr already entered the gravel zone and the ground water. Elevated inventories of the radionuclides were observed for the recharge site. The soil of the recharge field exhibited a threefold higher activity of 137 Cs compared to the reference soil. Also for 239+240 Pu higher inventories where observed for the recharge sites (40%). 90 Sr behaved differently, showing similar inventories between reference and recharge site. We estimate that 75-89% of the total inventory of 137 Cs in the soil at the recharge site (7.000 Bq/m 2 ) originated from the fallout of the Chernobyl accident and from emissions of Swiss NPPs. This estimate is based on the

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

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

PubMed

Blaha-Nelson, David; Krüger, Dennis M; Szeler, Klaudia; Ben-David, Moshe; Kamerlin, Shina Caroline Lynn

2017-01-25

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 k cat 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.

Forward osmosis as an approach to manage oil sands tailings water and on-site basal depressurization water.

PubMed

Zhu, Shu; Li, Mingyu; Gamal El-Din, Mohamed

2017-04-05

As the volume of oil sands process-affected water (OSPW) stored in tailings ponds increases, it is urgent to seek for water management approaches to alleviate the environmental impact caused by large quantity of toxic water. Forward osmosis (FO) utilizes osmotic pressure difference between two solutions, thereby giving a potential to manage two wastewaters. In this study, FO was proposed to manage OSPW, using on-site waste basal depressurization water (BDW) as draw solution. To investigate its feasibility, both short and long-term OSPW desalination experiments were carried out. By applying this process, the volume of OSPW was decreased>40% and high rejections were achieved, especially, the major organic toxicity source - naphthenic acids (NAs). Although comparative low water flux (≤3L/m 2 h) was obtained, water flux caused by membrane fouling can be completely recovered using water physical cleaning. Moreover, calcium carbonate precipitation was observed on the OSPW-oriented membrane side. With respect to flux decline, the active layer facing the feed solution (FO mode) and active layer facing draw solution (PRO mode) did not demonstrate a significant difference on anti-fouling performance. The advantages provided by this approach include zero draw solution cost, less reversible membrane fouling and beneficial reuse/recycle of diluted BDW. Copyright © 2016 Elsevier B.V. All rights reserved.

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

, a noncatalytic arrangement of the catalytic triad is dominant. Unnatural truncated substrates are inactive because of the lack of protein-protein interactions provided by the ACP. Directed evolution is able to gradually restore the catalytic organization of the active site by motion of the protein backbone that alters the active site geometry. In the third case, we demonstrate the key role of MD in combination with crystallography to identify the origins of substrate-dependent stereoselectivities in a number of Codexis-engineered ketoreductases, one of which is used commercially for the production of the antibiotic sulopenem. Here, mutations alter the shape of the active site as well as the accessibility of water to different regions of it. Each of these examples reveals something different about how mutations can influence enzyme activity and shows that directed evolution, like natural evolution, can increase catalytic activity in a variety of remarkable and often subtle ways.

Bacterial biomass and activity in the deep waters of the eastern Atlantic—evidence of a barophilic community

NASA Astrophysics Data System (ADS)

Patching, J. W.; Eardly, D.

1997-09-01

Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlantic, of similar depth (4560-4800 m), but varying in their nutritional status. The Northern (N) site was eutrophic and subject to a strong seasonal input of surface derived organic matter (phytodetritus) to the sediment. The Southern (S) site was oligotrophic. Deep water at this site does not appear to receive any strong seasonal input. Bacterial numbers in the deep water column at the N site showed no significant seasonal variation but were greater than those at the S site. Deep water bacteria were typically small and free-living. From biovolume determinations, it was estimated that mean concentrations of bacterial organic carbon at depths greater than 500 m were 0.12 (0.03-0.29) μg C 1 -1 and 0.02 (0.01-0.04) μg C 1 -1 at the N and S sites, respectively. Rates of thymidine and leucine incorporation were used as indicators of bacterial activity. Bacterial communities in water in contact with the sediment (SCW; sediment contact water) at both sites (but especially at the S site) were strongly barophilic at in situ temperatures (2.5-4.1°C). The barophilic response of thymidine incorporation was enhanced when SCW samples from the N site were incubated at 11.5°C. It is proposed that this result indicated an elevating effect of pressure on cardinal temperatures and that the SCW community was obligately psychrophilic when unpressurised. Comparison of cell-specific incorporation rates determined under in situ conditions showed bacteria in the SCW to have levels of activity comparable with bacteria from a depth of 150 m. Thymidine incorporation rates were highest in SCW samples taken at the N site in May 1988 and September 1989. Thymidine incorporation by SCW samples taken immediately before (10 April 1994) the main spring-bloom-associated deposition of phytodetritus was significantly lower and comparable with that determined for the oligotrophic S site. The attributes

Field demonstration of on-site analytical methods for TNT and RDX in ground water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craig, H.; Ferguson, G.; Markos, A.

1996-12-31

A field demonstration was conducted to assess the performance of eight commercially-available and emerging colorimetric, immunoassay, and biosensor on-site analytical methods for explosives 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in ground water and leachate at the Umatilla Army Depot Activity, Hermiston, Oregon and US Naval Submarine Base, Bangor, Washington, Superfund sites. Ground water samples were analyzed by each of the on-site methods and results compared to laboratory analysis using high performance liquid chromatography (HPLC) with EPA SW-846 Method 8330. The commercial methods evaluated include the EnSys, Inc., TNT and RDX colorimetric test kits (EPA SW-846 Methods 8515 and 8510) with amore » solid phase extraction (SPE) step, the DTECH/EM Science TNT and RDX immunoassay test kits (EPA SW-846 Methods 4050 and 4051), and the Ohmicron TNT immunoassay test kit. The emerging methods tested include the antibody-based Naval Research Laboratory (NRL) Continuous Flow Immunosensor (CFI) for TNT and RDX, and the Fiber Optic Biosensor (FOB) for TNT. Accuracy of the on-site methods were evaluated using linear regression analysis and relative percent difference (RPD) comparison criteria. Over the range of conditions tested, the colorimetric methods for TNT and RDX showed the highest accuracy of the emerging methods for TNT and RDX. The colorimetric method was selected for routine ground water monitoring at the Umatilla site, and further field testing on the NRL CFI and FOB biosensors will continue at both Superfund sites.« less

CONTAMINATION OF PUBLIC GROUND WATER SUPPLIES BY SUPERFUND SITES

EPA Science Inventory

Multiple sources of contamination can affect ground water supplies, including municipal landfills, industrial operations, leaking underground storage tanks, septic tank systems, and prioritized uncontrolled hazardous waste sites known as “Superfund” sites. A review of Superfund R...

Practical data collection : establishing methods and procedures for measuring water clarity and turbidity of storm water run-off from active major highway construction sites.

DOT National Transportation Integrated Search

2014-09-12

In anticipation of regulation involving numeric turbidity limit at highway construction sites, research was : done into the most appropriate, affordable methods for surface water monitoring. Measuring sediment : concentration in streams may be conduc...

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

PubMed

Sen, Kakali; Horrell, Sam; Kekilli, Demet; Yong, Chin W; Keal, Thomas W; Atakisi, Hakan; Moreau, David W; Thorne, Robert E; Hough, Michael A; Strange, Richard W

2017-07-01

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Surface-Water Quality Conditions and Long-Term Trends at Selected Sites within the Ambient Water-Quality Monitoring Network in Missouri, Water Years 1993-2008

USGS Publications Warehouse

Barr, Miya N.; Davis, Jerri V.

2010-01-01

The U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources, collects data pertaining to the surface-water resources of Missouri. These data are collected as part of the Missouri Ambient Water-Quality Monitoring Network and constitute a valuable source of reliable, impartial, and timely information for developing an improved understanding of water resources in the State. Six sites from the Ambient Water-Quality Monitoring Network, with data available from the 1993 through 2008 water years, were chosen to compare water-quality conditions and long-term trends of dissolved oxygen, selected physical properties, total suspended solids, dissolved nitrate plus nitrite as nitrogen, total phosphorous, fecal indicator bacteria, and selected trace elements. The six sites used in the study were classified in groups corresponding to the physiography, main land use, and drainage basin size, and represent most stream types in Missouri. Long-term trends in this study were analyzed using flow-adjusted and non-flow adjusted models. Highly censored datasets (greater than 5 percent but less than 50 percent censored values) were not flow-adjusted. Trends that were detected can possibly be related to changes in agriculture or urban development within the drainage basins. Trends in nutrients were the most prevalent. Upward flow-adjusted trends in dissolved nitrate plus nitrite (as nitrogen) concentrations were identified at the Elk River site, and in total phosphorus concentrations at the South Fabius and Grand River sites. A downward flow-adjusted trend was identified in total phosphorus concentrations from Wilson Creek, the only urban site in the study. The downward trend in phosphorus possibly was related to a phosphorus reduction system that began operation in 2001 at a wastewater treatment plant upstream from the sampling site. Total suspended solids concentrations indicated an upward non-flow adjusted trend at the two northern sites (South Fabius

User's manual for the national water information system of the U.S. Geological Survey: Ground-water site-inventory system

USGS Publications Warehouse

,

2004-01-01

The Ground-Water Site-Inventory (GWSI) System is a ground-water data storage and retrieval system that is part of the National Water Information System (NWIS) developed by the U.S. Geological Survey (USGS). The NWIS is a distributed water database in which data can be processed over a network of workstations and file servers at USGS offices throughout the United States. This system comprises the GWSI, the Automated Data Processing System (ADAPS), the Water-Quality System (QWDATA), and the Site-Specific Water-Use Data System (SWUDS). The GWSI System provides for entering new sites and updating existing sites within the local database. In addition, the GWSI provides for retrieving and displaying ground-water and sitefile data stored in the local database. Finally, the GWSI provides for routine maintenance of the local and national data records. This manual contains instructions for users of the GWSI and discusses the general operating procedures for the programs found within the GWSI Main Menu.

Evaluation of surface waters associated with animal feeding operations for estrogenic chemicals and activity

USDA-ARS?s Scientific Manuscript database

Estrogens and estrogenic activity (EA) were evaluated in surface waters associated with animal feeding operations. Water was sampled at 19 sites in 12 states using discrete (n=41) and POCIS (n=19) sampling methods. Estrogenic chemicals measured in unfiltered water by GC/MS2 included: estrone (E1),17...

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 (CeO 2) and sodium-modified ceria (Ce-Na) were prepared through combustion synthesis. Palladium was deposited onto the supports (Pd/CeO 2 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/CeO 2. 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 supportmore » and independent of 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

Characterization of Missouri surface waters near point sources of pollution reveals potential novel atmospheric route of exposure for bisphenol A and wastewater hormonal activity pattern.

PubMed

Kassotis, Christopher D; Alvarez, David A; Taylor, Julia A; vom Saal, Frederick S; Nagel, Susan C; Tillitt, Donald E

2015-08-15

Surface water contamination by chemical pollutants increasingly threatens water quality around the world. Among the many contaminants found in surface water, there is growing concern regarding endocrine disrupting chemicals, based on their ability to interfere with some aspect of hormone action in exposed organisms, including humans. This study assessed water quality at several sites across Missouri (near wastewater treatment plants and airborne release sites of bisphenol A) based on hormone receptor activation potencies and chemical concentrations present in the surface water. We hypothesized that bisphenol A and ethinylestradiol would be greater in water near permitted airborne release sites and wastewater treatment plant inputs, respectively, and that these two compounds would be responsible for the majority of activities in receptor-based assays conducted with water collected near these sites. Concentrations of bisphenol A and ethinylestradiol were compared to observed receptor activities using authentic standards to assess contribution to total activities, and quantitation of a comprehensive set of wastewater compounds was performed to better characterize each site. Bisphenol A concentrations were found to be elevated in surface water near permitted airborne release sites, raising questions that airborne releases of BPA may influence nearby surface water contamination and may represent a previously underestimated source to the environment and potential for human exposure. Estrogen and androgen receptor activities of surface water samples were predictive of wastewater input, although the lower sensitivity of the ethinylestradiol ELISA relative to the very high sensitivity of the bioassay approaches did not allow a direct comparison. Wastewater-influenced sites also had elevated anti-estrogenic and anti-androgenic equivalence, while sites without wastewater discharges exhibited no antagonist activities. Published by Elsevier B.V.

Characterization of Missouri surface waters near point sources of pollution reveals potential novel atmospheric route of exposure for bisphenol A and wastewater hormonal activity pattern

USGS Publications Warehouse

Kassotis, Christopher D.; Alvarez, David A.; Taylor, Julia A.; vom Saal, Frederick S.; Nagel, Susan C.; Tillitt, Donald E.

2015-01-01

Surface water contamination by chemical pollutants increasingly threatens water quality around the world. Among the many contaminants found in surface water, there is growing concern regarding endocrine disrupting chemicals, based on their ability to interfere with some aspect of hormone action in exposed organisms, including humans. This study assessed water quality at several sites across Missouri (near wastewater treatment plants and airborne release sites of bisphenol A) based on hormone receptor activation potencies and chemical concentrationspresent in the surface water. We hypothesized that bisphenol A and ethinylestradiol would be greater in water near permitted airborne release sites and wastewater treatment plant inputs, respectively, and that these two compounds would be responsible for the majority of activities in receptor-based assays conducted with water collected near these sites. Concentrations of bisphenol A and ethinylestradiol were compared to observed receptor activities using authentic standards to assess contribution to total activities, and quantitation of a comprehensive set of wastewater compounds was performed to better characterize each site. Bisphenol A concentrations were found to be elevated in surface water near permitted airborne release sites, raising questions that airborne releases of BPA may influence nearby surface water contamination and may represent a previously underestimated source to the environment and potential for human exposure. Estrogen and androgen receptor activities of surface water samples were predictive of wastewater input, although the lower sensitivity of the ethinylestradiol ELISA relative to the very high sensitivity of the bioassay approaches did not allow a direct comparison. Wastewater-influenced sites also had elevated anti-estrogenic and anti-androgenic equivalence, while sites without wastewater discharges exhibited no antagonist activities.

Trends in major-ion constituents and properties for selected sampling sites in the Tongue and Powder River watersheds, Montana and Wyoming, based on data collected during water years 1980-2010

USGS Publications Warehouse

Sando, Steven K.; Vecchia, Aldo V.; Barnhart, Elliott P.; Sando, Thomas R.; Clark, Melanie L.; Lorenz, David L.

2014-01-01

The primary purpose of this report is to present information relating to flow-adjusted temporal trends in major-ion constituents and properties for 16 sampling sites in the Tongue and Powder River watersheds based on data collected during 1980–2010. In association with this primary purpose, the report presents background information on major-ion characteristics (including specific conductance, calcium, magnesium, potassium, sodium adsorption ratio, sodium, alkalinity, chloride, fluoride, dissolved sulfate, and dissolved solids) of the sampling sites and coal-bed methane (CBM) produced water (groundwater pumped from coal seams) in the site watersheds, trend analysis methods, streamflow conditions, and factors that affect trend results. The Tongue and Powder River watersheds overlie the Powder River structural basin (PRB) in northeastern Wyoming and southeastern Montana. Limited extraction of coal-bed methane (CBM) from the PRB began in the early 1990’s, and increased dramatically during the late 1990’s and early 2000’s. CBM-extraction activities produce discharges of water with high concentrations of dissolved solids (particularly sodium and bicarbonate ions) relative to most stream water in the Tongue and Powder River watersheds. Water-quality of CBM produced water is of concern because of potential effects of sodium on agricultural soils and potential effects of bicarbonate on aquatic biota. Two parametric trend-analysis methods were used in this study: the time-series model (TSM) and ordinary least squares regression (OLS) on time, streamflow, and season. The TSM was used to analyze trends for 11 of the 16 study sites. For five sites, data requirements of the TSM were not met and OLS was used to analyze trends. Two primary 10-year trend-analysis periods were selected. Trend-analysis period 1 (water years 1986–95; hereinafter referred to as period 1) was selected to represent variability in major-ion concentrations in the Tongue and Powder River

Air-water exchange of PAHs and OPAHs at a superfund mega-site.

PubMed

Tidwell, Lane G; Blair Paulik, L; Anderson, Kim A

2017-12-15

Chemical fate is a concern at environmentally contaminated sites, but characterizing that fate can be difficult. Identifying and quantifying the movement of chemicals at the air-water interface are important steps in characterizing chemical fate. Superfund sites are often suspected sources of air pollution due to legacy sediment and water contamination. A quantitative assessment of polycyclic aromatic hydrocarbons (PAHs) and oxygenated PAH (OPAHs) diffusive flux in a river system that contains a Superfund Mega-site, and passes through residential, urban and agricultural land, has not been reported before. Here, passive sampling devices (PSDs) were used to measure 60 polycyclic aromatic hydrocarbons (PAHs) and 22 oxygenated PAH (OPAHs) in air and water. From these concentrations the magnitude and direction of contaminant flux between these two compartments was calculated. The magnitude of PAH flux was greater at sites near or within the Superfund Mega-site than outside of the Superfund Mega-site. The largest net individual PAH deposition at a single site was naphthalene at a rate of -14,200 (±5780) (ng/m 2 )/day. The estimated one-year total flux of phenanthrene was -7.9×10 5 (ng/m 2 )/year. Human health risk associated with inhalation of vapor phase PAHs and dermal exposure to PAHs in water were assessed by calculating benzo[a]pyrene equivalent concentrations. Excess lifetime cancer risk estimates show potential increased risk associated with exposure to PAHs at sites within and in close proximity to the Superfund Mega-site. Specifically, estimated excess lifetime cancer risk associated with dermal exposure and inhalation of PAHs was above 1 in 1 million within the Superfund Mega-site. The predominant depositional flux profile observed in this study suggests that the river water in this Superfund site is largely a sink for airborne PAHs, rather than a source. Copyright © 2017 Elsevier B.V. All rights reserved.

Phosphorylation regulates the water channel activity of the seed-specific aquaporin alpha-TIP.

PubMed

Maurel, C; Kado, R T; Guern, J; Chrispeels, M J

1995-07-03

The vacuolar membrane protein alpha-TIP is a seed-specific protein of the Major Intrinsic Protein family. Expression of alpha-TIP in Xenopus oocytes conferred a 4- to 8-fold increase in the osmotic water permeability (Pf) of the oocyte plasma membrane, showing that alpha-TIP forms water channels and is thus a new aquaporin. alpha-TIP has three putative phosphorylation sites on the cytoplasmic side of the membrane (Ser7, Ser23 and Ser99), one of which (Ser7) has been shown to be phosphorylated. We present several lines of evidence that the activity of this aquaporin is regulated by phosphorylation. First, mutation of the putative phosphorylation sites in alpha-TIP (Ser7Ala, Ser23Ala and Ser99Ala) reduced the apparent water transport activity of alpha-TIP in oocytes, suggesting that phosphorylation of alpha-TIP occurs in the oocytes and participates in the control of water channel activity. Second, exposure of oocytes to the cAMP agonists 8-bromoadenosine 3',5'-cyclic monophosphate, forskolin and 3-isobutyl-1-methylxanthine, which stimulate endogenous protein kinase A (PKA), increased the water transport activity of alpha-TIP by 80-100% after 60 min. That the protein can be phosphorylated by PKA was demonstrated by phosphorylating alpha-TIP in isolated oocyte membranes with the bovine PKA catalytic subunit. Third, the integrity of the three sites at positions 7, 23 and 99 was necessary for the cAMP-dependent increase in the Pf of oocytes expressing alpha-TIP, as well as for in vitro phosphorylation of alpha-TIP. These findings demonstrate that the alpha-TIP water channel can be modulated via phosphorylation of Ser7, Ser23 and Ser99.(ABSTRACT TRUNCATED AT 250 WORDS)

Estrogen and androgen receptor activities of hydraulic fracturing chemicals and surface and ground water in a drilling-dense region

USGS Publications Warehouse

Kassotis, Christopher D.; Tillitt, Donald E.; Davis, J. Wade; Hormann, Anette M.; Nagel, Susan C.

2014-01-01

The rapid rise in natural gas extraction using hydraulic fracturing increases the potential for contamination of surface and ground water from chemicals used throughout the process. Hundreds of products containing more than 750 chemicals and components are potentially used throughout the extraction process, including more than 100 known or suspected endocrine-disrupting chemicals. We hypothesized thataselected subset of chemicalsusedin natural gas drilling operationsandalso surface and ground water samples collected in a drilling-dense region of Garfield County, Colorado, would exhibit estrogen and androgen receptor activities. Water samples were collected, solid-phase extracted, and measured for estrogen and androgen receptor activities using reporter gene assays in human cell lines. Of the 39 unique water samples, 89%, 41%, 12%, and 46% exhibited estrogenic, antiestrogenic, androgenic, and antiandrogenic activities, respectively. Testing of a subset of natural gas drilling chemicals revealed novel antiestrogenic, novel antiandrogenic, and limited estrogenic activities. The Colorado River, the drainage basin for this region, exhibited moderate levels of estrogenic, antiestrogenic, and antiandrogenic activities, suggesting that higher localized activity at sites with known natural gas–related spills surrounding the river might be contributing to the multiple receptor activities observed in this water source. The majority of water samples collected from sites in a drilling-dense region of Colorado exhibited more estrogenic, antiestrogenic, or antiandrogenic activities than reference sites with limited nearby drilling operations. Our data suggest that natural gas drilling operationsmayresult in elevated endocrine-disrupting chemical activity in surface and ground water.

EPA GROUND WATER ISSUE: Ground Water Sample Preservation at ISCO Sites – Recommended Guidelines

EPA Science Inventory

In-situ chemical oxidation (ISCO) involves the introduction of a chemical oxidant into the subsurface for the purpose of transforming ground water contaminants into harmless byproducts. Due to oxidant persistence, ground water samples collected at hazardous waste sites may contai...

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

PubMed Central

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

2015-01-01

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. PMID:25999343

Where's water? The many binding sites of hydantoin.

PubMed

Gruet, Sébastien; Pérez, Cristóbal; Steber, Amanda L; Schnell, Melanie

2018-02-21

Prebiotic hydantoin and its complexes with one and two water molecules are investigated using high-resolution broadband rotational spectroscopy in the 2-8 GHz frequency range. The hyperfine structure due to the nuclear quadrupole coupling of the two 14 N atoms is analysed for the monomer and the complexes. This characteristic hyperfine structure will support a definitive assignment from low frequency radioastronomy data. Experiments with H 2 18 O provide accurate experimental information on the preferred binding sites of water, which are compared with quantum-chemically calculated coordinates. In the 2-water complexes, the water molecules bind to hydantoin as a dimer instead of individually, indicating the strong water-water interactions. This information provides first insight on how hydantoin interacts with water on the molecular level.

Evaluation of potential water conservation using site-specific irrigation

USDA-ARS?s Scientific Manuscript database

With the advent of site-specific variable-rate irrigation (VRI) systems, irrigation can be spatially managed within sub-field-sized zones. Spatial irrigation management can optimize spatial water use efficiency and may conserve water. Spatial VRI systems are currently being managed by consultants ...

Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

PubMed

Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

2015-04-01

Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach. Copyright © 2015 Elsevier B.V. All rights reserved.

User's Manual for the National Water Information System of the U.S. Geological Survey: Ground-water site-inventory system

USGS Publications Warehouse

,

2005-01-01

The Ground-Water Site-Inventory (GWSI) System is a ground-water data storage and retrieval system that is part of the National Water Information System (NWIS) developed by the U.S. Geological Survey (USGS). The NWIS is a distributed water database in which data can be processed over a network of workstations and file servers at USGS offices throughout the United States. This system comprises the GWSI, the Automated Data Processing System (ADAPS), the Water-Quality System (QWDATA), and the Site- Specific Water-Use Data System (SWUDS). The GWSI System provides for entering new sites and updating existing sites within the local database. In addition, the GWSI provides for retrieving and displaying groundwater and Sitefile data stored in the local database. Finally, the GWSI provides for routine maintenance of the local and national data records. This manual contains instructions for users of the GWSI and discusses the general operating procedures for the programs found within the GWSI Main Menu.

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

Effects of produced waters at oilfield production sites on the Osage Indian Reservation, northeastern Oklahoma

USGS Publications Warehouse

Otton, James K.; Asher-Bolinder, Sigrid; Owen, Douglass E.; Hall, Laurel

1997-01-01

The authors conducted limited site surveys in the Wildhorse and Burbank oilfields on the Osage Indian Reservation, northeastern Oklahoma. The purpose was to document salt scarring, erosion, and soil and water salinization, to survey for radioactivity in oilfield equipment, and to determine if trace elements and naturally occurring radioactive materials (NORM) were present in soils affected by oilfield solid waste and produced waters. These surveys were also designed to see if field gamma spectrometry and field soil conductivity measurements were useful in screening for NORM contamination and soil salinity at these sites. Visits to oilfield production sites in the Wildhorse field in June of 1995 and 1996 confirmed the presence of substantial salt scarring, soil salinization, and slight to locally severe erosion. Levels of radioactivity on some oil field equipment, soils, and road surfaces exceed proposed state standards. Radium activities in soils affected by tank sludge and produced waters also locally exceed proposed state standards. Laboratory analyses of samples from two sites show moderate levels of copper, lead, and zinc in brine-affected soils and pipe scale. Several sites showed detectable levels of bromine and iodine, suggesting that these trace elements may be present in sufficient quantity to inhibit plant growth. Surface waters in streams at two sampled sites exceed total dissolved solid limits for drinking waters. At one site in the Wildhorse field, an EM survey showed that saline soils in the upper 6m extend from a surface salt scar downvalley about 150 m. (Photo [95k]: Dead oak trees and partly revegetated salt scar at Site OS95-2 in the Wildhorse field, Osage County, Oklahoma.) In the Burbank field, limited salt scarring and slight erosion occurs in soils at some sites and low to moderate levels of radioactivity were observed in oil field equipment at some sites. The levels of radioactivity and radium observed in some soils and equipment at these

Ecological-site based assessments of wind and water erosion: informing management of accelerated soil erosion in rangelands

NASA Astrophysics Data System (ADS)

Webb, N.; Herrick, J.; Duniway, M.

2013-12-01

This work explores how soil erosion assessments can be structured in the context of ecological sites and site dynamics to inform systems for managing accelerated soil erosion. We evaluated wind and water erosion rates for five ecological sites in southern New Mexico, USA, using monitoring data and rangeland-specific wind and water erosion models. Our results show that wind and water erosion can be highly variable within and among ecological sites. Plots in shrub-encroached and shrub-dominated states were consistently susceptible to both wind and water erosion. However, grassland plots and plots with a grass-succulent mix had a high indicated susceptibility to wind and water erosion respectively. Vegetation thresholds for controlling erosion are identified that transcend the ecological sites and their respective states. The thresholds define vegetation cover levels at which rapid (exponential) increases in erosion rates begin to occur, suggesting that erosion in the study ecosystem can be effectively controlled when bare ground cover is <20% of a site or total ground cover is >50%. Similarly, our results show that erosion can be controlled when the cover of canopy interspaces >50 cm in length reaches ~50%, the cover of canopy interspaces >100 cm in length reaches ~35% or the cover of canopy interspaces >150 cm in length reaches ~20%. This process-based understanding can be applied, along with knowledge of the differential sensitivity of vegetation states, to improve erosion management systems. Land use and management activities that alter cover levels such that they cross thresholds, and/or drive vegetation state changes, may increase the susceptibility of sites to erosion. Land use impacts that are constrained within the natural variability of sites should not result in accelerated soil erosion. Evaluating land condition against the erosion thresholds and natural variability of ecological sites will enable improved identification of where and when accelerated soil

Water balance at a low-level radioactive-waste disposal site

USGS Publications Warehouse

Healy, R.W.; Gray, J.R.; De Vries, G. M.; Mills, P.C.

1989-01-01

The water balance at a low-level radioactive-waste disposal site in northwestern Illinois was studied from July 1982 through June 1984. Continuous data collection allowed estimates to be made for each component of the water-balance equation independent of other components. The average annual precipitation was 948 millimeters. Average annual evapotranspiration was estimated at 637 millimeters, runoff was 160 millimeters, change in water storage in a waste-trench cover was 24 millimeters, and deep percolation was 208 millimeters. The magnitude of the difference between precipitation and all other components (81 millimeters per year) indicates that, in a similar environment, the water-budget method would be useful in estimating evapotranspiration, but questionable for estimation of other components. Precipitation depth and temporal distribution had a very strong effect on all other components of the water-balance equation. Due to the variability of precipitation from year to year, it appears that two years of data are inadequate for characterization of the long-term average water balance at the site.

Water resources activities, Georgia District, 1986

USGS Publications Warehouse

Casteel, Carolyn A.; Ballew, Mary D.

1987-01-01

The U.S. Geological Survey, through its Water Resources Division , investigates the occurrence, quantity, quality, distribution, and movement of the surface and underground water that composes the Nation 's water resources. Much of the work is a cooperative effort in which planning and financial support are shared by state and local governments and other federal agencies. This report contains a brief description of the water-resources investigations in Georgia in which the Geological Survey participates, and a list of selected references. Water-resources data for the 1985 water year for Georgia consists of records of stage, discharge, and water quality of streams; stage and contents of lakes and reservoirs; and groundwater levels. These data include discharge records for 108 gaging stations; water quality for 43 continuous stations, 109 periodic stations, and miscellaneous sites; peak stage and discharge only for 130 crest-stage partial-record stations and 44 miscellaneous sites; and water levels of 27 observation wells. Nineteen Georgia District projects are summarized. (Lantz-PTT)

RATES OF IRON OXIDATION AND ARSENIC SORPTION DURING GROUND WATER-SURFACE WATER MIXING AT A HAZARDOUS WASTE SITE

EPA Science Inventory

The fate of arsenic discharged from contaminated ground water to a pond at a hazardous waste site is controlled, in part, by the rate of ferrous iron oxidation-precipitation and arsenic sorption. Laboratory experiments were conducted using site-derived water to assess the impact...

Water-level altitudes and continuous and discrete water quality at and near an aquifer storage and recovery site, Bexar, Atascosa, and Wilson Counties, Texas, June 2004-September 2011

USGS Publications Warehouse

Crow, Cassi L.

2012-01-01

The U.S. Geological Survey (USGS), in cooperation with the San Antonio Water System (SAWS), collected data during 2004–11 to characterize the quality of native groundwater from the San Antonio segment of the Edwards aquifer (hereinafter, Edwards aquifer) and preinjection and postinjection water from the Carrizo aquifer (informal name commonly applied to the upper part of the Carrizo-Wilcox aquifer in the area) at and near an aquifer storage and recovery (ASR) site in Bexar, Atascosa, and Wilson Counties, Texas. Daily mean water-level altitude, water temperature, and specific conductance were measured continuously in a monitoring well on the ASR site to determine how injection and withdrawal at the ASR site might affect local groundwater. Groundwater samples were collected and analyzed for selected physical properties and constituents to characterize the quality of native groundwater from the Edwards aquifer and preinjection and postinjection water from the Carrizo aquifer near the ASR site to provide a better understanding of possible changes in the quality of groundwater near an active ASR site that might result from the mixing of water from different aquifers. During injection periods, the water-level altitude in the monitoring well generally increased as the amount of water being injected into all wells at the ASR site increased and decreased as the amount of water being injected into all wells at the ASR site decreased. During withdrawal periods, the water-level altitude in the monitoring well generally increased as the total volume of water being withdrawn from all wells at the ASR site decreased and generally decreased as the total volume of water being withdrawn from all wells increased. Daily mean water temperature fluctuated by less than 1 degree Celsius and was determined to be independent of injection or withdrawal conditions at the ASR site. Changes in daily mean specific-conductance values measured at four depths in the monitoring well at the ASR

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP).

PubMed

Vanommeslaeghe, Kenno; Van Alsenoy, Christian; De Proft, Frank; Martins, José C; Tourwé, Dirk; Geerlings, Paul

2003-08-21

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.

Intercomparison of atmospheric water vapour measurements at a Canadian High Arctic site

NASA Astrophysics Data System (ADS)

Weaver, Dan; Strong, Kimberly; Schneider, Matthias; Rowe, Penny M.; Sioris, Chris; Walker, Kaley A.; Mariani, Zen; Uttal, Taneil; McElroy, C. Thomas; Vömel, Holger; Spassiani, Alessio; Drummond, James R.

2017-08-01

Water vapour is a critical component of the Earth system. Techniques to acquire and improve measurements of atmospheric water vapour and its isotopes are under active development. This work presents a detailed intercomparison of water vapour total column measurements taken between 2006 and 2014 at a Canadian High Arctic research site (Eureka, Nunavut). Instruments include radiosondes, sun photometers, a microwave radiometer, and emission and solar absorption Fourier transform infrared (FTIR) spectrometers. Close agreement is observed between all combination of datasets, with mean differences ≤ 1.0 kg m-2 and correlation coefficients ≥ 0.98. The one exception in the observed high correlation is the comparison between the microwave radiometer and a radiosonde product, which had a correlation coefficient of 0.92.A variety of biases affecting Eureka instruments are revealed and discussed. A subset of Eureka radiosonde measurements was processed by the Global Climate Observing System (GCOS) Reference Upper Air Network (GRUAN) for this study. Comparisons reveal a small dry bias in the standard radiosonde measurement water vapour total columns of approximately 4 %. A recently produced solar absorption FTIR spectrometer dataset resulting from the MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) retrieval technique is shown to offer accurate measurements of water vapour total columns (e.g. average agreement within -5.2 % of GRUAN and -6.5 % of a co-located emission FTIR spectrometer). However, comparisons show a small wet bias of approximately 6 % at the high-latitude Eureka site. In addition, a new dataset derived from Atmospheric Emitted Radiance Interferometer (AERI) measurements is shown to provide accurate water vapour measurements (e.g. average agreement was within 4 % of GRUAN), which usefully enables measurements to be taken during day and night (especially valuable during polar night).

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 abovegroundmore » 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)« less

Isotopic composition of water from a mine drainage site in Creede County in south central Colorado

NASA Astrophysics Data System (ADS)

Michel, R. L.; Williams, M. W.; Krupicka, A.; Wireman, M.; Graves, J.

2011-12-01

Creede County in South Central Colorado was an active area of silver mining beginning in the early 1890s. To relieve flooding in some of the mines, the Nelson Tunnel was built in the late 1890s. This tunnel still exists and acid mine drainage from the tunnel eventually flows into the Willow Creek Watershed which eventually flows into the Upper Rio Grande. The water coming out of the tunnel is high in toxic metals and the area has become part of an EPA Superfund site in an effort to find a suitable method to remediate the metal problems. Among the approaches used in the program is the use of isotopes of water and carbon to identify sources and estimate ages of the water in the drainage. Samples were collected for analysis of isotopic ratios and tritium concentrations at a series of sites within the tunnel complex from 2008-2010. In 2009 samples were also collected for analysis of isotopes in groundwater and surface water. In 2010 sampling was expanded to include four precipitation and one snow sample. Tritium concentrations in precipitation and snowfall in 2010 ranged from 3-6 tritium units with the lowest concentration found in the snow sample. The 18O isotopic ratios in precipitation for this site ranged from an average of -8.9 o/oo in summer to about -19 o/oo in winter. The six groundwater samples collected in 2009 had an average 18O isotopic concentration of -15 o/oo and tritium concentrations ranging from 7.4-9.3 TU. These results suggest that the groundwater sampled is composed largely of a mixture of summer and winter precipitation with the latter source being dominant. The tritium concentrations in groundwater exceed recent precipitation concentrations, suggesting the presence of water from the bomb-tritium transient and an age of a decade or more for the groundwater. Eight sites in the tunnel were sampled I from 2008-2010, although not all sites were sampled every year. The sampling sites included waters seeping into the tunnel as well as the outlet water

Greenhouse Gas Fluxes at the Tablelands, NL, Canada: A Site of Active Serpentinization

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Morrissey, L. S.; Cumming, E.

2016-12-01

Active sites of serpentinization have been proposed as sites for carbon capture and storage (CCS) projects. However, in addition to their ability to convert carbon dioxide to carbonate rock, sites of serpentinization also have the potential release methane, which is a more power greenhouse gas than carbon dioxide. Very little is known about the natural flux of carbon dioxide sequestered and methane released into the atmosphere from active sites of serpentinization. In this study we measured carbon dioxide, methane, and nitrous oxide gas fluxes at a pool of ultra-basic water discharging from serpentinized rock in Winterhouse Canyon, Gros Morne, Newfoundland. We found that the flux of methane released was 4.6 x 10-7 mol/m2/min and the carbon dioxide sequestered was 1.9 x 10-5 mol/m2/min, while the concentrations of nitrous oxide showed little change. Based on these fluxes we calculated predictive climate change parameters such as net radiative forcing and global warming potential which predicted that despite the methane being released the site still had an overall long-term atmospheric cooling effect based on the natural rate of carbon dioxide sequestration.

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

USGS Publications Warehouse

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

2006-01-01

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

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.

Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

PubMed Central

2015-01-01

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 kcat/Kphe value is down 104 for the mutant enzyme, and the Km 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. PMID:25453233

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.

Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase.

PubMed

Schwans, Jason P; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-11-05

Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural

Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase†

PubMed Central

Schwans, Jason P.; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-01-01

Within the idiosyncratic enzyme active site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near to charged groups or within hydrophobic pockets, Tyr57 of a P. putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semi-synthesis, 13C NMR spectroscopy, absorbance spectroscopy, and x-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from introduction of nearby anionic groups arise from accompanying active site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen bond donors, two Tyr side chains and a water molecule, positioned by other side chains and by a water-mediated hydrogen bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions, rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can

Impact of Zeolite Aging in Hot Liquid Water on Activity for Acid-Catalyzed Dehydration of Alcohols.

PubMed

Vjunov, Aleksei; Derewinski, Miroslaw A; Fulton, John L; Camaioni, Donald M; Lercher, Johannes A

2015-08-19

The location and stability of Brønsted acid sites catalytically active in zeolites during aqueous phase dehydration of alcohols were studied on the example of cyclohexanol. The catalytically active hydronium ions originate from Brønsted acid sites (BAS) of the zeolite that are formed by framework tetrahedral Si atom substitution by Al. Al K-edge extended X-ray absorption fine structure (EXAFS) and (27)Al magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopies in combination with density functional theory (DFT) calculations are used to determine the distribution of tetrahedral Al sites (Al T-sites) both qualitatively and quantitatively for both parent and HBEA catalysts aged in water prior to catalytic testing. The aging procedure leads to partial degradation of the zeolite framework evidenced from the decrease of material crystallinity (XRD) as well as sorption capacity (BET). With the exception of one commercial zeolite sample, which had the highest concentration of framework silanol-defects, there is no evidence of Al coordination modification after aging in water. The catalyst weight-normalized dehydration rate correlated best with the sum of strong and weak Brønsted acidic protons both able to generate the hydrated hydronium ions. All hydronium ions were equally active for the acid-catalyzed reactions in water. Zeolite aging in hot water prior to catalysis decreased the weight normalized dehydration reaction rate compared to that of the parent HBEA, which is attributed to the reduced concentration of accessible Brønsted acid sites. Sites are hypothesized to be blocked due to reprecipitation of silica dissolved during framework hydrolysis in the aging procedure.

THE TREATMENT OF CONTAMINATED WATER AT REMEDIAL WOOD PRESERVING SITES

EPA Science Inventory

Contaminated groundwater and surface water have posed a great challenge in restoring wood preserving sites to beneficial use. Often contaminated groundwater plumes extend far beyond the legal property limits, adversely impacting drinking water supplies and crop lands. To contain,...

Non-competitive inhibition by active site binders.

PubMed

Blat, Yuval

2010-06-01

Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.

Removal of bromide and iodide anions from drinking water by silver-activated carbon aerogels.

PubMed

Sánchez-Polo, M; Rivera-Utrilla, J; Salhi, E; von Gunten, U

2006-08-01

The aim of this study is to analyze the use of Ag-doped activated carbon aerogels for bromide and iodide removal from drinking water and to study how the activation of Ag-doped aerogels affects their behavior. It has been observed that the carbonization treatment and activation process of Ag-doped aerogels increased the surface area value ( [Formula: see text] ), whereas the volume of meso-(V(2)) and macropores (V(3)) decreased slightly. Chemical characterization of the materials revealed that carbonization and especially activation process considerably increased the surface basicity of the sample. Original sample (A) presented acidic surface properties (pH(PZC)=4.5) with 21% surface oxygen, whereas the sample that underwent activation showed mainly basic surface chemical properties (pH(PZC)=9.5) with only 6% of surface oxygen. Carbonization and especially, activation process considerable increased the adsorption capacity of bromide and iodide ions. This would mainly be produced by (i) an increase in the microporosity of the sample, which increases Ag-adsorption sites available to halide anions, and (ii) a rise of the basicity of the sample, which produces an increase in attractive electrostatic interactions between the aerogel surface, positively charged at the working pH (pH(solution)water treatment, adsorption of bromide and iodide was studied under dynamic conditions using waters from Lake Zurich. Results obtained showed that the carbonization and activation processes increased the adsorptive capacity of the aerogel sample. However, results showed that the adsorption capacity of the aerogel samples studied was considerably lower in water from Lake Zurich. Results showed X(0.02) (amount adsorbed to initial breakthrough) values of 0.1 and 4.3 mg/g for chloride anion and dissolved organic carbon (DOC), respectively, during bromide adsorption process in water from Lake Zurich

Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 materialmore » 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.« less

Amine binding and oxidation at the catalytic site for photosynthetic water oxidation

PubMed Central

Ouellette, Anthony J. A.; Anderson, Lorraine B.; Barry, Bridgette A.

1998-01-01

Photosynthetic water oxidation occurs at the Mn-containing catalytic site of photosystem II (PSII). By the use of 14C-labeled amines and SDS-denaturing PAGE, covalent adducts derived from primary amines and the PSII subunits, CP47, D2/D1, and the Mn-stabilizing protein, can be observed. When PSII contains the 18- and 24-kDa extrinsic proteins, which restrict access to the active site, no 14C labeling is obtained. NaCl, but not Na2SO4, competes with 14C labeling in Mn-containing PSII preparations, and the concentration dependence of this competition parallels the activation of oxygen evolution. Formation of 14C-labeled adducts is observed in the presence or in the absence of a functional manganese cluster. However, no significant Cl− effect on 14C labeling is observed in the absence of the Mn cluster. Isolation and quantitation of the 14C-labeled aldehyde product, produced from [14C]benzylamine, gives yields of 1.8 ± 0.3 mol/mol PSII and 2.9 ± 0.2 mol/mol in Mn-containing and Mn-depleted PSII, respectively. The corresponding specific activities are 0.40 ± 0.07 μmol(μmol PSII-hr)−1 and 0.64 ± 0.04 μmol(μmol PSII-hr)−1. Cl− suppresses the production of [14C]benzaldehyde in Mn-containing PSII, but does not suppress the production in Mn-depleted preparations. Control experiments show that these oxidation reactions do not involve the redox-active tyrosines, D and Z. Our results suggest the presence of one or more activated carbonyl groups in protein subunits that form the active site of PSII. PMID:9482863

Water-resources activities in New England, fiscal year 1993

USGS Publications Warehouse

Orlando, M.F.

1994-01-01

The U.S. Geological Survey has 82 active or complete-except-report projects of hydrologic investigations ongoing within the New England Program Area. Of this total, 23 are data projects. Data projects contain statistics and data on the conditions of surface water, ground water, water quality and (or) water use for the study area. There currently are six data projects in Connecticut, five in Maine, four in Massachusetts, four in Rhode Island, and four in New Hampshire and Vermont. The remaining 59 of these projects are interpretive projects. Interpretive projects include research, aerial appraisal, and other hydrologic studies and include projects as diverse as (1) determining the direction of ground-water flow at a toxic site, (2) predicting the effect of acid rain on water quality of a reservoir, and (3) estimating yields of aquifers on Cape Cod. Of the interpretive projects, 26 are in Massachusetts, 17 in Connecticut, 17 are in New Hampshire and Vermont, 6 are in Maine, and 3 in Rhode Island. The report is compiled from project descriptions for fiscal year 1993. It briefly describes the water-resources activities and projects that were active in each District of the USGS, Water Resources Division, New England Program Area of September 30, 1993. Cooperator or funding source, problem statements, objectives, approaches, progress, and plans for next year are described for each project. The project area is located on a map of the appropriate State(s). The report contains a bibliography, by District and by author, of reports completed since 1977.

ICR SS protozoan data site-by-site: a picture of Cryptosporidium and Giardia in U.S. surface water.

PubMed

Ongerth, Jerry E

2013-09-17

The U.S. Environmental Protection Agency (USEPA) Information Collection Rule Supplemental Survey (ICR SS) required analysis of Cryptosporidium and Giardia in 10 L surface water samples twice a week for a year by USEPA Method 1623 at 80 representative U.S. public water systems (PWS). The resulting data are examined site-by-site in relation to objectives of the Federal drinking water regulation, The Long-Term (2) Enhanced Surface Water Treatment Rule (LT2), currently under formal 6-year review by the USEPA. The data describe Cryptosporidium and Giardia in watersheds nation-wide over a single annual cycle. Due to limited recovery efficiency measurement results are not fully quantified. In the required sample volumes of 10 L no Cryptosporidium were found in 86% of samples and no Giardia were found in 67% of samples. Yet, organisms were found in enough samples at 34 of 80 sites to detail a specrtum of occurrence and variability for both organisms. The data are shown to describe indivudual site risk essential for guidance of watershed and water treatment management by PWSs. The span of median occurrence for both organisms was about 2 orders of magnitude above the limit of detection (LD), ca. 0.05 raw no's/L for Cryptosporidium and ca. 0.10 raw no's/L for Giardia. Data analysis illustrates key features of Cryptosporidium and Giardia in surface water: presence is continuous not intermittent; zeros indicate presence below the LD; occurrence level and variations depend on watershed sources; risk depends on both magnitude and variability of concentration; accurate estimation of risk requires routine measurement of recovery efficiency and calculation of concentration. The data and analysis illustrate features of Cryptosporidium and Giardia occurrence in surface water relevant to their effective regulation for public health protection.

Location and site characteristics of the ambient ground-water-quality-monitoring network in West Virginia

USGS Publications Warehouse

Kozar, M.D.; Brown, D.P.

1995-01-01

Ground-water-quality-monitoring sites have been established in compliance with the 1991 West Virginia "Groundwater Protection Act." One of the provisions of the "Groundwater Protection Act" is to conduct ground-water sampling, data collection, analyses, and evaluation with sufficient frequency so as to ascertain the characteristics and quality of ground water and the sufficiency of the ground- water protection programs established pursuant to the act (Chapter 20 of the code of West Virginia, 1991, Article 5-M). Information for 26 monitoring sites (wells and springs) which comprise the Statewide ambient ground-water-quality-monitoring network is presented. Areas in which monitoring sites were needed were determined by the West Virginia Division of Environmental Protection, Office of Water Resources in consultation with the U.S. Geological Survey (USGS). Initial sites were chosen on the basis of recent hydrogeologic investigations conducted by the USGS and from data stored in the USGS Ground Water Site Inventory database. Land use, aquifer setting, and areal coverage of the State are three of the more important criteria used in site selection. A field reconnaissance was conducted to locate and evaluate the adequacy of selected wells and springs. Descriptive information consisting of site, geologic, well construction, and aquifer-test data has been compiled. The 26 sites will be sampled periodically for iron, manganese, most common ions (for example, calcium, magnesium, sodium, potassium, sulfate, chloride, bicarbonate), volatile and semivolatile organic compounds (for example, pesticides and industrial solvents), and fecal coliform and fecal streptococcus bacteria. Background information explaining ground-water systems and water quality within the State has been included.

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.

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.

Heterogeneous water oxidation: surface activity versus amorphization activation in cobalt phosphate catalysts.

PubMed

González-Flores, Diego; Sánchez, Irene; Zaharieva, Ivelina; Klingan, Katharina; Heidkamp, Jonathan; Chernev, Petko; Menezes, Prashanth W; Driess, Matthias; Dau, Holger; Montero, Mavis L

2015-02-16

Is water oxidation catalyzed at the surface or within the bulk volume of solid oxide materials? This question is addressed for cobalt phosphate catalysts deposited on inert electrodes, namely crystallites of pakhomovskyite (Co3(PO4)2⋅8 H2O, Pak) and phosphate-containing Co oxide (CoCat). X-ray spectroscopy reveals that oxidizing potentials transform the crystalline Pak slowly (5-8 h) but completely into the amorphous CoCat. Electrochemical analysis supports high-TOF surface activity in Pak, whereas its amorphization results in dominating volume activity of the thereby formed CoCat material. In the directly electrodeposited CoCat, volume catalysis prevails, but not at very low levels of the amorphous material, implying high-TOF catalysis at surface sites. A complete picture of heterogeneous water oxidation requires insight in catalysis at the electrolyte-exposed "outer surface", within a hydrated, amorphous volume phase, and modes and kinetics of restructuring upon operation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of water levels in the Frenchman Flat area, Nevada Test Site

USGS Publications Warehouse

Bright, D.J.; Watkins, S.A.; Lisle, B.A.

2001-01-01

Analysis of water levels in 21 wells in the Frenchman Flat area, Nevada Test Site, provides information on the accuracy of hydraulic-head calculations, temporal water-level trends, and potential causes of water-level fluctuations. Accurate hydraulic heads are particularly important in Frenchman Flat where the hydraulic gradients are relatively flat (less than 1 foot per mile) in the alluvial aquifer. Temporal water-level trends with magnitudes near or exceeding the regional hydraulic gradient may have a substantial effect on ground-water flow directions. Water-level measurements can be adjusted for the effects of barometric pressure, formation water density (from water-temperature measurements), borehole deviation, and land-surface altitude in selected wells in the Frenchman Flat area. Water levels in one well were adjusted for the effect of density; this adjustment was significantly greater (about 17 feet) than the adjustment of water levels for barometric pressure, borehole deviation, or land-surface altitude (less than about 4 feet). Water-level measurements from five wells exhibited trends that were statistically and hydrologically significant. Statistically significant water-level trends were observed for three wells completed in the alluvial aquifer (WW-5a, UE-5n, and PW-3), for one well completed in the carbonate aquifer (SM-23), and for one well completed in the quartzite confining unit (Army-6a). Potential causes of water-level fluctuations in wells in the Frenchman Flat area include changes in atmospheric conditions (precipitation and barometric pressure), Earth tides, seismic activity, past underground nuclear testing, and nearby pumping. Periodic water-level measurements in some wells completed in the carbonate aquifer indicate cyclic-type water-level fluctuations that generally correlate with longer term changes (more than 5 years) in precipitation. Ground-water pumping fromthe alluvial aquifer at well WW-5c and pumping and discharge from well RNM-2s

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Water-Quality Assessment of the Yellowstone River Basin, Montana and Wyoming-Water Quality of Fixed Sites, 1999-2001

USGS Publications Warehouse

Miller, Kirk A.; Clark, Melanie L.; Wright, Peter R.

2005-01-01

The National Water-Quality Assessment Program of the U.S. Geological Survey initiated an assessment in 1997 of the quality of water resources in the Yellowstone River Basin. Water-quality samples regularly were collected during 1999-2001 at 10 fixed sites on streams representing the major environmental settings of the basin. Integrator sites, which are heterogeneous in land use and geology, were established on the mainstem of the Yellowstone River (4 sites) and on three major tributaries?Clarks Fork Yellowstone River (1 site), the Bighorn River (1 site), and the Powder River (1 site). Indicator sites, which are more homogeneous in land use and geology than the integrator sites, were located on minor tributaries with important environmental settings?Soda Butte Creek in a mineral resource area (1 site), the Tongue River in a forested area (1 site), and the Little Powder River in a rangeland area (1 site). Water-quality sampling frequency generally was at least monthly and included field measurements and laboratory analyses of fecal-indicator bacteria, major ions, dissolved solids, nutrients, trace elements, pesticides, and suspended sediment. Median concentrations of fecal coliform and Escherichia coli were largest for basins that were predominantly rangeland and smallest for basins that were predominantly forested. Concentrations of fecal coliform and Escherichia coli significantly varied by season (p-value <0.001); the smallest median concentrations were during January?March and the largest median concentrations were during April?June. Fecal-coliform concentrations exceeded the U.S. Environmental Protection Agency recommended limit for a single sample of 400 colonies per 100 milliliters in 2.6 percent of all samples. Escherichia coli concentrations exceeded the U.S. Environmental Protection Agency recommended limit for a single sample of 298 colonies per 100 milliliters for moderate use, full-body contact recreation in 7.6 percent of all samples. Variations in

Soil-water movement under natural-site and waste-site conditions: A multiple-year field study in the Mojave Desert, Nevada

USGS Publications Warehouse

Andraski, Brian J.

1997-01-01

Soil-water movement under natural-site and simulated waste-site conditions were compared by monitoring four experimental sites in the Mojave Desert, Nevada, during a 5-year period: one vegetated soil profile, one soil profile where vegetation was removed, and two nonvegetated test trenches. Precipitation ranged from 14 to 162 mm/yr. Temporal changes in water content measured by neutron probe were limited to the upper 0.5–1 m; values ranged from 0.01 to 0.19 m3/m3. Water potential and temperature were measured by thermocouple psychrometers; 77% remained operable for ≥4.5 years. For vegetated soil, precipitation that accumulated in the upper 0.75 m of soil was removed by evapotranspiration: water potentials decreased seasonally by 4 to >8 MPa. During 2 years with below-average precipitation, water potentials below the app arent root zone decreased by 2.3 (1.2-m depth) to 0.4 MPa (5-m depth), and the gradients became predominantly upward. Water potentials then rebounded during 2 years with near- and above-average precipitation, and seasonally variant water potential gradients were reestablished above the 4.2-m depth. Under nonvegetated waste-site conditions, data indicated the long-term accumulation and shallow, but continued, penetration of precipitation: water potentials showed moisture penetration to depths of 0.75−1.85 m. The method of simulated-waste drum placement (stacked versus random) and the associated differences in subsidence showed no measurable influence on the water balance of the trenches: subsidence totaled ≤13 mm during the study. Water potentials below the trenches and below the 2-m depth for the nonvegetated soil remained low (≈−5.5 to −7.5 MPa) and indicated the persistence of typically upward driving forces for isothermal water flow. Water fluxes estimated from water potential and temperature data suggested that isothermal liquid, isothermal vapor, and nonisothermal vapor flow need to be considered in the conceptualization of

Variations in water balance and recharge potential at three western desert sites

USGS Publications Warehouse

Gee, G.W.; Wierenga, P.J.; Andraski, Brian J.; Young, M.H.; Fayer, M.J.; Rockhold, M.L.

1994-01-01

Radioactive and hazardous waste landfills exist at numerous desert locations in the USA. At these locations, annual precipitation is low and soils are generally dry, yet little is known about recharge of water and transport of contaminants to the water table. Recent water balance measurements made at three desert locations, Las Cruces, NM, Beatty, NV, and the U.S. Department of Energy's Hanford Site in the state of Washington, provide information on recharge potential under three distinctly different climate and soil conditions. All three sites show water storage increases with time when soils are coarse textured and plants are removed from the surface, the rate of increase being influenced by climatic variables such as precipitation, radiation, temperature, and wind. Lysimeter data from Hanford and Las Cruces indicate that deep drainage (recharge) from bare, sandy soils can range from 10 to >50% of the annual precipitation. At Hanford, when desert plants are present on sandy or gravelly surface soils, deep drainage is reduced but not eliminated. When surface soils are silt loams, deep drainage is eliminated whether plants are present or not. At Las Cruces and Beatty, the presence of plants eliminated deep drainage at the measurement sites. Differences in water balance between sites are attributed to precipitation quantity and distribution and to soil and vegetation types. The implication for waste management at desert locations is that surface soil properties and plant characteristics must be considered in waste site design in order to minimize recharge potential.

Litter type affects the activity of aerobic decomposers in a boreal peatland more than site nutrient and water level regimes

NASA Astrophysics Data System (ADS)

Straková, P.; Niemi, R. M.; Freeman, C.; Peltoniemi, K.; Toberman, H.; Heiskanen, I.; Fritze, H.; Laiho, R.

2011-02-01

Peatlands are carbon (C) storage ecosystems sustained by a high water level (WL). High WL creates anoxic conditions that suppress the activity of aerobic decomposers and provide conditions for peat accumulation. Peatland function can be dramatically affected by WL drawdown caused by land-use and/or climate change. Aerobic decomposers are directly affected by WL drawdown through environmental factors such as increased oxygenation and nutrient availability. Additionally, they are indirectly affected via changes in plant community composition and litter quality. We studied the relative importance of direct and indirect effects of WL drawdown on aerobic decomposer activity in plant litter. We did this by profiling 11 extracellular enzymes involved in the mineralization of organic C, nitrogen, phosphorus and sulphur. Our study sites represented a three-stage chronosequence from pristine (undrained) to short-term (years) and long-term (decades) WL drawdown conditions under two nutrient regimes. The litter types included reflected the prevalent vegetation, i.e., Sphagnum mosses, graminoids, shrubs and trees. WL drawdown had a direct and positive effect on microbial activity. Enzyme allocation shifted towards C acquisition, which caused an increase in the rate of decomposition. However, litter type overruled the direct effects of WL drawdown and was the main factor shaping microbial activity patterns. Our results imply that changes in plant community composition in response to persistent WL drawdown will strongly affect the C dynamics of peatlands.

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Impact of waste dump on surface water quality and aquatic insect diversity of Deepor Beel (Ramsar site), Assam, North-east India.

PubMed

Choudhury, Dharitri; Gupta, Susmita

2017-10-06

Water and aquatic insects were collected seasonally from site 1, the low-lying area of the dump near Deepor Beel, and from sites 2 and 3 of the main wetland and analysed. While dissolved oxygen (DO) increased from site 1 to site 3 in each season, electrical conductivity (EC), total dissolved solid (TDS), total alkalinity (TA) and free CO 2 (F-CO 2 ) decreased. Pb and Cd were found to exceed the limits set for drinking water in all the sites and seasons. Species richness (SpR) was found highest (23) at site 2 and lowest (14) at site 1. Sensitive species was absent. The Shannon (H') values at site 1 were < 1 while at sites 2 and 3 were > 1 in most of the seasons. Biological monitoring scores (Biological Monitoring Working Party and Stream Invertebrate Grade Number-Average Level) in different sites and seasons inferred severely poor to moderate water quality. At site 1, significant negative correlations were seen for Pb and Cr with SpR while Ni and Cu with insect density (ID). At site 2, TA had highly significant positive correlations with SpR and ID while Cu showed negative correlation with SpR. At site 3, ID had significant negative relationships with air temperature, water temperature, depth, TA, F-CO 2 , PO 4 3- and Cr. Canonical correspondence analysis triplot has clearly separated site 1 associated with tolerant species and highly influenced by TA, TDS, EC, F-CO 2, Cr, Ni, Cd and Zn confirming high anthropogenic activities on that site. Tolerant and semitolerant species were present at site 2 (influenced by depth and transparency) and site 3 (influenced by Pb and WT) both. Results of this study discerned that the dump site is the point source of pollution.

Quantifying Fast and Slow Responses of Terrestrial Carbon Exchange across a Water Availability Gradient in North American Flux Sites

NASA Astrophysics Data System (ADS)

Biederman, J. A.; Scott, R. L.; Goulden, M.

2014-12-01

Climate change is predicted to increase the frequency and severity of water limitation, altering terrestrial ecosystems and their carbon exchange with the atmosphere. Here we compare site-level temporal sensitivity of annual carbon fluxes to interannual variations in water availability against cross-site spatial patterns over a network of 19 eddy covariance flux sites. This network represents one order of magnitude in mean annual productivity and includes western North American desert shrublands and grasslands, savannahs, woodlands, and forests with continuous records of 4 to 12 years. Our analysis reveals site-specific patterns not identifiable in prior syntheses that pooled sites. We interpret temporal variability as an indicator of ecosystem response to annual water availability due to fast-changing factors such as leaf stomatal response and microbial activity, while cross-site spatial patterns are used to infer ecosystem adjustment to climatic water availability through slow-changing factors such as plant community and organic carbon pools. Using variance decomposition, we directly quantify how terrestrial carbon balance depends on slow- and fast-changing components of gross ecosystem production (GEP) and total ecosystem respiration (TER). Slow factors explain the majority of variance in annual net ecosystem production (NEP) across the dataset, and their relative importance is greater at wetter, forest sites than desert ecosystems. Site-specific offsets from spatial patterns of GEP and TER explain one third of NEP variance, likely due to slow-changing factors not directly linked to water, such as disturbance. TER and GEP are correlated across sites as previously shown, but our site-level analysis reveals surprisingly consistent linear relationships between these fluxes in deserts and savannahs, indicating fast coupling of TER and GEP in more arid ecosystems. Based on the uncertainty associated with slow and fast factors, we suggest a framework for improved

Trigger values for investigation of hormonal activity in drinking water and its sources using CALUX bioassays.

PubMed

Brand, Walter; de Jongh, Cindy M; van der Linden, Sander C; Mennes, Wim; Puijker, Leo M; van Leeuwen, Cornelis J; van Wezel, Annemarie P; Schriks, Merijn; Heringa, Minne B

2013-05-01

To screen for hormonal activity in water samples, highly sensitive in vitro CALUX bioassays are available which allow detection of estrogenic (ERα), androgenic (AR), progestagenic (PR), and glucocorticoid (GR) activities. This paper presents trigger values for the ERα, AR, PR, and GR CALUX bioassays for agonistic hormonal activities in (drinking) water, which define a level above which human health risk cannot be waived a priori and additional examination of specific endocrine activity may be warranted. The trigger values are based on 1) acceptable or tolerable daily intake (ADI/TDI) values of specific compounds, 2) pharmacokinetic factors defining their bioavailability, 3) estimations of the bioavailability of unknown compounds with equivalent hormonal activity, 4) relative endocrine potencies, and 5) physiological, and drinking water allocation factors. As a result, trigger values of 3.8ng 17β-estradiol (E2)-equivalents (eq)/L, 11ng dihydrotestosterone (DHT)-eq/L, 21ng dexamethasone (DEX)-eq/L, and 333ng Org2058-eq/L were derived. Benchmark Quotient (BQ) values were derived by dividing hormonal activity in water samples by the derived trigger using the highest concentrations detected in a recent, limited screening of Dutch water samples, and were in the order of (value) AR (0.41)>ERα (0.13)>GR (0.06)>PR (0.04). The application of trigger values derived in the present study can help to judge measured agonistic hormonal activities in water samples using the CALUX bioassays and help to decide whether further examination of specific endocrine activity followed by a subsequent safety evaluation may be warranted, or whether concentrations of such activity are of low priority with respect to health concerns in the human population. For instance, at one specific drinking water production site ERα and AR (but no GR and PR) activities were detected in drinking water, however, these levels are at least a factor 83 smaller than the respective trigger values, and

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Measuring water potential (activity) from free water to oven dryness.

PubMed

Wiebe, H H

1981-12-01

Water activities (potentials) in plant materials were measured over the range from free water to oven dryness with a Spanner thermocouple psychrometer. In a two-step procedure, water was first condensed on the thermocouple junction for several minutes. The sample was then inserted under the wet thermocouple and the maximum psychrometric cooling was measured in about 10 seconds. Calibration was with saturated salt slurries of known water activities. Psychrometric cooling was a nearly linear function of the water activity and of the negative log of the water potential. The psychrometric cooling to water activity relationship agreed with wetbulb temperature depression to relative humidity relationships given in tables. Water activities of wheat grains and leaves decreased sharply in a curvilinear fashion as their water contents decreased. Some problems of the procedure are discussed.

Photosynthesis, water relations, and growth of planted Pinus strobus L. on burned sites in the southern Appalachians

Treesearch

Katherine J. Elliott; James M. Vose

1994-01-01

We measured net photosynthesis,leaf conductance, xylem water potential, and growth of Pinus strbus L. seedlings two years after planting on two clear-cut and burned sites in the southern Appalachians. Multiple regression analysis was used to relate seedling net pholosynthesis to vapor pressure deficit, seedling crown temperature, photosynthetically active radiation (...

Amplified Rate Acceleration by Simultaneous Up-Regulation of Multiple Active Sites in an Endo-Functionalized Porous Capsule.

PubMed

Kopilevich, Sivil; Müller, Achim; Weinstock, Ira A

2015-10-14

Using the hydrolysis of epoxides in water as a model reaction, the effect of multiple active sites on Michaelis-Menten compliant rate accelerations in a porous capsule is demonstrated. The capsule is a water-soluble Ih-symmetry Keplerate-type complex of the form, [{Mo(VI)6O21(H2O)6}12{Mo(V)2O4(L)}30](42-), in which 12 pentagonal "ligands," {(Mo(VI))Mo(VI)5O21(H2O)6}(6-), are coordinated to 30 dimolybdenum sites, {Mo(V)2O4L}(1+) (L = an endohedrally coordinated η(2)-bound carboxylate anion), resulting in 20 Mo9O9 pores. When "up-regulated" by removal of ca. one-third of the blocking ligands, L, an equal number of dimolybdenum sites are activated, and the newly freed-up space allows for encapsulation of nearly twice as many substrate guests, leading to a larger effective molarity (amplification), and an increase in the rate acceleration (k(cat)/k(uncat)) from 16,000 to an enzyme-like value of 182,800.

Drinking water in California child care sites before and after 2011-2012 beverage policy.

PubMed

Ritchie, Lorrene D; Yoshida, Sallie; Sharma, Sushma; Patel, Anisha; Vitale, Elyse Homel; Hecht, Ken

2015-06-04

Drinking water is promoted to improve beverage nutrition and reduce the prevalence of obesity. The aims of this study were to identify how water was provided to young children in child care and to determine the extent to which water access changed after a federal and state child care beverage policy was instituted in 2011 and 2012 in California. Two independent cross-sectional samples of licensed child care providers completed a self-administered survey in 2008 (n = 429) and 2012 (n = 435). Logistic regression was used to analyze data for differences between 2008 and 2012 survey responses, after adjustment for correlations among the measurements in each of 6 child care categories sampled. A significantly larger percentage of sites in 2012 than in 2008 always served water at the table with meals or snacks (47.0% vs 28.0%, P = .001). A significantly larger percentage of child care sites in 2012 than in 2008 made water easily and visibly available for children to self-serve both indoors (77.9% vs 69.0%, P = .02) and outside (78.0% vs 69.0%, P = .03). Sites that participated in the federal Child and Adult Care Food Program had greater access to water indoors and outside than sites not in the program. In 2012 most (76.1%) child care providers reported no barriers to serving water to children. Factors most frequently cited to facilitate serving water were information for families (39.0% of sites), beverage policy (37.0%), and lessons for children (37.9%). Water provision in California child care improved significantly between samples of sites studied in 2008 and 2012, but room for improvement remains after policy implementation. Additional training for child care providers and parents should be considered.

Radionuclide transport in the "sediments - water - plants" system of the water bodies at the Semipalatinsk test site.

PubMed

Aidarkhanova, A K; Lukashenko, S N; Larionova, N V; Polevik, V V

2018-04-01

This paper provides research data on levels and character of radionuclide contamination distribution in the «sediments- water - plants » system of objects of the Semipalatinsk test site (STS). As the research objects there were chosen water bodies of man-made origin which located at the territory of "Experimental Field", "Balapan", "Telkem" and "Sary-Uzen" testing sites. For research the sampling of bottom sediments, water, lakeside and water plants was taken. Collected samples were used to determine concentration of anthropogenic radionuclides 90 Sr, 239+240 Pu, 241 Am, 137 Cs. The distribution coefficient (K d ) was calculated as the ratio of the content of radionuclides in the sediments to the content in water, and the concentration ratio (F V ) was calculated as the ratio of radionuclide content in plants to the content in sediments or soil. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.

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 uponmore » 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.« less

Evolution of a designed retro-aldolase leads to complete active site remodeling

PubMed Central

Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

2013-01-01

Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that dramatic molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400 fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate, and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. PMID:23748672

Effects of livestock watering sites on alien and native plants in the Mojave Desert, USA

USGS Publications Warehouse

Brooks, M.L.; Matchett, J.R.; Berry, K.H.

2006-01-01

Increased livestock densities near artificial watering sites create disturbance gradients called piospheres. We studied responses of alien and native annual plants and native perennial plants within 9 piospheres in the Mojave Desert of North America. Absolute and proportional cover of alien annual plants increased with proximity to watering sites, whereas cover and species richness of native annual plants decreased. Not all alien species responded the same, as the alien forb Erodium cicutarium and the alien grass Schismus spp. increased with proximity to watering sites, and the alien annual grass Bromus madritensis ssp. rubens decreased. Perennial plant cover and species richness also declined with proximity to watering sites, as did the structural diversity of perennial plant cover classes. Significant effects were focused within 200 m of the watering sites, suggesting that control efforts for alien annual plants and restoration efforts for native plants should optimally be focused within this central part of the piosphere gradient.

Estimates of cloud water deposition at Mountain Acid Deposition Program sites in the Appalachian Mountains.

PubMed

Baumgardner, Ralph E; Isil, Selma S; Lavery, Thomas F; Rogers, Christopher M; Mohnen, Volker A

2003-03-01

Cloud water deposition was estimated at three high-elevation sites in the Appalachian Mountains of the eastern United States (Whiteface Mountain, NY; Whitetop Mountain, VA; and Clingman's Dome, TN) from 1994 through 1999 as part of the Mountain Acid Deposition Program (MADPro). This paper provides a summary of cloud water chemistry, cloud liquid water content, cloud frequency, estimates of cloud water deposition of sulfur and nitrogen species, and estimates of total deposition of sulfur and nitrogen at these sites. Other cloud studies in the Appalachians and their comparison to MADPro are also summarized. Whiteface Mountain exhibited the lowest mean and median concentrations of sulfur and nitrogen ions in cloud water, while Clingman's Dome exhibited the highest mean and median concentrations. This geographic gradient is partly an effect of the different meteorological conditions experienced at northern versus southern sites in addition to the difference in pollution content of air masses reaching the sites. All sites measured seasonal cloud water deposition rates of SO4(2-) greater than 50 kg/ha and NO3(-) rates of greater than 25 kg/ha. These high-elevation sites experienced additional deposition loading of SO4(2-) and NO3(-) on the order of 6-20 times greater compared with lower elevation Clean Air Status and Trends Network (CASTNet) sites. Approximately 80-90% of this extra loading is from cloud deposition.

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

PubMed

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

2016-06-17

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

Methods for computing water-quality loads at sites in the U.S. Geological Survey National Water Quality Network

USGS Publications Warehouse

Lee, Casey J.; Murphy, Jennifer C.; Crawford, Charles G.; Deacon, Jeffrey R.

2017-10-24

The U.S. Geological Survey publishes information on concentrations and loads of water-quality constituents at 111 sites across the United States as part of the U.S. Geological Survey National Water Quality Network (NWQN). This report details historical and updated methods for computing water-quality loads at NWQN sites. The primary updates to historical load estimation methods include (1) an adaptation to methods for computing loads to the Gulf of Mexico; (2) the inclusion of loads computed using the Weighted Regressions on Time, Discharge, and Season (WRTDS) method; and (3) the inclusion of loads computed using continuous water-quality data. Loads computed using WRTDS and continuous water-quality data are provided along with those computed using historical methods. Various aspects of method updates are evaluated in this report to help users of water-quality loading data determine which estimation methods best suit their particular application.

Heavy metal contamination of soil and water in the vicinity of an abandoned e-waste recycling site: implications for dissemination of heavy metals.

PubMed

Wu, Qihang; Leung, Jonathan Y S; Geng, Xinhua; Chen, Shejun; Huang, Xuexia; Li, Haiyan; Huang, Zhuying; Zhu, Libin; Chen, Jiahao; Lu, Yayin

2015-02-15

Illegal e-waste recycling activity has caused heavy metal pollution in many developing countries, including China. In recent years, the Chinese government has strengthened enforcement to impede such activity; however, the heavy metals remaining in the abandoned e-waste recycling site can still pose ecological risk. The present study aimed to investigate the concentrations of heavy metals in soil and water in the vicinity of an abandoned e-waste recycling site in Longtang, South China. Results showed that the surface soil of the former burning and acid-leaching sites was still heavily contaminated with Cd (>0.39 mg kg(-1)) and Cu (>1981 mg kg(-1)), which exceeded their respective guideline levels. The concentration of heavy metals generally decreased with depth in both burning site and paddy field, which is related to the elevated pH and reduced TOM along the depth gradient. The pond water was seriously acidified and contaminated with heavy metals, while the well water was slightly contaminated since heavy metals were mostly retained in the surface soil. The use of pond water for irrigation resulted in considerable heavy metal contamination in the paddy soil. Compared with previous studies, the reduced heavy metal concentrations in the surface soil imply that heavy metals were transported to the other areas, such as pond. Therefore, immediate remediation of the contaminated soil and water is necessary to prevent dissemination of heavy metals and potential ecological disaster. Copyright © 2014 Elsevier B.V. All rights reserved.

Potential For Denitrification near Reclaimed Water Application Sites in Orange County, Florida, 2009

USGS Publications Warehouse

Byrne, Michael J.; Smith, Richard L.; Repert, Deborah A.

2012-01-01

The potential for denitrification was tested in water samples from four Upper Floridan aquifer wells near a reclaimed water application site, in west Orange County Florida, and two adjacent springs. Results of the study indicate that denitrifying bacteria are present in the groundwater and spring water samples, and that these bacteria can readily denitrify the waters when suitable geochemical conditions exist. The acetylene block technique was used to assess nitrous oxide in the samples that was produced by denitrification. The laboratory incubation experiment consisted of four different treatments to each of the six samples: (1) ambient water (no added nitrate or glucose), (2) ambient water amended with 1.4 milligrams per liter (mg/L) nitrate as nitrogen (N), (3) ambient water amended with 5.0 mg/L nitrate as N, and (4) ambient water amended with 5.0 mg/L nitrate as N and 10 mg/L glucose as C6H12O6. A companion set of incubations using treatment 2 tracked changes in nitrate and nitrite concentration with time. The rate of denitrification in treatment 2 ranged from 0.059 to 0.124 milligram per liter per day nitrogen [(mg/L)/d N] and in treatment 3 ranged from 0.071 to 0.226 (mg/L)/d N. At all of the sampling sites, treatment 4 yielded denitrification rates at least an order of magnitude greater than those measured for the other treatments; rates ranged from 2.3 to 4.4 (mg/L)/d N. The electron donor supply, dissolved organic carbon, in the groundwater and springwater is sufficient to remove at least 1.1-1.4 mg/L nitrate as N in 20 to 30 days, as indicated by nitrous oxide production rates under ambient conditions (treatment 1). The even higher nitrate removal observed with addition of supplemental carbon in treatment 4 suggests that carbon is a limiting nutrient in this reaction. Denitrifying activity might explain the low ambient nitrate concentrations in the Upper Floridan aquifer in this area.

Recreational use assessment of water-based activities, using time-lapse construction cameras.

PubMed

Sunger, Neha; Teske, Sondra S; Nappier, Sharon; Haas, Charles N

2012-01-01

Recreational exposure to surface waters during periods of increased pathogen concentration may lead to a significantly higher risk of illness. However, estimates of elementary exposure factors necessary to evaluate health risk (i.e., usage distributions and exposure durations) are not available for many non-swimming water-related activities. No prior studies have assessed non-swimming water exposure with respect to factors leading to impaired water quality from increased pathogen concentration, such as weather condition (rain events produce increased runoff and sewer overflows) and type of day (heavy recreational periods). We measured usage patterns and evaluated the effect of weather and type of day at eight water sites located within Philadelphia, by using a novel "time lapse photography" technology during three peak recreational seasons (May-September) 2008-2010. Camera observations validated with simultaneous in-person surveys exhibited a strong correlation (R(2)=0.81 to 0.96) between the two survey techniques, indicating that the application of remote photography in collecting human exposure data was appropriate. Recreational activities usage varied more on a temporal basis than due to inclement weather. Only 14% (6 out of 44) of the site-specific activity combinations showed dry weather preference, whereas 41.5% (17 out of 41) of the combinations indicated greater usage on weekends as compared with weekday. In general, the log normal distribution described the playing and wading duration distribution, while the gamma distribution was the best fit for fishing durations. Remote photography provided unbiased, real-time human exposure data and was less personnel intensive compared with traditional survey methods. However, there are potential limitations associated with remote surveillance data related to its limited view. This is the first study to report that time lapse cameras can be successfully applied to assess water-based human recreational patterns and can

Survival and activity of Streptococcus faecalis and Escherichia coli in petroleum-contaminated tropical marine waters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santo Domingo, J.W.; Fuentes, F.A.; Hazen, T.C.

1987-12-31

The in situ survival and activity of Streptococcus faecalis and Escherichia coli were studied using membrane diffusion chambers in tropical marine waters receiving oil refinery effluents. Protein synthesis, DNA synthesis, respiration or fermentation, INT reduced per cell, and ATP per cell were used to measure physiological activity. Cell densities decreased significantly over time at both sites for both S. faecalis and E. coli; however, no significant differences in survival pattern were observed between S. faecalis and E.coli. Differences in protein synthesis between the two were only observed at a study site which was not heavily oiled. Although fecal streptococci havemore » been suggested as a better indicator of fecal contamination than fecal coliforms in marine waters, in this study both E. coli and S. faecalis survived and remained physiologically active for extended periods of time. These results suggest that the fecal streptococci group is not a better indicator of fecal contamination in tropical marine waters than the fecal coliform group, especially when that environment is high in long-chained hydrocarbons.« less

Near-bottom pelagic bacteria at a deep-water sewage sludge disposal site.

PubMed

Takizawa, M; Straube, W L; Hill, R T; Colwell, R R

1993-10-01

The epibenthic bacterial community at deep-ocean sewage sludge disposal site DWD-106, located approximately 106 miles (ca. 196 km) off the coast of New Jersey, was assessed for changes associated with the introduction of large amounts of sewage sludge. Mixed cultures and bacterial isolates obtained from water overlying sediment core samples collected at the deep-water (2,500 m) municipal sewage disposal site were tested for the ability to grow under in situ conditions of temperature and pressure. The responses of cultures collected at a DWD-106 station heavily impacted by sewage sludge were compared with those of samples collected from a station at the same depth which was not contaminated by sewage sludge. Significant differences were observed in the ability of mixed bacterial cultures and isolates from the two sites to grow under deep-sea pressure and temperature conditions. The levels of sludge contamination were established by enumerating Clostridium perfringens, a sewage indicator bacterium, in sediment samples from the two sites. The results of hybridization experiments in which DNAs extracted directly from the water overlying sediment core samples were used indicate that the reference site epibenthic community, the disposal site epibenthic community, and the community in a surface sludge plume share many members. Decreased culturability of reference site mixed cultures in the presence of sewage sludge was observed. Thus, the culturable portions of both the autochthonous and allochthonous bacterial communities at the disposal site may be inhibited in situ, the former by sewage sludge and the latter by high pressure and low temperature.

Measuring and computing natural ground-water recharge at sites in south-central Kansas

USGS Publications Warehouse

Sophocleous, M.A.; Perry, C.A.

1987-01-01

To measure the natural groundwater recharge process, two sites in south-central Kansas were instrumented with sensors and data microloggers. The atmospheric-boundary layer and the unsaturated and saturated soil zones were monitored as a single regime. Direct observations also were used to evaluate the measurements. Atmospheric sensors included an anemometer, a tipping-bucket rain gage, an air-temperature thermistor, a relative-humidity probe, a net radiometer, and a barometric-pressure transducer. Sensors in the unsaturated zone consisted of soil-temperature thermocouples, tensiometers coupled with pressure transducers and dial gages, gypsum blocks, and a neutron-moisture probe. The saturated-zone sensors consisted of a water-level pressure transducer, a conventional float gage connected to a variable potentiometer, soil thermocouples, and a number of multiple-depth piezometers. Evaluation of the operation of these sensors and recorders indicates that certain types of equipment, such as pressure transducers, are very sensitive to environmental conditions. A number of suggestions aimed at improving instrumentation of recharge investigations are outlined. Precipitation and evapotranspiration data, taken together with soil moisture profiles and storage changes, water fluxes in the unsaturated zone and hydraulic gradients in the saturated zone at various depths, soil temperature, water table hydrographs, and water level changes in nearby wells, describe the recharge process. Although the two instrumented sites are located in sand-dune environments in area characterized by a shallow water table and a sub-humid continental climate, a significant difference was observed in the estimated total recharge. The estimates ranged from less than 2.5 mm at the Zenith site to approximately 154 mm at the Burrton site from February to June 1983. The principal reasons that the Burrton site had more recharge than the Zenith site were more precipitation, less evapotranspiration, and a

Water-quality assessment of the Sacramento River basin, California : water quality of fixed sites, 1996-1998

USGS Publications Warehouse

Domagalski, Joseph L.; Dileanis, Peter D.

2000-01-01

Water-quality samples were collected from 12 sites in the Sacramento River Basin, Cali-fornia, from February 1996 through April 1998. Field measurements (dissolved oxygen, pH, specific conductance, alkalinity, and water tem-perature) were completed on all samples, and laboratory analyses were done for suspended sediments, nutrients, dissolved and particulate organic carbon, major ions, trace elements, and mercury species. Samples were collected at four types of locations on the Sacramento River?large tributaries to the Sacramento River, agricul-tural drainage canals, an urban stream, and a flood control channel. The samples were collected across a range of flow conditions representative of those sites during the timeframe of the study. The water samples from the Sacramento River indi-cate that specific conductance increases slightly downstream but that the water quality is indicative of dilute water. Water temperature of the Sacramento River increases below Shasta Lake during the spring and summer irrigation season owing to diversion of water out of the river and subsequent lower flow. All 12 sites had generally low concentrations of nutrients, but chlorophyll concentrations were not measured; therefore, the actual consequences of nutrient loading could not be adequately assessed. Concentrations of dis-solved organic carbon in samples from the Sacramento River and the major tributaries were generally low; the formation of trihalomethanes probably does not currently pose a problem when water from the Sacramento River and its major tributaries is chlorinated for drinking-water purposes. However, dissolved organic carbon concentrations were higher in the urban stream and in agricultural drainage canals, but were diluted upon mixing with the Sacramento River. The only trace element that currently poses a water-quality problem in the Sacramento River is mercury. A federal criterion for the protection of aquatic life was exceeded during this study, and floodwater

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

DOE PAGES

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

2017-09-01

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

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

PubMed

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

2017-10-16

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

Water at Biological Phase Boundaries: Its Role in Interfacial Activation of Enzymes and Metabolic Pathways.

PubMed

Damodaran, Srinivasan

2015-01-01

Many life-sustaining activities in living cells occur at the membrane-water interface. The pertinent questions that we need to ask are, what are the evolutionary reasons in biology for choosing the membrane-water interface as the site for performing and/or controlling crucial biological reactions, and what is the key physical principle that is very singular to the membrane-water interface that biology exploits for regulating metabolic processes in cells? In this chapter, a hypothesis is developed, which espouses that cells control activities of membrane-bound enzymes through manipulation of the thermodynamic activity of water in the lipid-water interfacial region. The hypothesis is based on the fact that the surface pressure of a lipid monolayer is a direct measure of the thermodynamic activity of water at the lipid-water interface. Accordingly, the surface pressure-dependent activation or inactivation of interfacial enzymes is directly related to changes in the thermodynamic activity of interfacial water. Extension of this argument suggests that cells may manipulate conformations (and activities) of membrane-bound enzymes by manipulating the (re)activity of interfacial water at various locations in the membrane by localized compression or expansion of the interface. In this respect, cells may use the membrane-bound hormone receptors, lipid phase transition, and local variations in membrane lipid composition as effectors of local compression and/or expansion of membrane, and thereby local water activity. Several experimental data in the literature will be reexamined in the light of this hypothesis.

Water vapor and aerosol lidar measurements within an atmospheric instrumental super site to study the aerosols and the tropospheric trace gases in rome

NASA Astrophysics Data System (ADS)

Dionisi, D.; Iannarelli, A. M.; Scoccione, A.; Liberti, G. L.; Cacciani, M.; Argentini, S.; Baldini, L.; Barnaba, F.; Campanelli, M.; Casasanta, G.; Diémoz, H.; Di Liberto, L.; Gobbi, G. P.; Petenko, I.; Siani, A. M.; Von Bismarck, J.; Casadio, S.

2018-04-01

A joint instrumental Super Site, combining observation in urban ("Sapienza" University) and semi-rural (ESA-ESRIN and CNR-ISAC) environment, for atmospheric studies and satellites Cal/Val activities, has been set-up in the Rome area (Italy). Ground based active and passive remote sensing instruments located in both sites are operating in synergy, offering information for a wide range of atmospheric parameters. In this work, a comparison of aerosol and water vapor measurements derived by the Rayleigh-Mie-Raman (RMR) lidars, operating simultaneously in both experimental sites, is presented.

Effect of water availability in opening containers of breeding site on Aedes aegypti life cycle

NASA Astrophysics Data System (ADS)

Tokachil, Najir; Yusoff, Nuraini; Saaid, Alif; Appandi, Najwa; Harun, Farhana

2017-11-01

The distribution of rainfall is one of the factors which contribute to the development of Aedes aegypti life cycle. The fluctuation of rainfall might influence the acceleration of Aedes aegypti growth by providing sufficient breeding sites. In this research, the availability of water in an opening container of the breeding site is considered as a significant variable which affects the distinct stages structure in mosquito life cycle which egg, larva, pupa, and adult. A stage-structured Lefkovitch matrix model was used by considering the quantity of water contains in an opening container and life cycle of Aedes aegypti. The maximum depth of water in the container was also taken into account in order to find the time duration of mosquito life cycle to complete. We found that the maximum depth of water availability in mosquito breeding site influenced the abundance of the mosquito population. Hence, the containers are filled with sufficient water be able to stand from hot temperature for several days before drying out might continue to provide mosquito breeding site. In the future, it is recommended to consider other factors which affect the quantity of water in mosquito breeding sites such as heavy rain and wind blows.

Water-activated graphite felt as a high-performance electrode for vanadium redox flow batteries

NASA Astrophysics Data System (ADS)

Kabtamu, Daniel Manaye; Chen, Jian-Yu; Chang, Yu-Chung; Wang, Chen-Hao

2017-02-01

A simple, green, novel, time-efficient, and potentially cost-effective water activation method was employed to enhance the electrochemical activity of graphite felt (GF) electrodes for vanadium redox flow batteries (VRFBs). The GF electrode prepared with a water vapor injection time of 5 min at 700 °C exhibits the highest electrochemical activity for the VO2+/VO2+ couple among all the tested electrodes. This is attributed to the small, controlled amount of water vapor that was introduced producing high contents of oxygen-containing functional groups, such as sbnd OH groups, on the surface of the GF fibers, which are known to be electrochemically active sites for vanadium redox reactions. Charge-discharge tests further confirm that only 5 min of GF water activation is required to improve the efficiency of the VRFB cell. The average coulombic efficiency, voltage efficiency, and energy efficiency are 95.06%, 87.42%, and 83.10%, respectively, at a current density of 50 mA cm-2. These voltage and energy efficiencies are determined to be considerably higher than those of VRFB cells assembled using heat-treated GF electrodes without water activation and pristine GF electrodes.

Surface-Water Hydrology and Quality at the Pike Hill Superfund Site, Corinth, Vermont, October 2004 to December 2005

USGS Publications Warehouse

Kiah, Richard G.; Deacon, Jeffrey R.; Piatak, Nadine M.; Seal, Robert R.; Coles, James F.; Hammarstrom, Jane M.

2007-01-01

The hydrology and quality of surface water in and around the Pike Hill Brook watershed, in Corinth, Vermont, was studied from October 2004 to December 2005 by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency (USEPA). Pike Hill was mined intermittently for copper from 1847 to 1919 and the site is known to be contributing trace elements and acidity to Pike Hill Brook and an unnamed tributary to Cookville Brook. The site has been listed as a Superfund site since 2004. Streamflow, specific conductance, pH, and water temperature were measured continuously and monthly at three sites on Pike Hill Brook to determine the variation in these parameters over an annual cycle. Synoptic water-quality sampling was done at 10 stream sites in October 2004, April 2005, and June 2005 and at 13 stream sites in August 2005 to characterize the quality of surface water in the watershed on a seasonal and spatial basis, as well as to assess the effects of wetlands on water quality. Samples for analysis of benthic macroinvertebrate populations were collected at 11 stream sites in August 2005. Water samples were analyzed for 5 major ions and 32 trace elements. Concentrations of trace elements at sites in the Pike Hill Brook watershed exceeded USEPA National Recommended Water Quality Criteria acute and chronic toxicity standards for aluminum, iron, cadmium, copper, and zinc. Concentrations of copper exceeded the chronic criteria in an unnamed tributary to Cookville Brook in one sample. Concentrations of sulfate, calcium, aluminum, iron, cadmium, copper, and zinc decreased with distance from a site directly downstream from the mine (site 1), as a result of dilution and through sorption and precipitation of the trace elements. Maximum concentrations of aluminum, iron, cadmium, copper, and zinc were observed during spring snowmelt. Concentrations of sulfate, calcium, cadmium, copper, and zinc, and instantaneous loads of calcium and aluminum were

Active Layer and Water Geochemistry Dynamics throughout the Yukon River Basin

NASA Astrophysics Data System (ADS)

Mutter, E. A.; Toohey, R.; Herman-Mercer, N. M.; Schuster, P. F.

2017-12-01

The hydrology of the Yukon River Basin has changed over the last several decades as evidenced by a variety of discharge, gravimetric, and geochemical analyses. The Indigenous Observation Network (ION), a community-based project, was initiated by the Yukon River Inter-Tribal Watershed Council and USGS. Capitalizing on existing USGS monitoring and research infrastructure and supplementing USGS collected data, ION investigates changes in surface water geochemistry and active layer dynamics throughout the Yukon River Basin. Over 1600 samples of surface water geochemistry (i.e., major ions, dissolved organic carbon, and 18O and 2H) have been collected at 35 sites throughout the Yukon River and its major tributaries over the past 15 years. Active layer dynamics (maximum thaw depth, soil temperature and moisture) have been collected at 20 sites throughout the Yukon River Basin for the past eight years. Important regional differences in geochemistry and active layer parameters linked to permafrost continuity and tributaries will be highlighted. Additionally, annual trends and seasonal dynamics describing the spatial and temporal heterogeneity of the watershed will be presented in the context of observed hydrological changes. These data assist the global effort to characterize arctic river fluxes and their relationship to the carbon cycle, weathering and permafrost degradation.

Measuring Water Potential (Activity) from Free Water to Oven Dryness 1

PubMed Central

Wiebe, Herman H.

1981-01-01

Water activities (potentials) in plant materials were measured over the range from free water to oven dryness with a Spanner thermocouple psychrometer. In a two-step procedure, water was first condensed on the thermocouple junction for several minutes. The sample was then inserted under the wet thermocouple and the maximum psychrometric cooling was measured in about 10 seconds. Calibration was with saturated salt slurries of known water activities. Psychrometric cooling was a nearly linear function of the water activity and of the negative log of the water potential. The psychrometric cooling to water activity relationship agreed with wetbulb temperature depression to relative humidity relationships given in tables. Water activities of wheat grains and leaves decreased sharply in a curvilinear fashion as their water contents decreased. Some problems of the procedure are discussed. Images PMID:16662081

Litter type affects the activity of aerobic decomposers in a boreal peatland more than site nutrient and water table regimes

NASA Astrophysics Data System (ADS)

Straková, P.; Niemi, R. M.; Freeman, C.; Peltoniemi, K.; Toberman, H.; Heiskanen, I.; Fritze, H.; Laiho, R.

2011-09-01

Peatlands are carbon (C) storage ecosystems sustained by a high water table (WT). High WT creates anoxic conditions that suppress the activity of aerobic decomposers and provide conditions for peat accumulation. Peatland function can be dramatically affected by WT drawdown caused by climate and/or land-use change. Aerobic decomposers are directly affected by WT drawdown through environmental factors such as increased oxygenation and nutrient availability. Additionally, they are indirectly affected via changes in plant community composition and litter quality. We studied the relative importance of direct and indirect effects of WT drawdown on aerobic decomposer activity in plant litter at two stages of decomposition (incubated in the field for 1 or 2 years). We did this by profiling 11 extracellular enzymes involved in the mineralization of organic C, nitrogen (N), phosphorus (P) and sulphur. Our study sites represented a three-stage chronosequence from pristine to short-term (years) and long-term (decades) WT drawdown conditions under two nutrient regimes (bog and fen). The litter types included reflected the prevalent vegetation: Sphagnum mosses, graminoids, shrubs and trees. Litter type was the main factor shaping microbial activity patterns and explained about 30 % of the variation in enzyme activities and activity allocation. Overall, enzyme activities were higher in vascular plant litters compared to Sphagnum litters, and the allocation of enzyme activities towards C or nutrient acquisition was related to the initial litter quality (chemical composition). Direct effects of WT regime, site nutrient regime and litter decomposition stage (length of incubation period) summed to only about 40 % of the litter type effect. WT regime alone explained about 5 % of the variation in enzyme activities and activity allocation. Generally, enzyme activity increased following the long-term WT drawdown and the activity allocation turned from P and N acquisition towards C

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. © 2010 The Authors Journal compilation © 2010 FEBS.

Jumping to (fatal) conclusions? An analysis of video film on a social networking web site of recreational jumping from height into water.

PubMed

Moran, Kevin

2014-01-01

In high-income countries, death as a consequence of recreational jumping into water from height has not been well investigated partly because it traditionally has been a covert activity within youth culture. An observational study of video recordings posted on the YouTube web site was used to gather data on the nature of jumping activity in New Zealand and Australia. An analytical framework was developed to identify site- participant- social characteristics (10 variables) and online feedback (4 variables). Of the 389 videos recorded in New Zealand (n = 210) and Australia (n = 179), 929 jumpers were observed, and rivers were the most frequently reported site of jumping activity (New Zealand 47%; Australia 35%). One fifth (20%) of the jumps in New Zealand and one third (33%) in Australia were from heights estimated to be more than 12 m. The YouTube website portraying jumps from height were visited almost half a million times (495,686 hits). Ways of reducing recreational jumping risk via targeted education interventions may be best directed at young male adults. Use of social network sites to foster safe behaviours may be an effective way to educate young people of the inherent risks of jumping from height into water.

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Drinking Water in California Child Care Sites Before and After 2011–2012 Beverage Policy

PubMed Central

Yoshida, Sallie; Sharma, Sushma; Patel, Anisha; Vitale, Elyse Homel; Hecht, Ken

2015-01-01

Introduction Drinking water is promoted to improve beverage nutrition and reduce the prevalence of obesity. The aims of this study were to identify how water was provided to young children in child care and to determine the extent to which water access changed after a federal and state child care beverage policy was instituted in 2011 and 2012 in California. Methods Two independent cross-sectional samples of licensed child care providers completed a self-administered survey in 2008 (n = 429) and 2012 (n = 435). Logistic regression was used to analyze data for differences between 2008 and 2012 survey responses, after adjustment for correlations among the measurements in each of 6 child care categories sampled. Results A significantly larger percentage of sites in 2012 than in 2008 always served water at the table with meals or snacks (47.0% vs 28.0%, P = .001). A significantly larger percentage of child care sites in 2012 than in 2008 made water easily and visibly available for children to self-serve both indoors (77.9% vs 69.0%, P = .02) and outside (78.0% vs 69.0%, P = .03). Sites that participated in the federal Child and Adult Care Food Program had greater access to water indoors and outside than sites not in the program. In 2012 most (76.1%) child care providers reported no barriers to serving water to children. Factors most frequently cited to facilitate serving water were information for families (39.0% of sites), beverage policy (37.0%), and lessons for children (37.9%). Conclusion Water provision in California child care improved significantly between samples of sites studied in 2008 and 2012, but room for improvement remains after policy implementation. Additional training for child care providers and parents should be considered. PMID:26043304

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect

Computerized stratified random site-selection approaches for design of a ground-water-quality sampling network

USGS Publications Warehouse

Scott, J.C.

1990-01-01

Computer software was written to randomly select sites for a ground-water-quality sampling network. The software uses digital cartographic techniques and subroutines from a proprietary geographic information system. The report presents the approaches, computer software, and sample applications. It is often desirable to collect ground-water-quality samples from various areas in a study region that have different values of a spatial characteristic, such as land-use or hydrogeologic setting. A stratified network can be used for testing hypotheses about relations between spatial characteristics and water quality, or for calculating statistical descriptions of water-quality data that account for variations that correspond to the spatial characteristic. In the software described, a study region is subdivided into areal subsets that have a common spatial characteristic to stratify the population into several categories from which sampling sites are selected. Different numbers of sites may be selected from each category of areal subsets. A population of potential sampling sites may be defined by either specifying a fixed population of existing sites, or by preparing an equally spaced population of potential sites. In either case, each site is identified with a single category, depending on the value of the spatial characteristic of the areal subset in which the site is located. Sites are selected from one category at a time. One of two approaches may be used to select sites. Sites may be selected randomly, or the areal subsets in the category can be grouped into cells and sites selected randomly from each cell.

Baseline risk assessment of ground water contamination at the uranium mill tailings site near Durango, Colorado. Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-09-01

For the UMTRA Project site located near Durango, Colorado (the Durango site), the Surface Project cleanup occurred from 1986 to 1991. An evaluation was made to determine whether exposure to ground water contaminated by uranium processing could affect people`s health. Exposure could occur from drinking water pumped from a hypothetical well drilled in the contaminated ground water area. In addition, environmental risks may result if plants or animals are exposed to contaminated ground water, or surface water that has mixed with contaminated ground water. This risk assessment report is the first site-specific document prepared for the UMTRA Ground Water Projectmore » at the Durango site. The results of this report and further site characterization of the Durango site will be used to determine what is necessary to protect public health and the environment, and to comply with the EPA standards.« less

Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

PubMed

Miner, Kyle D; Kurtz, Donald M

2016-02-16

HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

Post-Remediation Biomonitoring of Pesticides in Marine Waters Near the United Heckathorn Site, Richmond, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antrim, Liam D.; Kohn, Nancy P.

Marine sediment remediation at the United Heckathorn Superfund Site was completed in April 1997. Water and mussel tissues were sampled in January 1998 from four stations near Lauritzen Canal in Richmond, California, for the first post-remediation monitoring of marine areas near the United Heckathorn Site. Dieldrin and DDT were analyzed in water samples, tissue samples from resident mussels, and tissue samples from transplanted mussels deployed for 4 months. Concentrations of dieldrin and total DDT in water and total DDT in tissue were compared to pre-remediation data available from the California State Mussel Watch program (tissues) and the Ecological Risk Assessmentmore » for the United Heckathorn Superfund Site (tissues and water). Biomonitoring results indicated that pesticides were still bioavailable in the water column, and have not been reduced from pre-remediation levels. Annual biomonitoring will continue to assess the effectiveness of remedial actions at the United Heckathorn Site.« less

Hydrogeology and physical characteristics of water samples at the Red River aluminum site, Stamps, Arkansas, April 2001

USGS Publications Warehouse

Czarnecki, John B.; Stanton, Gregory P.; Freiwald, David A.

2001-01-01

The Red River Aluminum site near Stamps, Arkansas, contains waste piles of salt cake and metal byproducts from the smelting of aluminum. The waste piles are subjected to about 50 inches of rainfall a year, resulting in the dissolution of the salts and metal. To assess the potential threat to underlying ground-water resources at the site, its hydrogeology was characterized by measuring water levels and field parameters of water quality in 23 wells and at 2 surface-water sites. Seventeen of these monitor wells were constructed at various depths for this study to allow for the separate characterization of the shallow and deep ground-water systems, the calculation of vertical gradients, and the collection of water samples at different depths within the flow system. Lithologic descriptions from drill-hole cuttings and geophysical logs indicate the presence of interbedded sands, gravels, silts, and clays to depths of 65 feet. The regionally important Sparta aquifer underlies the site. Water levels in shallow wells indicate radial flow away from the salt-cake pile located near the center of the site. Flow in the deep system is to the west and southwest toward Bodcau Creek. Water-level data from eight piezometer nests indicate a downward hydraulic gradient from the shallow to deep systems across the site. Values of specific conductance (an indicator of dissolved salts) ranged from 215 to 196,200 microsiemens per centimeter and indicate that saline waters are being transported horizontally and vertically downward away from the site

Site observational work plan for the UMTRA Project site at Monument Valley, Arizona

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-09-01

The site observational work plan (SOWP) for the Monument Valley, Arizona, US Department of Energy (DOE) Uranium Mill Tailings Remedial Action (UMTRA) Project site is one of the first site-specific documents developed to achieve ground water compliance at the site. This SOWP applies information about the Monument Valley site to a regulatory compliance framework that identifies strategies that could be used to meet ground water compliance. The compliance framework was developed in the UMTRA Ground Water programmatic environmental impact statement (DOE, 1995). The DOE`s goal is to implement a cost-effective site strategy that complies with the US Environmental Protection Agencymore » (EPA) ground water standards and protects human health and the environment. The compliance strategy that emerges in the final version of the SOWP will assess potential environmental impacts and provide stakeholder a forum for review and comment. When the compliance strategy is acceptable, it will be detailed in a remedial action plan that will be subject to review by the state and/or tribe and concurrence by the US Nuclear Regulatory Commission (NRC). Information available for the preparation of this SOWP indicates active remediation is the most likely compliance strategy for the Monument Valley site. Additional data are needed to determine the most effective remediation technology.« less

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.

Quality-assurance plan for groundwater activities, U.S. Geological Survey, Washington Water Science Center

USGS Publications Warehouse

Kozar, Mark D.; Kahle, Sue C.

2013-01-01

This report documents the standard procedures, policies, and field methods used by the U.S. Geological Survey’s (USGS) Washington Water Science Center staff for activities related to the collection, processing, analysis, storage, and publication of groundwater data. This groundwater quality-assurance plan changes through time to accommodate new methods and requirements developed by the Washington Water Science Center and the USGS Office of Groundwater. The plan is based largely on requirements and guidelines provided by the USGS Office of Groundwater, or the USGS Water Mission Area. Regular updates to this plan represent an integral part of the quality-assurance process. Because numerous policy memoranda have been issued by the Office of Groundwater since the previous groundwater quality assurance plan was written, this report is a substantial revision of the previous report, supplants it, and contains significant additional policies not covered in the previous report. This updated plan includes information related to the organization and responsibilities of USGS Washington Water Science Center staff, training, safety, project proposal development, project review procedures, data collection activities, data processing activities, report review procedures, and archiving of field data and interpretative information pertaining to groundwater flow models, borehole aquifer tests, and aquifer tests. Important updates from the previous groundwater quality assurance plan include: (1) procedures for documenting and archiving of groundwater flow models; (2) revisions to procedures and policies for the creation of sites in the Groundwater Site Inventory database; (3) adoption of new water-level forms to be used within the USGS Washington Water Science Center; (4) procedures for future creation of borehole geophysics, surface geophysics, and aquifer-test archives; and (5) use of the USGS Multi Optional Network Key Entry System software for entry of routine water-level data

Comparison of balance of tritium activity in waste water from nuclear power plants and at selected monitoring sites in the Vltava River, Elbe River and Jihlava (Dyje) River catchments in the Czech Republic.

PubMed

Hanslík, Eduard; Marešová, Diana; Juranová, Eva; Sedlářová, Barbora

2017-12-01

During the routine operation, nuclear power plants discharge waste water containing a certain amount of radioactivity, whose main component is the artificial radionuclide tritium. The amounts of tritium released into the environment are kept within the legal requirements, which minimize the noxious effects of radioactivity, but the activity concentration is well measurable in surface water of the recipient. This study compares amount of tritium activity in waste water from nuclear power plants and the tritium activity detected at selected relevant sites of surface water quality monitoring. The situation is assessed in the catchment of the Vltava and Elbe Rivers, affected by the Temelín Nuclear Power Plant as well as in the Jihlava River catchment (the Danube River catchment respectively), where the waste water of the Dukovany Nuclear Power Plant is discharged. The results show a good agreement of the amount of released tritium stated by the power plant operator and the tritium amount detected in the surface water and highlighted the importance of a robust independent monitoring of tritium discharged from a nuclear power plant which could be carried out by water management authorities. The outputs of independent monitoring allow validating the values reported by a polluter and expand opportunities of using tritium as e.g. tracer. Copyright © 2017 Elsevier Ltd. All rights reserved.

KatB, a cyanobacterial Mn-catalase with unique active site configuration: Implications for enzyme function.

PubMed

Bihani, Subhash C; Chakravarty, Dhiman; Ballal, Anand

2016-04-01

Manganese catalases (Mn-catalases), a class of H2O2 detoxifying proteins, are structurally and mechanistically distinct from the commonly occurring catalases, which contain heme. Active site of Mn-catalases can serve as template for the synthesis of catalase mimetics for therapeutic intervention in oxidative stress related disorders. However, unlike the heme catalases, structural aspects of Mn-catalases remain inadequately explored. The genome of the ancient cyanobacterium Anabaena PCC7120, shows the presence of two Mn-catalases, KatA and KatB. Here, we report the biochemical and structural characterization of KatB. The KatB protein (with a C-terminal his-tag) was over-expressed in Escherichia coli and purified by affinity chromatography. On the addition of Mn(2+) to the E. coli growth medium, a substantial increase in production of the soluble KatB protein was observed. The purified KatB protein was an efficient catalase, which was relatively insensitive to inhibition by azide. Crystal structure of KatB showed a hexameric assembly with four-helix bundle fold, characteristic of the Ferritin-like superfamily. With canonical Glu4His2 coordination geometry and two terminal water ligands, the KatB active site was distinctly different from that of other Mn-catalases. Interestingly, the KatB active site closely resembled the active sites of ruberythrin/bacterioferritin, bi-iron members of the Ferritin-like superfamily. The KatB crystal structure provided fundamental insights into the evolutionary relationship within the Ferritin-like superfamily and further showed that Mn-catalases can be sub-divided into two groups, each with a distinct active site configuration. Copyright © 2016 Elsevier Inc. All rights reserved.

HTO and OBT activity concentrations in soil at the historical atmospheric HT release site (Chalk River Laboratories).

PubMed

Kim, S B; Bredlaw, M; Korolevych, V Y

2012-01-01

Tritium is routinely released by the Chalk River Laboratories (CRL) nuclear facilities. Three International HT release experiments have been conducted at the CRL site in the past. The site has not been disturbed since the last historical atmospheric testing in 1994 and presents an opportunity to assess the retention of tritium in soil. This study is devoted to the measurement of HTO and OBT activity concentration profiles in the subsurface 25 cm of soil. In terms of soil HTO, there is no evidence from the past HT release experiments that HTO was retained. The HTO activity concentration in the soil pore water appears similar to concentrations found in background areas in Ontario. In contrast, OBT activity concentrations in soil at the same site were significantly higher than HTO activity concentrations in soil. Elevated OBT appears to reside in the top layer of the soil (0-5 cm). In addition, OBT activity concentrations in the top soil layer did not fluctuate much with season, again, quite in contrast with soil HTO. This result suggests that OBT activity concentrations retained the signature of the historical tritium releases. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Characterization and relation of precipitation, streamflow, and water-quality data at the U.S. Army Garrison Fort Carson and Piñon Canyon Maneuver Site, Colorado, water years 2013–14

USGS Publications Warehouse

Holmberg, Michael J.; Stogner, Sr., Robert W.; Bruce, James F.

2016-11-29

To evaluate the influence of military training activities on streamflow and water quality, the U.S. Geological Survey, in cooperation with the U.S. Department of the Army, began a hydrologic data collection network on the U.S. Army Garrison Fort Carson in 1978 and on the Piñon Canyon Maneuver Site in 1983. This report is a summary and characterization of the precipitation, streamflow, and water-quality data collected at 43 sites between October 1, 2012, and September 30, 2014 (water years 2013 and 2014).Variations in the frequency of daily precipitation, seasonal distribution, and seasonal and annual precipitation at 5 stations at the U.S. Army Garrison Fort Carson and 18 stations at or near the Piñon Canyon Maneuver Site were evaluated. Isohyetal diagrams indicated a general pattern of increase in total annual precipitation from east to west at the U.S. Army Garrison Fort Carson and the Piñon Canyon Maneuver Site. Between about 54 and 79 percent of daily precipitation was 0.1 inch or less in magnitude. Precipitation events were larger and more frequent between July and September.Daily streamflow data from 16 sites were used to evaluate temporal and spatial variations in streamflow for the water years 2013 and 2014. At all sites, median daily mean streamflow for the 2-year period ranged from 0.0 to 9.60 cubic feet per second. Daily mean streamflow hydrographs are included in this report. Five sites on the Piñon Canyon Maneuver Site were monitored for peak stage using crest-stage gages.At the Piñon Canyon Maneuver Site, five sites had a stage recorder and precipitation gage, providing a paired streamflow-precipitation dataset. There was a statistically significant correlation between precipitation and streamflow based on Spearman’s rho correlation (rho values ranged from 0.17 to 0.35).Suspended-sediment samples were collected in April through October for water years 2013–14 at one site at the U.S. Army Garrison Fort Carson and five sites at the Pi

Inversion of sonobuoy data from shallow-water sites with simulated annealing.

PubMed

Lindwall, Dennis; Brozena, John

2005-02-01

An enhanced simulated annealing algorithm is used to invert sparsely sampled seismic data collected with sonobuoys to obtain seafloor geoacoustic properties at two littoral marine environments as well as for a synthetic data set. Inversion of field data from a 750-m water-depth site using a water-gun sound source found a good solution which included a pronounced subbottom reflector after 6483 iterations over seven variables. Field data from a 250-m water-depth site using an air-gun source required 35,421 iterations for a good inversion solution because 30 variables had to be solved for, including the shot-to-receiver offsets. The sonobuoy derived compressional wave velocity-depth (Vp-Z) models compare favorably with Vp-Z models derived from nearby, high-quality, multichannel seismic data. There are, however, substantial differences between seafloor reflection coefficients calculated from field models and seafloor reflection coefficients based on commonly used Vp regression curves (gradients). Reflection loss is higher at one field site and lower at the other than predicted from commonly used Vp gradients for terrigenous sediments. In addition, there are strong effects on reflection loss due to the subseafloor interfaces that are also not predicted by Vp gradients.

ColiSense, today's sample today: A rapid on-site detection of β-D-Glucuronidase activity in surface water as a surrogate for E. coli.

PubMed

Heery, Brendan; Briciu-Burghina, Ciprian; Zhang, Dian; Duffy, Gillian; Brabazon, Dermot; O'Connor, Noel; Regan, Fiona

2016-01-01

A sensitive field-portable fluorimeter with incubating capability and triplicate sample chambers was designed and built. The system was optimised for the on-site analysis of E. coli in recreational waters using fluorescent based enzyme assays. The target analyte was β-D-Glucuronidase (GUS) which hydrolyses a synthetic substrate 6-Chloro-4-Methyl-Umbelliferyl-β-D-Glucuronide (6-CMUG) to release the fluorescent molecule 6-Chloro-4-Methyl-Umbelliferyl (6-CMU). The system was calibrated with 6-CMU standards. A LOD of 5 nM and a resolution of less than 1 nM was determined while enzyme kinetic tests showed detection of activities below 1 pmol min(-1) mL(-1) of sample. A field portable sample preparation, enzyme extraction protocol and continuous assay were applied with the system to analyse freshwater and marine samples. Results from a one day field trial are shown which demonstrated the ability of the system to deliver results on-site within a 75 min period. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

PubMed

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial Activities and Dissolved Organic Matter Dynamics in Oil-Contaminated Surface Seawater from the Deepwater Horizon Oil Spill Site

PubMed Central

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L.; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities. PMID:22509359

Direct instrumental identification of catalytically active surface sites

NASA Astrophysics Data System (ADS)

Pfisterer, Jonas H. K.; Liang, Yunchang; Schneider, Oliver; Bandarenka, Aliaksandr S.

2017-09-01

The activity of heterogeneous catalysts—which are involved in some 80 per cent of processes in the chemical and energy industries—is determined by the electronic structure of specific surface sites that offer optimal binding of reaction intermediates. Directly identifying and monitoring these sites during a reaction should therefore provide insight that might aid the targeted development of heterogeneous catalysts and electrocatalysts (those that participate in electrochemical reactions) for practical applications. The invention of the scanning tunnelling microscope (STM) and the electrochemical STM promised to deliver such imaging capabilities, and both have indeed contributed greatly to our atomistic understanding of heterogeneous catalysis. But although the STM has been used to probe and initiate surface reactions, and has even enabled local measurements of reactivity in some systems, it is not generally thought to be suited to the direct identification of catalytically active surface sites under reaction conditions. Here we demonstrate, however, that common STMs can readily map the catalytic activity of surfaces with high spatial resolution: we show that by monitoring relative changes in the tunnelling current noise, active sites can be distinguished in an almost quantitative fashion according to their ability to catalyse the hydrogen-evolution reaction or the oxygen-reduction reaction. These data allow us to evaluate directly the importance and relative contribution to overall catalyst activity of different defects and sites at the boundaries between two materials. With its ability to deliver such information and its ready applicability to different systems, we anticipate that our method will aid the rational design of heterogeneous catalysts.

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Water-quality data from an earthen dam site in southern Westchester County, New York, 2015

USGS Publications Warehouse

Chu, Anthony; Noll, Michael L.

2017-10-11

The U.S. Geological Survey, in cooperation with the New York City Department of Environmental Protection, sampled 37 sites in the reservoir area for nutrients, major ions, metals, pesticides and their degradates, volatile organic compounds, temperature, pH, and specific conductance during fall 2015. Data collection was done to characterize the local groundwater-flow system and identify potential sources of seeps from the southern embankment at the Hillview Reservoir. Water-quality samples were collected in accordance with standard U.S. Geological Survey methods at 37 sites in and adjacent to Hillview Reservoir. These 37 sites were sampled to determine (1) baseline water-quality conditions of the saturated, low-permeability sediments that compose the earthen embankment that surrounds the reservoir, (2) water-quality conditions in the southwestern part of the study area in relation to the seeps on the embankment, and (3) temporal variation of water-quality conditions between 2006 and 2015 (not included in this report). The physical parameters and the results of the water-quality analysis from the 37 sites are included in this report and can be downloaded from the U.S. Geological Survey National Water Information System website.

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

PubMed

Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana

2012-01-01

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

Isotope geochemistry of waters affected by acid mine drainage in old labour sites (SE, Spain).

NASA Astrophysics Data System (ADS)

Pérez-Sirvent, Carmen; Martinez-Sanchez, Maria Jose; Garcia-Lorenzo, Maria Luz; Agudo, Ines; Hernandez-Cordoba, Manuel; Recio, Clemente

2015-04-01

The ore deposits of this zone have iron, lead and zinc as the main metal components. Iron is present in oxides, hydroxides, sulfides, sulfates, carbonates, and silicates; lead and zinc occur in sulfides (galena and sphalerite, respectively), carbonates, sulfates, and lead or zinc-bearing (manganese, iron) oxides. Mining started with the Romans and activity peaked in the second half of the 19th century and throughout the 20th century until the 1980's. From 1940 to 1957, mineral concentration was made by froth flotation and, prior to this, by gravimetric techniques. The mining wastes, or tailings, with a very fine particle size were deposited inland (tailings dams) and, since 1957, huge releases were made in directly the sea coast. The objective of this work was to evaluate processes affecting waters from abandoned mine sites by way of stable isotopic analysis, particularly H and O stable isotopes from water and S and O from dissolved sulfates. Several common chemical and physical processes, such as evaporation, water-rock interaction and mixing could alter water isotopic composition. Evaporation, which causes an enrichment in δD and δ18O in the residual water, is an important process in semiarid areas. The results obtained indicate that, for sites near the coast, waters are meteoric, and marine infiltration only takes place in the deepest layers near the shore or if water remains stagnated in sediments with low permeability. The main source of sulfate was the oxidation of sulfides, resulting in the liberation of acid, sulfate and metals. In order to assess the mechanism responsible for sulfide oxidation, the stoichiometric isotope balance model and the general isotope balance model were tested, suggesting that the oxidation via Fe3+ was predominant in the surface, and controlled by A. ferrooxidans, while at depth, sulfate reduction occurred.

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 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 waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 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 active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

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 waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 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 waste...

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 waste...

Life at low water activity.

PubMed Central

Grant, W D

2004-01-01

Two major types of environment provide habitats for the most xerophilic organisms known: foods preserved by some form of dehydration or enhanced sugar levels, and hypersaline sites where water availability is limited by a high concentration of salts (usually NaCl). These environments are essentially microbial habitats, with high-sugar foods being dominated by xerophilic (sometimes called osmophilic) filamentous fungi and yeasts, some of which are capable of growth at a water activity (a(w)) of 0.61, the lowest a(w) value for growth recorded to date. By contrast, high-salt environments are almost exclusively populated by prokaryotes, notably the haloarchaea, capable of growing in saturated NaCl (a(w) 0.75). Different strategies are employed for combating the osmotic stress imposed by high levels of solutes in the environment. Eukaryotes and most prokaryotes synthesize or accumulate organic so-called 'compatible solutes' (osmolytes) that have counterbalancing osmotic potential. A restricted range of bacteria and the haloarchaea counterbalance osmotic stress imposed by NaCl by accumulating equivalent amounts of KCl. Haloarchaea become entrapped and survive for long periods inside halite (NaCl) crystals. They are also found in ancient subterranean halite (NaCl) deposits, leading to speculation about survival over geological time periods. PMID:15306380

Identification of B. anthracis N(5)-carboxyaminoimidazole ribonucleotide mutase (PurE) active site binding compounds via fragment library screening.

PubMed

Lei, Hao; Jones, Christopher; Zhu, Tian; Patel, Kavankumar; Wolf, Nina M; Fung, Leslie W-M; Lee, Hyun; Johnson, Michael E

2016-02-15

The de novo purine biosynthesis pathway is an attractive target for antibacterial drug design, and PurE from this pathway has been identified to be crucial for Bacillus anthracis survival in serum. In this study we adopted a fragment-based hit discovery approach, using three screening methods-saturation transfer difference nucleus magnetic resonance (STD-NMR), water-ligand observed via gradient spectroscopy (WaterLOGSY) NMR, and surface plasmon resonance (SPR), against B. anthracis PurE (BaPurE) to identify active site binding fragments by initially testing 352 compounds in a Zenobia fragment library. Competition STD NMR with the BaPurE product effectively eliminated non-active site binding hits from the primary hits, selecting active site binders only. Binding affinities (dissociation constant, KD) of these compounds varied between 234 and 301μM. Based on test results from the Zenobia compounds, we subsequently developed and applied a streamlined fragment screening strategy to screen a much larger library consisting of 3000 computationally pre-selected fragments. Thirteen final fragment hits were confirmed to exhibit binding affinities varying from 14μM to 700μM, which were categorized into five different basic scaffolds. All thirteen fragment hits have ligand efficiencies higher than 0.30. We demonstrated that at least two fragments from two different scaffolds exhibit inhibitory activity against the BaPurE enzyme. Published by Elsevier Ltd.

Subsurface imaging of water electrical conductivity, hydraulic permeability and lithology at contaminated sites by induced polarization

NASA Astrophysics Data System (ADS)

Maurya, P. K.; Balbarini, N.; Møller, I.; Rønde, V.; Christiansen, A. V.; Bjerg, P. L.; Auken, E.; Fiandaca, G.

2018-05-01

At contaminated sites, knowledge about geology and hydraulic properties of the subsurface and extent of the contamination is needed for assessing the risk and for designing potential site remediation. In this study, we have developed a new approach for characterizing contaminated sites through time-domain spectral induced polarization. The new approach is based on: (1) spectral inversion of the induced polarization data through a reparametrization of the Cole-Cole model, which disentangles the electrolytic bulk conductivity from the surface conductivity for delineating the contamination plume; (2) estimation of hydraulic permeability directly from the inverted parameters using a laboratory-derived empirical equation without any calibration; (3) the use of the geophysical imaging results for supporting the geological modelling and planning of drilling campaigns. The new approach was tested on a data set from the Grindsted stream (Denmark), where contaminated groundwater from a factory site discharges to the stream. Two overlapping areas were covered with seven parallel 2-D profiles each, one large area of 410 m × 90 m (5 m electrode spacing) and one detailed area of 126 m × 42 m (2 m electrode spacing). The geophysical results were complemented and validated by an extensive set of hydrologic and geologic information, including 94 estimates of hydraulic permeability obtained from slug tests and grain size analyses, 89 measurements of water electrical conductivity in groundwater, and four geological logs. On average the IP-derived and measured permeability values agreed within one order of magnitude, except for those close to boundaries between lithological layers (e.g. between sand and clay), where mismatches occurred due to the lack of vertical resolution in the geophysical imaging. An average formation factor was estimated from the correlation between the imaged bulk conductivity values and the water conductivity values measured in groundwater, in order to

Baseline risk assessment of ground water contamination at the uranium mill tailings site near Durango, Colorado

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1995-02-01

This risk assessment evaluates the possibility of health and environmental risks from contaminated ground water at the uranium mill tailings site near Durango, Colorado. The former uranium processing site`s contaminated soil and material were removed and placed at a disposal site located in Body Canyon, Colorado, during 1986--1991 by the US Departments of Energy`s Uranium Mill Tailings Remedial Action (UMTRA) Project. Currently, the UMTRA Project is evaluating the nature and extent of ground water contamination at the site. This risk assessment follows an approach similar to that used by the US Environmental Protection Agency. The first step is to determinemore » what site-related contaminants are found in ground water samples. The next step in the risk assessment is to determine how much of these contaminants people might ingest if they got their drinking water from a well on the site. In accordance with standard practice for this type of risk assessment, the highest contaminant concentrations from the most contaminated wells are used. The risk assessment then explains the possible health problems that could result from this amount of contamination.« less

Remediation System Evaluation, Savage Municipal Water Supply Superfund Site (PDF)

EPA Pesticide Factsheets

The Savage Municipal Water Supply Superfund Site, located on the western edge of Milford, New Hampshire, consists of a source area and an extended plume that is approximately 6,000 feet long and 2,500 feet wide.

Direct Conversion of Methane to Methanol on Ni-Ceria Surfaces: Metal-Support Interactions and Water-enabled Catalytic Conversion by Site Blocking

DOE PAGES

Lustemberg, Pablo G.; Palomino, Robert M.; Gutierrez, Ramon A.; ...

2018-05-28

The transformation of methane into methanol or higher alcohols at moderate temperature and pressure conditions is of great environmental interest and remains a challenge despite many efforts. Extended surfaces of metallic nickel are inactive for a direct CH 4 → CH 3OH conversion. This experimental and computational study provides clear evidence that low Ni loadings on a CeO 2(111) support can perform a direct catalytic cycle for the generation of methanol at low temperature using oxygen and water as reactants, with a higher selectivity than ever reported for ceria-based catalysts. On the basis of ambient pressure X-ray photoemission spectroscopy andmore » density functional theory calculations, we demonstrate that water plays a crucial role in blocking catalyst sites where methyl species could fully decompose, an essential factor for diminishing the production of CO and CO 2, and in generating sites on which methoxy species and ultimately methanol can form. In addition to water-site blocking, one needs the effects of metal-support interactions to bind and activate methane and water. Lastly, these findings should be considered when designing metal/oxide catalysts for converting methane to value-added chemicals and fuels.« less

Direct Conversion of Methane to Methanol on Ni-Ceria Surfaces: Metal-Support Interactions and Water-enabled Catalytic Conversion by Site Blocking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lustemberg, Pablo G.; Palomino, Robert M.; Gutierrez, Ramon A.

The transformation of methane into methanol or higher alcohols at moderate temperature and pressure conditions is of great environmental interest and remains a challenge despite many efforts. Extended surfaces of metallic nickel are inactive for a direct CH 4 → CH 3OH conversion. This experimental and computational study provides clear evidence that low Ni loadings on a CeO 2(111) support can perform a direct catalytic cycle for the generation of methanol at low temperature using oxygen and water as reactants, with a higher selectivity than ever reported for ceria-based catalysts. On the basis of ambient pressure X-ray photoemission spectroscopy andmore » density functional theory calculations, we demonstrate that water plays a crucial role in blocking catalyst sites where methyl species could fully decompose, an essential factor for diminishing the production of CO and CO 2, and in generating sites on which methoxy species and ultimately methanol can form. In addition to water-site blocking, one needs the effects of metal-support interactions to bind and activate methane and water. Lastly, these findings should be considered when designing metal/oxide catalysts for converting methane to value-added chemicals and fuels.« less

In situ Visualization of Electrocatalytic Reaction Activity at Quantum Dots for Water Oxidation.

PubMed

Chen, Ying; Fu, Jiaju; Cui, Chen; Jiang, Dechen; Chen, Zixuan; Chen, Hong-Yuan; Zhu, Jun-Jie

2018-06-11

Exploring electrocatalytic reactions on nanomaterial surface can give crucial information for the development of robust catalysts. Here, electrocatalytic reaction activity at single quantum dots (QDs) loaded silica micro-particles involved in water oxidation is visualized using electrochemiluminescence (ECL) microscopy. Under positive potential, the active redox centers at QDs induce the generation of hydroperoxide surface intermediates as coreactant to remarkably enhance ECL emission from luminol derivative for imaging. For the first time, in situ visualization of catalytic activity in water oxidation at QDs catalyst was achieved, supported by a linear relation between ECL intensity and turn over frequency. A very slight diffusion trend attributed to only luminol species proved in situ capture of hydroperoxide surface intermediates at catalytic active sites of QDs. This work provides tremendous potential in on-line imaging of electrocatalytic reaction and visual evaluation of catalyst performance.

Site clearance working group

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The Gulf of Mexico and Louisiana continue to be areas with a high level of facility removal, and the pace of removal is projected to increase. Regulations were promulgated for the Gulf of Mexico and Louisiana requiring that abandoned sites be cleared of debris that could interfere with fishing and shrimping activities. The site clearance regulations also required verification that the sites were clear. Additionally, government programs were established to compensate fishermen for losses associated with snagging their equipment on oil and gas related objects that remained on the water bottoms in areas other than active producing sites and sitesmore » that had been verified as clear of obstructions and snags. The oil and gas industry funds the compensation programs. This paper reviews the regulations and evolving operating practices in the Gulf of Mexico and Louisiana where site clearance and fisherman`s gear compensation regulations have been in place for a number of years. Although regulations and guidelines may be in place elsewhere in the world, this paper focuses on the Gulf of Mexico and Louisiana. Workshop participants are encouraged to bring up international issues during the course of the workshop. Additionally, this paper raises questions and focuses on issues that are of concern to the various Gulf of Mexico and Louisiana water surface and water bottom stakeholders. This paper does not have answers to the questions or issues. During the workshop participants will debate the questions and issues in an attempt to develop consensus opinions and/or make suggestions that can be provided to the appropriate organizations, both private and government, for possible future research or policy adjustments. Site clearance and facility removal are different activities. Facility removal deals with removal of the structures used to produce oil and gas including platforms, wells, casing, piles, pipelines, well protection structures, etc.« less

Water-resources activities in Ohio, 1986 (water fact sheet)

USGS Publications Warehouse

Hindall, S.M.

1986-01-01

The Ohio District of the Water Resources Division, U.S. Geological Survey, provides information on Ohio 's water resources for the overall benefit of the State and the Nation. An integral part of the Survey 's mission is to conduct investigations of the Nation 's land, mineral, and water resources, and to publish and disseminate the information needed to understand, to plan the use of, and to manage these resources. The activities fall into eight broad categories: collection of hydrologic data; water resources investigations and assessments; basic and problem-oriented hydrologic and water related research; acquisition of information useful in predicting and delineating water related natural hazards; coordination of the activities of all Federal agencies in the acquisition of water data, and operation of water information centers; dissemination of data and the results of investigations; provision of scientific and technical assistance in hydrologic studies; and the administration of the State Water Resources Research Institute Program and the National Water Resources Research Grant Program. (Lantz-PTT)

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

Chemosynthetic microbial activity at Mid-Atlantic Ridge hydrothermal vent sites

NASA Astrophysics Data System (ADS)

Wirsen, Carl O.; Jannasch, Holger W.; Molyneaux, Stephen J.

1993-06-01

Chemosynthetic production of microbial biomass, determined by 14CO2 fixation and enzymatic (RuBisCo) activity, at the Mid-Atlantic Ridge (MAR) 23° and 26°N vent sites was found in various niches: warm water emissions, loosely rock-attached flocculent material, dense morphologically diverse bacterial mats covering the surfaces of polymetal sulfide deposits, and filamentous microbes on the carapaces of shrimp (Rimicaris exoculata). The bacterial mats on polymetal sulfide surfaces contained unicellular and filamentous bacteria which appeared to use as their chemolithotrophic electron or energy source either dissolved reduced minerals from vent emissions, mainly sulfur compounds, or solid metal sulfide deposits, mainly pyrite. Moderately thermophilic Chemosynthetic activity was observed in carbon dioxide fixation experiments and in enrichments, but no thermophilic aerobic sulfur oxidizers could be isolated. Both obligate and facultative chemoautotrophs growing at mesophilic temperatures were isolated from all chemosynthetically active surface scrapings. The obligate autotrophs could oxidize sterilized MAR natural sulfide deposits as well as technical pyrite at near neutral pH, in addition to dissolved reduced sulfur compounds. While the grazing by shrimp on the surface mats of MAR metal sulfide deposits was observed and deemed important, the animals' primary occurrence in dense swarms near vent emissions suggests that they were feeding at these sites, where conditions for Chemosynthetic growth of their filamentous microbial epiflora were optimal. The data show that the transformation of geothermal energy at the massive polymetal sulfide deposits of the MAR is based on the lithoautotrophic oxidation of soluble sulfides and pyrites into microbial biomass.

Occurrence of active and inactive herbicide ingredients at selected sites in Iowa

USGS Publications Warehouse

Wang, W.; Liszewski, M.; Buchmiller, R.; Cherryholmes, K.

1995-01-01

Herbicides were detected in 50% of water samples, ranging from 78% of water samples from the Ames site to 25% from the Walnut Creek site. Among herbicides detected, listed in decreasing order of frequency, were atrazine > alachlor > cyanazine > metolachlor > metribuzin. Volatile organic compounds were detected in 11% of water samples. Among the compounds detected, listed in decreasing order of frequency, were xylene > toluene > acetone. One sample contained a detectable amount of aliphatic compound(s), with the empirical formula of C8H18. Results from the Deer Creek site showed that herbicides were detected primarily in the top layer (1.2 m), whereas xylene and other alkylbenzenes were detected at 2.1 m or deeper. Apparently, physico-chemical and other factors are separating herbicides and volatile organic compounds in the shallow unsaturated zone.

Diel Sampling of Groundwater and Surface Water for Trace Elements and Select Water-Quality Constituents at a Former Zinc Smelter Site near Hegeler, Illinois, August 1-3, 2007

USGS Publications Warehouse

Kay, Robert T.; Groschen, George E.; Dupre, David H.; Drexler, Timothy D.; Thingvold, Karen L.; Rosenfeld, Heather J.

2009-01-01

Surface water can exhibit substantial diel variations in the concentration of a number of constituents. Sampling regimens that do not characterize diel variations in water quality can result in an inaccurate understanding of site conditions and of the threat posed by the site to human health and the environment. Surface- and groundwater affected by acid drainage were sampled every 60 to 90 minutes over a 48-hour period at a former zinc smelter known as the Hegeler Zinc Superfund Site, in Hegeler, Ill. Groundwater-quality data from a well at the site indicate stable, low pH, weakly oxidizing geochemical conditions in the aquifer. With the exceptions of temperature and pH, no constituents exhibited diel variations in groundwater. Variations in temperature and pH likely were not representative of conditions in the aquifer. Surface water was sampled at a site on Grape Creek. Diel variations were observed in temperature, dissolved oxygen, pH, and specific conductance, and in the concentrations of nitrite, barium, iron, lead, vanadium, and possibly uranium. Concentrations during the diel cycles varied by about an order of magnitude for nitrite and varied by about a factor of two for barium, iron, lead, vanadium, and uranium. Temperature, dissolved oxygen, specific conductance, nitrite, barium, lead, and uranium generally reached maximum values during the afternoon and minimum values during the night. Iron, vanadium, and pH generally reached minimum values during the afternoon and maximum values during the night. These variations would need to be accounted for during sampling of surface-water quality in similar hydrologic settings. The temperature variations in surface water were affected by variations in air temperature. Concentrations of dissolved oxygen were affected by variations in the intensity of photosynthetic activity and respiration. Nitrite likely was formed by the oxidation of ammonium by dissolved oxygen and degraded by its anaerobic oxidation by ammonium or

A Site-sPecific Agricultural water Requirement and footprint Estimator (SPARE:WATER 1.0)

NASA Astrophysics Data System (ADS)

Multsch, S.; Al-Rumaikhani, Y. A.; Frede, H.-G.; Breuer, L.

2013-07-01

The agricultural water footprint addresses the quantification of water consumption in agriculture, whereby three types of water to grow crops are considered, namely green water (consumed rainfall), blue water (irrigation from surface or groundwater) and grey water (water needed to dilute pollutants). By considering site-specific properties when calculating the crop water footprint, this methodology can be used to support decision making in the agricultural sector on local to regional scale. We therefore developed the spatial decision support system SPARE:WATER that allows us to quantify green, blue and grey water footprints on regional scale. SPARE:WATER is programmed in VB.NET, with geographic information system functionality implemented by the MapWinGIS library. Water requirements and water footprints are assessed on a grid basis and can then be aggregated for spatial entities such as political boundaries, catchments or irrigation districts. We assume inefficient irrigation methods rather than optimal conditions to account for irrigation methods with efficiencies other than 100%. Furthermore, grey water is defined as the water needed to leach out salt from the rooting zone in order to maintain soil quality, an important management task in irrigation agriculture. Apart from a thorough representation of the modelling concept, we provide a proof of concept where we assess the agricultural water footprint of Saudi Arabia. The entire water footprint is 17.0 km3 yr-1 for 2008, with a blue water dominance of 86%. Using SPARE:WATER we are able to delineate regional hot spots as well as crop types with large water footprints, e.g. sesame or dates. Results differ from previous studies of national-scale resolution, underlining the need for regional estimation of crop water footprints.

Water resources activities of the USGS, 1987

USGS Publications Warehouse

Moore, John E.; Cardin, C. William

1987-01-01

Effective management of water resources requires an understanding of hydrologic systems and the factors that determine the distribution, availability, and quality of water. Within the Federal Government, the U.S. Geological Survey has the principal responsibility for providing hydrologic information and for appraising the Nation's water resources. The water resources activities of the U.S. Geological Survey are diverse, ranging from research investigations of specific aspects of the hydrologic cycle to large programs of regional water-resources investigations, such as the Regional Aquifer System Analyses.This report describes the U.S. Geological Survey's water resources activities. Some activities, such as the acid rain program, are mandated by line items in the Survey's fiscal year 1987 budget. Others, such as floods, sediment, and snow and ice, are topics of general interest to the water resources community. Still others are related to current water issues, such as nonpoint sources of pollution, the irrigation drainage problem of the western San Joaquin Valley, and national ground-water protection.In many cases, there is considerable overlap in the topical descrip-tions. The Survey's water resources research program, for example, conducts investigations that are applicable to virtually all of the activities listed in this book. Similarly, projects in the Federal-State Cooperative Program cover multiple aspects of water resources. For these reasons, the sums associated with funding for each of the activities listed exceeds by a considerable amount the Survey's budget for water resources activities.The report first describes the water-resources mission of the U.S. Geological Survey and discusses the principal sources of funds that support the activities. The remainder of the report consists of descriptions of 39 of the most significant water resources activities. An index appears at the end of the report.Each description of a significant water activity has the

Magnificent Ground Water Connection. [Sample Activities].

ERIC Educational Resources Information Center

Environmental Protection Agency, Washington, DC.

Water conservation and usage is an important concept in science. This document, geared specifically to New England, provides many activities for protecting and discussing ground water situations. Sample activities for grades K-6 include: (1) All the Water in the World; (2) The Case of the Disappearing Water; (3) Deep Subjects--Wells and Ground…

Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.

PubMed

Chung, Ivy Yeuk Wah; Paetzel, Mark

2013-05-03

Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water.

Computational study of ibuprofen removal from water by adsorption in realistic activated carbons.

PubMed

Bahamon, Daniel; Carro, Leticia; Guri, Sonia; Vega, Lourdes F

2017-07-15

Molecular simulations using the Grand Canonical Monte Carlo (GCMC) method have been performed in order to obtain physical insights on how the interaction between ibuprofen (IBP) and activated carbons (ACs) in aqueous mixtures affects IBP removal from water by ACs. A nanoporous carbon model based on units of polyaromatic molecules with different number of rings, defects and polar-oxygenated sites is described. Individual effects of factors such as porous features and chemical heterogeneities in the adsorbents are investigated and quantified. Results are in good agreement with experimental adsorption data, highlightening the ability of GCMC simulation to describe the macroscopic adsorption performance in drug removal applications, while also providing additional insights into the IBP/water adsorption mechanism. The simulation results allow finding the optimal type of activated carbon material for separating this pollutant in water treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Impact of prolonged storm activity on the Ecological Status of intertidal benthic habitats within oyster (Crassostrea gigas) trestle cultivation sites.

PubMed

O'Carroll, Jack P J; Quinn, Christina; Forde, James; Patterson, Adrian; O'Beirn, Francis X; Kennedy, Robert

2016-09-15

The Ecological Status (ES; sensu the Water Framework Directive) of intertidal benthic communities within six oyster trestle cultivation sites was found to be negatively impacted along the access routes to trestles in a 2013 study. All cultivation sites occur within Natura 2000 sites. The current study revisited four of the 2013 cultivation sites in February 2014 one month after the storm activity of winter 2013/14 to test if the compaction effect along access routes persisted after the storms. Three levels of the fixed factor treatment were sampled; immediately below the trestles, along the access route and 300m away from any anthropogenic activity. The compaction effect at the Access treatment persisted in spite of the major storm activity. The current study showed the IQI to be effective for assessing the impacts of aquaculture and highlights the IQI as a tool for monitoring Conservation Status of intertidal communities under the Habitats Directive. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of effluent spray irrigation on ground water at a test site near Tarpon Springs, Florida

USGS Publications Warehouse

Brown, D.P.

1982-01-01

Secondary-treated effluent was applied to a 7.2-acre test site near Tarpon Springs, Fla., for about 1 year at an average rate of 0.06 million gallons per day and 3 years at 0.11 million gallons per day. Chemical fertilizer was applied periodically to the test site and adjacent areas. Periodic mounding of the water table occurred due to effluent irrigation, inducing radial flow from the test site. Physical, geochemical, biochemical processes effectively reduced total nitrogen concentration 90% and total phosphorous concentration more than 95% in the ground water of the surficial aquifer about 300 feet downgradient from the test site from that of the applied effluent. Downgradient, total nitrogen averaged 2.4 milligrams per liter and total phosphorus averaged 0.17 milligrams per liter. Substantial increases in total phosphorus were observed when the pH of the ground water increased. Total coliform bacteria in the ground water of the surficial aquifer were generally less than 100 colonies per 100 milliliters. Fecal coliform bacteria were generally less than 25 colonies per 100 milliliters at the test site and were not detected downgradient or near the test site. Fecal streptococcal bacteria were generally less than 100 colonies per 100 milliliters at the test site, but were detected on three occasions near the test site. (USGS)

A technique to minimize uncertainties in load duration curves (LDCs) for water quality-impaired ungauged sites

EPA Science Inventory

For many water quality-impaired stream segments, streamflow and water quality monitoring sites are not available. Lack of available streamflow data at impaired ungauged sites leads to uncertainties in total maximum daily load (TMDL) estimation. We developed a technique to minimiz...

Optimal Site Characterization and Selection Criteria for Oyster Restoration using Multicolinear Factorial Water Quality Approach

NASA Astrophysics Data System (ADS)

Yoon, J.

2015-12-01

Elevated levels of nutrient loadings have enriched the Chesapeake Bay estuaries and coastal waters via point and nonpoint sources and the atmosphere. Restoring oyster beds is considered a Best Management Practice (BMP) to improve the water quality as well as provide physical aquatic habitat and a healthier estuarine system. Efforts include declaring sanctuaries for brood-stocks, supplementing hard substrate on the bottom and aiding natural populations with the addition of hatchery-reared and disease-resistant stocks. An economic assessment suggests that restoring the ecological functions will improve water quality, stabilize shorelines, and establish a habitat for breeding grounds that outweighs the value of harvestable oyster production. Parametric factorial models were developed to investigate multicolinearities among in situ water quality and oyster restoration activities to evaluate posterior success rates upon multiple substrates, and physical, chemical, hydrological and biological site characteristics to systematically identify significant factors. Findings were then further utilized to identify the optimal sites for successful oyster restoration augmentable with Total Maximum Daily Loads (TMDLs) and BMPs. Factorial models evaluate the relationship among the dependent variable, oyster biomass, and treatments of temperature, salinity, total suspended solids, E. coli/Enterococci counts, depth, dissolved oxygen, chlorophyll a, nitrogen and phosphorus, and blocks consist of alternative substrates (oyster shells versus riprap, granite, cement, cinder blocks, limestone marl or combinations). Factorial model results were then compared to identify which combination of variables produces the highest posterior biomass of oysters. Developed Factorial model can facilitate maximizing the likelihood of successful oyster reef restoration in an effort to establish a healthier ecosystem and to improve overall estuarine water quality in the Chesapeake Bay estuaries.

In vitro assessment of thyroid hormone disrupting activities in drinking water sources along the Yangtze River.

PubMed

Hu, Xinxin; Shi, Wei; Zhang, Fengxian; Cao, Fu; Hu, Guanjiu; Hao, Yingqun; Wei, Si; Wang, Xinru; Yu, Hongxia

2013-02-01

The thyroid hormone disrupting activities of drinking water sources from the lower reaches of Yangtze River were examined using a reporter gene assay based on African green monkey kidney fibroblast (CV-1) cells. None of the eleven tested samples showed thyroid receptor (TR) agonist activity. Nine water samples exhibited TR antagonist activities with the equivalents referring to Di-n-butyl phthalate (DNBP) (TR antagonist activity equivalents, ATR-EQ(50)s) ranging from 6.92 × 10(1) to 2.85 × 10(2) μg DNBP/L. The ATR-EQ(50)s and TR antagonist equivalent ranges (ATR-EQ(30-80) ranges) for TR antagonist activities indicated that the water sample from site WX-8 posed the greatest health risks. The ATR-EQ(80)s of the water samples ranging from 1.56 × 10(3) to 6.14 × 10(3) μg DNBP/L were higher than the NOEC of DNBP. The results from instrumental analysis showed that DNBP might be responsible for the TR antagonist activities in these water samples. Water sources along Yangtze River had thyroid hormone disrupting potential. Copyright © 2012 Elsevier Ltd. All rights reserved.

Integrated ground-water monitoring strategy for NRC-licensed facilities and sites: Case study applications

USGS Publications Warehouse

Price, V.; Temples, T.; Hodges, R.; Dai, Z.; Watkins, D.; Imrich, J.

2007-01-01

This document discusses results of applying the Integrated Ground-Water Monitoring Strategy (the Strategy) to actual waste sites using existing field characterization and monitoring data. The Strategy is a systematic approach to dealing with complex sites. Application of such a systematic approach will reduce uncertainty associated with site analysis, and therefore uncertainty associated with management decisions about a site. The Strategy can be used to guide the development of a ground-water monitoring program or to review an existing one. The sites selected for study fall within a wide range of geologic and climatic settings, waste compositions, and site design characteristics and represent realistic cases that might be encountered by the NRC. No one case study illustrates a comprehensive application of the Strategy using all available site data. Rather, within each case study we focus on certain aspects of the Strategy, to illustrate concepts that can be applied generically to all sites. The test sites selected include:Charleston, South Carolina, Naval Weapons Station,Brookhaven National Laboratory on Long Island, New York,The USGS Amargosa Desert Research Site in Nevada,Rocky Flats in Colorado,C-Area at the Savannah River Site in South Carolina, andThe Hanford 300 Area.A Data Analysis section provides examples of detailed data analysis of monitoring data.

A process to estimate net infiltration using a site-scale water-budget approach, Rainier Mesa, Nevada National Security Site, Nevada, 2002–05

USGS Publications Warehouse

Smith, David W.; Moreo, Michael T.; Garcia, C. Amanda; Halford, Keith J.; Fenelon, Joseph M.

2017-08-29

This report documents a process used to estimate net infiltration from precipitation, evapotranspiration (ET), and soil data acquired at two sites on Rainier Mesa. Rainier Mesa is a groundwater recharge area within the Nevada National Security Site where recharged water flows through bedrock fractures to a deep (450 meters) water table. The U.S. Geological Survey operated two ET stations on Rainier Mesa from 2002 to 2005 at sites characterized by pinyon-juniper and scrub-brush vegetative cover. Precipitation and ET data were corrected to remove measurement biases and gap-filled to develop continuous datasets. Net infiltration (percolation below the root zone) and changes in root-zone water storage were estimated using a monthly water-balance model.Site-scale water-budget results indicate that the heavily-fractured welded-tuff bedrock underlying thin (<40 centimeters) topsoil is a critical water source for vegetation during dry periods. Annual precipitation during the study period ranged from fourth lowest (182 millimeters [mm]) to second highest (708 mm) on record (record = 55 years). Annual ET exceeded precipitation during dry years, indicating that the fractured-bedrock reservoir capacity is sufficient to meet atmospheric-evaporative demands and to sustain vegetation through extended dry periods. Net infiltration (82 mm) was simulated during the wet year after the reservoir was rapidly filled to capacity. These results support previous conclusions that preferential fracture flow was induced, resulting in an episodic recharge pulse that was detected in nearby monitoring wells. The occurrence of net infiltration only during the wet year is consistent with detections of water-level rises in nearby monitoring wells that occur only following wet years.

Land utilization and water resource inventories over extended test sites

NASA Technical Reports Server (NTRS)

Hoffer, R. M.

1972-01-01

In addition to the work on the corn blight this year, several other analysis tests were completed which resulted in significant findings. These aspects are discussed as follows: (1) field spectral measurements of soil conditions; (2) analysis of extended test site data; this discussion involves three different sets of data analysis sequences; (3) urban land use analysis, for studying water runoff potentials; and (4) thermal data quality study, as an expansion of our water resources studies involving temperature calibration techniques.

[Assessment of Cyto- and Genotoxicity of Underground Waters from the Far Eastern Center on Radioactive Waste Treatment Site].

PubMed

Oudalova, A A; Pyatkova, S V; Geras'kin, S A; Kiselev, S M; Akhromeev, S V

2016-01-01

This study has been completed in the frames of activities on the environment assessment in the vicinity of the Far Eastern center (FEC) on radioactive waste treatment (a branch of Fokino, Sysoev Bay). Underground waters collected at the FEC technical site were surveyed both with instrumental techniques and bioassays. Concentrations of some chemicals (ranged to the third hazard category) in the samples collected are over the permitted limits. Activities of 137Cs and 90Sr in waters amount up to 3.8 and 16.2 Bq/l, correspondingly. The integral pollution index is over 1 in all the samples and could amount up to 165. The Allium-test application allows the detection of the sample points where underground waters have an enhanced mutagenic potential. Dependencies between biological effects and pollution levels are analyzed. The findings obtained could be used for the monitoring optimized and decision making on rehabilitation measures to decrease negative influence of the enterprise on the environment.

Event- and site-specific soil wetting and seasonal change in amount of soil water

USDA-ARS?s Scientific Manuscript database

Numerous studies have examined ways to characterize the central tendency of soil water within a field or watershed. Extreme changes in water content reveal more about water movement within the area. The purpose of this study was to determine if extreme soil water changes varied among sites, and to s...

Computer simulation of the active site of human serum cholinesterase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kefang Jiao; Song Li; Zhengzheng Lu

1996-12-31

The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positivemore » electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.« less

Summary of inorganic compositional data for groundwater, soil-water, and surface-water samples collected at the Headgate Draw subsurface drip irrigation site, Johnson County, Wyoming

USGS Publications Warehouse

Geboy, Nicholas J.; Engle, Mark A.; Schroeder, Karl T.; Zupancic, John W.

2011-01-01

As part of a 5-year project on the impact of subsurface drip irrigation (SDI) application of coalbed-methane (CBM) produced waters, water samples were collected from the Headgate Draw SDI site in the Powder River Basin, Wyoming, USA. This research is part of a larger study to understand short- and long-term impacts on both soil and water quality from the beneficial use of CBM waters to grow forage crops through use of SDI. This document provides a summary of the context, sampling methodology, and quality assurance and quality control documentation of samples collected prior to and over the first year of SDI operation at the site (May 2008-October 2009). This report contains an associated database containing inorganic compositional data, water-quality criteria parameters, and calculated geochemical parameters for samples of groundwater, soil water, surface water, treated CBM waters, and as-received CBM waters collected at the Headgate Draw SDI site.

Ground-water quality, water year 1995, and statistical analysis of ground-water-quality data, water years 1994-95, at the Chromic Acid Pit site, US Army Air Defense Artillery Center and Fort Bliss, El Paso, Texas

USGS Publications Warehouse

Abeyta, Cynthia G.; Roybal, R.G.

1996-01-01

The Chromic Acid Pit site is an inactive waste disposal site that is regulated by the Resource Conservation and Recovery Act of 1976. The 2.2-cubic-yard cement-lined pit was operated from 1980 to 1983 by a contractor to the U.S. Army Air Defense Artillery Center and Fort Bliss. The pit, located on the Fort Bliss military reservation in El Paso, Texas, was used for disposal and evaporation of chromic acid waste generated from chrome plating operations. The site was closed in 1989, and the Texas Natural Resources Conservation Commission issued permit number HW-50296 (U.S. Environmental Protection Agency number TX4213720101), which approved and implemented post-closure care for the Chromic Acid Pit site. In accordance with an approved post-closure plan, the U.S. Geological Survey is cooperating with the U.S. Army in monitoring and evaluating ground-water quality at the site. One upgradient ground-water monitoring well (MW1) and two downgradient ground-water monitoring wells (MW2 and MW3), installed adjacent to the chromic acid pit, are monitored on a quarterly basis. Ground-water sampling of these wells by the U.S. Geological Survey began in December 1993. The ground-water level, measured in a production well located approximately 1,700 feet southeast of the Chromic Acid Pit site, has declined about 29.43 feet from 1982 to 1995. Depth to water at the Chromic Acid Pit site in September 1995 was 284.2 to 286.5 feet below land surface; ground-water flow at the water table is assumed to be toward the southeast. Ground-water samples collected from monitoring wells at the Chromic Acid Pit site during water year 1995 contained dissolved- solids concentrations of 481 to 516 milligrams per liter. Total chromium concentrations detected above the laboratory reporting limit ranged from 0.0061 to 0.030 milligram per liter; dissolved chromium concentrations ranged from 0.0040 to 0.010 milligram per liter. Nitrate as nitrogen concentrations ranged from 2.1 to 2.8 milligrams per

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

In vitro antimicrobial activity of Medilox® super-oxidized water.

PubMed

Gunaydin, Murat; Esen, Saban; Karadag, Adil; Unal, Nevzat; Yanik, Keramettin; Odabasi, Hakan; Birinci, Asuman

2014-07-14

Super-oxidized water is one of the broad spectrum disinfectants, which was introduced recently. There are many researches to find reliable chemicals which are effective, inexpensive, easy to obtain and use, and effective for disinfection of microorganisms leading hospital infections. Antimicrobial activity of super-oxidized water is promising. The aim of this study was to investigate the in-vitro antimicrobial activity of different concentrations of Medilox® super-oxidized water that is approved by the Food and Drug Administration (FDA) as high level disinfectant. In this study, super-oxidized water obtained from Medilox® [Soosan E & C, Korea] device, which had been already installed in our hospital, was used. Antimicrobial activities of different concentrations of super-oxidized water (1/1, 1/2, 1/5, 1/10, 1/20, 1/50, 1/100) at different exposure times (1, 2, 5, 10, 30 min) against six ATCC strains, eight antibiotic resistant bacteria, yeasts and molds were evaluated using qualitative suspension test. Dey-Engley Neutralizing Broth [Sigma-Aldrich, USA] was used as neutralizing agent. Medilox® was found to be effective against all standard strains (Acinetobacter baumannii 19606, Escherichia coli 25922, Enterococcus faecalis 29212, Klebsiella pneumoniae 254988, Pseudomonas aeruginosa 27853, Staphylococcus aureus 29213), all clinical isolates (Acinetobacter baumannii, Escherichia coli, vancomycin-resistant Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, Bacillus subtilis, Myroides spp.), and all yeastsat 1/1 dilution in ≥1 minute. It was found to be effective on Aspergillus flavus at 1/1 dilution in ≥2 minutes and on certain molds in ≥5 minutes. Medilox® super-oxidized water is a broad spectrum, on-site producible disinfectant, which is effective on bacteria and fungi and can be used for the control of nosocomial infection.

Cs-137 in milk, vegetation, soil, and water near the former Soviet Union's Semipalatinsk Nuclear Test Site.

PubMed

Kakimov, Aitbek; Yessimbekov, Zhanibek; Kakimova, Zhainagul; Bepeyeva, Aigerim; Stuart, Marilyne

2016-03-01

The present study was carried out to evaluate Cs-137 activity concentration in soil, water, vegetation, and cow's milk at 10 locations within three regions (Abai, Ayaguz, and Urdzhar) to the southeast of the Semipalatinsk Nuclear Test Site (SNTS) in Kazakhstan. Cs-137 activity concentrations, determined using a pure Ge gamma-ray spectrometer, showed that, all samples collected did not exceed the National maximum allowable limits of 10,000 Bq/kg for soil, 100 Bq/kg for cow's milk, 74 Bq/kg for vegetation, and 11 Bq/kg for water. Cs-137 is, therefore, not considered a health hazard in these regions. The highest levels of contamination were found in the Abai region, where the highest activity concentration of Cs-137 was 18.0 ± 1.0 Bq/kg in soil, 7.60 ± 0.31 Bq/kg in cow's milk, 4.00 ± 0.14 Bq/kg in the vegetation, and 3.00 ± 0.24 Bq/kg in water. The lowest levels were measured within the Urdzhar region, where 4.00 ± 0.14 Bq/kg was found in the soil, 0.30 ± 0.02 Bq/kg in the cow's milk, 1.00 ± 0.03 Bq/kg in the vegetation, and 0.20 ± 0.02 Bq/kg in the water.

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

PubMed

Beuming, Thijs; Che, Ye; Abel, Robert; Kim, Byungchan; Shanmugasundaram, Veerabahu; Sherman, Woody

2012-03-01

Water plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high-energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site-free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high-energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure-based drug design efforts. Copyright © 2011 Wiley Periodicals, Inc.

Pathogen Treatment Guidance and Monitoring Approaches fro On-Site Non-Potable Water Reuse

EPA Science Inventory

On-site non-potable water reuse is increasingly used to augment water supplies, but traditional fecal indicator approaches for defining and monitoring exposure risks are limited when applied to these decentralized options. This session emphasizes risk-based modeling to define pat...

Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

USGS Publications Warehouse

Warren, Ean; Bekins, Barbara A.

2015-01-01

Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150–200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

Be Water Wise.

ERIC Educational Resources Information Center

Birch, Sandra K.; Pettus, Alvin M.

Various topics on water and water conservation are discussed, each general topic followed by a student activity. Topics include: (1) importance of water; (2) water in the environment; (3) getting water to and from homes (making water usable; treating wastewater; on-site systems, including water wells and septic tanks); (4) relationship between…

Impact of zeolite aging in hot liquid water on activity for acid-catalyzed dehydration of alcohols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vjunov, Aleksei; Derewinski, Miroslaw A.; Fulton, John L.

The catalytic performance of zeolite in aqueous medium depends on a multitude of factors, such as the concentration and distribution of active sites and framework integrity. Al K–edge extended X–ray absorption fine structure and 27Al MAS NMR spectroscopies in combination with DFT calculations are used to determine the distribution of tetrahedral Al sites both qualitatively and quantitatively for both parent and 48 h 160 ºC water treated HBEA catalysts. There is no evidence of Al coordination modification after aging in water. The distribution and concentration of Al T–sites, active centers for the dehydration of cyclohexanol, do not markedly impact themore » catalytic performance in water, because the Brønsted acidic protons are present in the form of hydrated hydronium ions and thus have very similar acid properties. The results suggest that all Brønsted acid sites are equally active in aqueous medium. The decrease of zeolite catalytic performance after water treatment is attributed to the reduced concentration of Brønsted acid sites. Increasing the stability of pore walls and decreasing the rate of Si–O–Si group hydrolysis may result in improved apparent zeolite catalytic performance in aqueous medium. Authors thank B. W. Arey (PNNL) for HIM measurements, T. Huthwelker for support during Al XAFS measurements at the Swiss Light Source (PSI, Switzerland), J. Z. Hu and S. D. Burton (PNNL) for support during NMR experiments. This work was supported by the U. S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. MD acknowledges support by the Materials Synthesis and Simulation Across Scales (MS3 Initiative) conducted under Laboratory Directed Research & Development Program at PNNL. HIM imaging and NMR experiments were performed at the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the DOE Office of Science, Office of

Improving surface-subsurface water budgeting for Brownfield study sites using high resolution satellite imagery

NASA Astrophysics Data System (ADS)

Dujardin, J.; Boel, S.; Anibas, C.; Batelaan, O.; Canters, F.

2009-04-01

Countries around the world have problems with contaminated brownfield sites as resulting from a relatively anarchic economical and industrial development during the 19th and 20th centuries. Since a few decades policy makers and stakeholders have become more aware of the risk posed by these sites because some of these sites present direct public hazards. Water is often the main vector of the mobility of contaminants. In order to propose remediation measures for the contaminated sites, it is required to describe and to quantify as accurately as possible the surface and subsurface water fluxes in the polluted site. In this research a modelling approach with integrated remote sensing analysis has been developed for accurately calculating water and contaminant fluxes on the polluted sites. Groundwater pollution in urban environments is linked to patterns of land use, so to identify the sources of contamination with great accuracy in urban environments it is essential to characterize the land cover in a detailed way. The use of high resolution spatial information is required because of the complexity of the urban land use. An object-oriented classification approach applied on high resolution satellite data has been adopted. Cluster separability analysis and visual interpretation of the image objects belonging to each cluster resulted in the selection of 8 land-cover categories (water, bare soil, meadow, mixed forest, grey urban surfaces, red roofs, bright roofs and shadow).To assign the image objects to one of the 8 selected classes a multiple layer perceptron (MLP) approach was adopted, using the NeuralWorks Predict software. After a post-classification shadow removal and a rule-based classification enhancement a kappa-value of 0.86 was obtained. Once the land cover was characterized, the groundwater recharge has been simulated using the spatially distributed WetSpass model and the subsurface water flow was simulated with GMS 6.0 in order to identify and budget the

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.

Uranium isotopes in well water samples as drinking sources in some settlements around the Semipalatinsk Nuclear Test Site, Kazakhstan.

PubMed

Yamamoto, Masayoshi; Tomita, Junpei; Sakaguchi, Aya; Ohtsuka, Yoshihito; Hoshi, Masaharu; Apsalikov, Kazbek N

Radiochemical results of U isotopes ( 234 U, 235 U and 238 U) and their activity ratios are reported for well waters as local sources of drinking waters collected from the ten settlements around the Semipalatinsk Nuclear Test Site (SNTS), Kazakhstan. The results show that 238 U varies widely from 3.6 to 356 mBq/L (0.3-28.7 μg/L), with a factor of about 100. The 238 U concentrations in some water samples from Dolon, Tailan, Sarzhal and Karaul settlements are comparable to or higher than the World Health Organization's restrictive proposed guideline of 15 μg (U)/L. The 234 U/ 238 U activity ratios in the measured water samples are higher than 1, and vary between 1.1 and 7.9, being mostly from 1.5 to 3. The measured 235 U/ 238 U activity ratios are around 0.046, indicating that U in these well waters is of natural origin. It is probable that the elevated concentration of 238 U found in some settlements around the SNTS is not due to the close-in fallout from nuclear explosions at the SNTS, but rather to the intensive weathering of rocks including U there. The calculated effective doses to adults resulting from consumption of the investigated waters are in the range 1.0-18.7 μSv/y. Those doses are lower than WHO and IAEA reference value (100 μSv/y) for drinking water.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.

PubMed

Zastrow, Melissa L; Pecoraro, Vincent L

2013-04-17

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

Active Sites Environmental Monitoring Program: Mid-FY 1991 report

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 ofmore » vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.« less

Presence of active pharmaceutical ingredients in the continuum of surface and ground water used in drinking water production.

PubMed

Ahkola, Heidi; Tuominen, Sirkku; Karlsson, Sanja; Perkola, Noora; Huttula, Timo; Saraperä, Sami; Artimo, Aki; Korpiharju, Taina; Äystö, Lauri; Fjäder, Päivi; Assmuth, Timo; Rosendahl, Kirsi; Nysten, Taina

2017-12-01

Anthropogenic chemicals in surface water and groundwater cause concern especially when the water is used in drinking water production. Due to their continuous release or spill-over at waste water treatment plants, active pharmaceutical ingredients (APIs) are constantly present in aquatic environment and despite their low concentrations, APIs can still cause effects on the organisms. In the present study, Chemcatcher passive sampling was applied in surface water, surface water intake site, and groundwater observation wells to estimate whether the selected APIs are able to end up in drinking water supply through an artificial groundwater recharge system. The API concentrations measured in conventional wastewater, surface water, and groundwater grab samples were assessed with the results obtained with passive samplers. Out of the 25 APIs studied with passive sampling, four were observed in groundwater and 21 in surface water. This suggests that many anthropogenic APIs released to waste water proceed downstream and can be detectable in groundwater recharge. Chemcatcher passive samplers have previously been used in monitoring several harmful chemicals in surface and wastewaters, but the path of chemicals to groundwater has not been studied. This study provides novel information on the suitability of the Chemcatcher passive samplers for detecting APIs in groundwater wells.

Ground-water quality in the vicinity of landfill sites, southern Franklin County, Ohio

USGS Publications Warehouse

De Roche, J.T.; Razem, A.C.

1981-01-01

The hydrogeology and ground-water quality in the vicinity of five landfills in southern Franklin County, Ohio, were investigated by use of data obtained from 46 existing wells, 1 seep, 1 surface-water site, and 1 leachate-collection site. Interpretation was based on data from the wells, a potentiometric-surface map, and chemical analyses. Four of the five landfills are in abandoned sand and gravel pits. Pumping of water from a quarry near the landfills has modified the local ground-water flow pattern, increased the hydraulic gradient, and lowered the water table. Ground water unaffected by the landfills is a hard, calcium bicarbonate type with concentrations of dissolved iron and dissolved sulfate as great as 3.0 milligrams per liter and 200 milligrams per liter, respectively. Water sampled from wells downgradient from two landfills shows an increase in sodium, chloride, and other constituents. The change in water quality cannot be traced directly to the landfills, however, because of well location and the presence of other potential sources of contamination. Chemical analysis of leachate from a collection unit at one landfill shows significant amounts of zinc, chromium, copper, and nickel, in addition to high total organic carbon, biochemical oxygen demand, and organic nitrogen. Concentrations of chloride, iron, lead, manganese and phenolic compounds exceed Ohio Environmental Protection Agency Water Quality Standards for drinking water. Water from unaffected wells within the study area have relatively small amounts of these constituents. (USGS)

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

PubMed

Mlýnský, Vojtěch; Walter, Nils G; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel

2015-01-07

The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg(2+) ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg(2+) ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg(2+) ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The deprotonation of the U-1(2'-OH) nucleophile and the nucleophilic attack of the resulting U-1(2'-O(-)) on the scissile phosphodiester are found to be separate steps, as deprotonation precedes the nucleophilic attack. This sequential mechanism of the HDV ribozyme differs from the concerted nucleophilic activation and attack suggested for the hairpin ribozyme. We estimate the pKa of the U-1(2'-OH) group to range from 8.8 to 11.2, suggesting that it is lowered by several units from that of a free ribose, comparable to and most likely smaller than the pKa of the solvated active site Mg(2+) ion. Our results thus support the notion that the structure of the HDV ribozyme, and particularly the positioning of the active site Mg(2+) ion, facilitate deprotonation and activation of the 2'-OH nucleophile.

Aquifer recharge with reclaimed water in the Llobregat Delta. Laboratory batch experiments and field test site.

NASA Astrophysics Data System (ADS)

Tobella, J.

2010-05-01

Summary Spain, as most other Mediterranean countries, faces near future water shortages, generalized pollution and loss of water dependent ecosystems. Aquifer recharge represents a promising option to become a source for indirect potable reuse purposes but presence of pathogens as well as organic and inorganic pollutants should be avoided. To this end, understanding the processes of biogeochemical degradation occurring within the aquifer during infiltration is capital. A set of laboratory batch experiments has been assembled in order to assess the behaviour of selected pesticides, drugs, estrogens, surfactant degradation products, biocides and phthalates under different redox conditions. Data collected during laboratory experiments and monitoring activities at the Sant Vicenç dels Horts test site will be used to build and calibrate a numerical model (i) of the physical-chemical-biochemical processes occurring in the batches and (ii) of multicomponent reactive transport in the unsaturated/saturated zone at the test site. Keywords Aquifer recharge, batch experiments, emerging micropollutants, infiltration, numerical model, reclaimed water, redox conditions, Soil Aquifer Treatment (SAT). 1. Introduction In Spain, the Llobregat River and aquifers, which supply water to Barcelona, have been overexploited for years and therefore, suffer from serious damages: the river dries up on summer, riparian vegetation has disappeared and seawater has intruded the aquifer. In a global context, solutions to water stress problems are urgently needed yet must be sustainable, economical and safe. Recent developments of analytical techniques detect the presence of the so-called "emerging" organic micropollutants in water and soils. Such compounds may affect living organisms when occurring in the environment at very low concentrations (microg/l or ng/l). In wastewater and drinking water treatment plants, a remarkable removal of these chemicals from water can be obtained only using

Quality of surface water at selected sites in the Suwannee River basin, Florida

USGS Publications Warehouse

Coffin, J.E.

1982-01-01

This report presents the results of analyses of water-quality samples collected from 14 surface-water sites in the Suwannee River basin in Florida from January through December 1980. The analyses of samples collected routinely included: nutrients, total organic carbon, and 5-day biochemical oxygen demand, bimonthly; and trace metals, annually. The array of constituents sampled was expanded in October 1978 at three of the original nine stations to provide quality-of-water information for streams draining an industrial area: Rocky Creek near Belmont, Hunter Creek near Belmont, and Swift Creek at Facil. Data collected at these three sites now include: major chemical constituents, six times per year: radium-226, two times per year; and trace metals, one time per year. These constituents are determined in addition to nutrients, total organic carbon, and bio-chemical oxygen demand which continue to be analyzed six times per year. All results of analyses of the water-quality samples collected from January through December 1980 remained within, or near, previously measured ranges and water-quality fluctuations were similar to those noted from data collected since 1971. (USGS)

Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.

PubMed

Sun, Zhizeng; Mehta, Shrenik C; Adamski, Carolyn J; Gibbs, Richard A; Palzkill, Timothy

2016-09-12

CphA is a Zn(2+)-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function.

Rainfall, evapotranspiration, total soil-water potential, and soil-water content at a sagebrush site and a replacement-vegetation site near Fort Defiance, Arizona, 1989-91

USGS Publications Warehouse

Thomas, C.L.

1994-01-01

The Navajo Nation Forestry Department established a growth of four species of native grasses and two species of native shrubs on formerly sagebrush- covered land about 6 miles north of Fort Defiance, Arizona. The native grasses and shrubs grew under conditions of natural precipitation and soil fertility. This provided alternate grazing areas for tribal livestock. Tribal livestock previously had been grazed on timber-producing land, killing seedlings planted for reforestation. Rainfall, evapotranspiration, total soil-water potential, and soil-water content at a sagebrush site and a site planted with grasses and shrubs north Fort Defiance, Arizona were monitored to document hydrologic conditions during the experiment. Daily rainfall during the April through November 1989- 91 data-collection period ranged from 0 to 1.21 inches (0 to 30.7 millimeters). Evapotranspiration during the data-collection period generally ranged from about 0.5 to 2 millimeters per day (0.02 to 0.08 inch per day), increasing to 2 to 5 millimeters per day (0.08 to 0.20 inch per day) after rainfall. The total soil-water content ranged from 5.7 to 65.9 percent. Soils were wetter during the April data-collection period than during the November data-collection periods.

Active site and laminarin binding in glycoside hydrolase family 55

DOE PAGES

Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; ...

2015-03-09

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. 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 themore » 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. Furthermore, application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.« less

Quality-Assurance Plan for Water-Quality Activities in the USGS Ohio Water Science Center

USGS Publications Warehouse

Francy, Donna S.; Shaffer, Kimberly H.

2008-01-01

In accordance with guidelines set forth by the Office of Water Quality in the Water Resources Discipline of the U.S. Geological Survey, a quality-assurance plan has been written for use by the Ohio Water Science Center in conducting water-quality activities. This quality-assurance plan documents the standards, policies, and procedures used by the Ohio Water Science Center for activities related to the collection, processing, storage, analysis, and publication of water-quality data. The policies and procedures documented in this quality-assurance plan for water-quality activities are meant to complement the Ohio Water Science Center quality-assurance plans for water-quality monitors, the microbiology laboratory, and surface-water and ground-water activities.

Diameter growth and phenology of trees on sites with high water tables

Treesearch

D.C. McClurkin

1965-01-01

On a site where the water table always was within the root zone, thinning had little effect on diameter growth of white ash or sweetgum but increased the growth of baldcypress. Thinning did not extend durating of growth into the fall, nor was growth related to seasonal fluctuations in the water table. In ash and sweetgum, growth initiation seemed related to soil...

Conformational coupling between the active site and residues within the K(C)-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase.

PubMed

Ahn, Young O; Mahinthichaichan, Paween; Lee, Hyun Ju; Ouyang, Hanlin; Kaluka, Daniel; Yeh, Syun-Ru; Arjona, Davinia; Rousseau, Denis L; Tajkhorshid, Emad; Adelroth, Pia; Gennis, Robert B

2014-10-21

The respiratory chains of nearly all aerobic organisms are terminated by proton-pumping heme-copper oxygen reductases (HCOs). Previous studies have established that C-family HCOs contain a single channel for uptake from the bacterial cytoplasm of all chemical and pumped protons, and that the entrance of the K(C)-channel is a conserved glutamate in subunit III. However, the majority of the K(C)-channel is within subunit I, and the pathway from this conserved glutamate to subunit I is not evident. In the present study, molecular dynamics simulations were used to characterize a chain of water molecules leading from the cytoplasmic solution, passing the conserved glutamate in subunit III and extending into subunit I. Formation of the water chain, which controls the delivery of protons to the K(C)-channel, was found to depend on the conformation of Y241(Vc), located in subunit I at the interface with subunit III. Mutations of Y241(Vc) (to A/F/H/S) in the Vibrio cholerae cbb3 eliminate catalytic activity, but also cause perturbations that propagate over a 28-Å distance to the active site heme b3. The data suggest a linkage between residues lining the K(C)-channel and the active site of the enzyme, possibly mediated by transmembrane helix α7, which contains both Y241(Vc) and the active site cross-linked Y255(Vc), as well as two CuB histidine ligands. Other mutations of residues within or near helix α7 also perturb the active site, indicating that this helix is involved in modulation of the active site of the enzyme.

Facile on-site detection of substituted aromatic pollutants in water using thin layer chromatography combined with surface-enhanced Raman spectroscopy.

PubMed

Li, Dawei; Qu, Lulu; Zhai, Wenlei; Xue, Jinqun; Fossey, John S; Long, Yitao

2011-05-01

A novel facile method for on-site detection of substituted aromatic pollutants in water using thin layer chromatography (TLC) combined with surface-enhanced Raman spectroscopy (SERS) was explored. Various substituted aromatics in polluted water were separated by a convenient TLC protocol and then detected using a portable Raman spectrometer with the prepared silver colloids serving as SERS-active substrates. The effects of operating conditions on detection efficacy were evaluated, and the application of TLC-SERS to on-site detection of artificial and real-life samples of aromatics/polluted water was systematically investigated. It was shown that commercially available Si 60-F(254) TLC plates were suitable for separation and displayed low SERS background and good separation efficiency, 2 mM silver colloids, 20 mM NaCl (working as aggregating agent), 40 mW laser power, and 50 s intergration time were appropriate for the detection regime. Furthermore, qualitative and quantitative detection of most of substituted aromatic pollutants was found to be readily accomplished using the developed TLC-SERS technique, which compared well with GC-MS in terms of identification ability and detection accuracy, and a limit of detection (LOD) less than 0.2 ppm (even at ppb level for some analytes) could be achieved under optimal conditions. The results reveal that the presented convenient method could be used for the effective separation and detection of the substituted aromatic pollutants of water on site, thus reducing possible influences of sample transportation and contamination while shortening the overall analysis time for emergency and routine monitoring of the substituted aromatics/polluted water.

Ground-water contamination by crude oil at the Bemidji, Minnesota, research site; US Geological Survey Toxic Waste--ground-water contamination study

USGS Publications Warehouse

Hult, M.F.

1984-01-01

The project site is near Bemidji in northern Minnesota where an accidental spill of 10,500 barrels of crude oil occurred when a pipeline broke on August 20, 1979. Regulatory and remedial actions have been completed. The site is in a remote area with neither man-made hydraulic stresses nor other anthropogenic sources of the compounds of interest. The spill is in the recharge area of a local flow system that discharges to a small closed lake approximately 1,000 feet down the hydraulic gradient. The aquifer is pitted outwash dissected by younger glacial channels and is underlain by poorly permeable till at a depth of about 80 feet. Ground water dissolves oil floating on the water table under the spill site and moves toward the lake. At the water table, ground water enters the lake through lacustrine sediments; at depth, flow may be underneath the lake through the outwash. Contaminant transport has been as rapid as 4 feet per day based on the rate of movement of contaminants monitored through wells installed within a few days of the spill, but average rates are undoubtedly much less.

Fraser River watershed, Colorado : assessment of available water-quantity and water-quality data through water year 1997

USGS Publications Warehouse

Apodaca, Lori Estelle; Bails, Jeffrey B.

1999-01-01

The water-quantity and water-quality data for the Fraser River watershed through water year 1997 were compiled for ground-water and surface-water sites. In order to assess the water-quality data, the data were related to land use/land cover in the watershed. Data from 81 water-quantity and water-quality sites, which consisted of 9 ground-water sites and 72 surface-water sites, were available for analysis. However, the data were limited and frequently contained only one or two water-quality analyses per site.The Fraser River flows about 28 miles from its headwaters at the Continental Divide to the confluence with the Colorado River. Ground-water resources in the watershed are used for residential and municipal drinking-water supplies. Surface water is available for use, but water diversions in the upper parts of the watershed reduce the flow in the river. Land use/land cover in the watershed is predominantly forested land, but increasing urban development has the potential to affect the quantity and quality of the water resources.Analysis of the limited ground-water data in the watershed indicates that changes in the land use/land cover affect the shallow ground-water quality. Water-quality data from eight shallow monitoring wells in the alluvial aquifer show that iron and manganese concentrations exceeded the U.S. Environmental Protection Agency secondary maximum contaminant level. Radon concentrations from these monitoring wells exceeded the U.S. Environmental Protection Agency proposed maximum contaminant level. The proposed radon contaminant level is currently being revised. The presence of volatile organic compounds at two monitoring wells in the watershed indicates that land use affects the shallow ground water. In addition, bacteria detected in three samples are at concentrations that would be a concern for public health if the water was to be used as a drinking supply. Methylene blue active substances were detected in the ground water at some sites and are a

Chemical and Isotopic Characterization of Surface Water and Active Layer Pore Water in a Tundra Landscape, Barrow, Alaska, USA

NASA Astrophysics Data System (ADS)

Newman, B. D.; Heikoop, J. M.; Throckmorton, H.; Arendt, C. A.; Graham, D. E.; Wilson, C. J.; Wullschleger, S. D.

2016-12-01

Studies conducted in the Barrow Environmental Observatory as part of the Next Generation Ecosystem Experiment (NGEE) - Arctic have demonstrated significant chemical and isotopic variability in surface water and active layer pore water of polygonal terrain located between drained thaw lake basins (DTLBs). In this study, we report on chemical and isotopic variation at the broader landscape scale that includes different age DTLBs and associated drainages, extant thaw lakes, and interlake regions. Fingerprint diagrams of major elements show a broader range of variation at the landscape scale relative to polygonal terrain. ANOVA analysis suggests that many of the polygonal and broader landscape scale sites have similar chemistry, suggesting a reasonably high degree of hydrologic connectivity. The most significant site-specific differences include higher d18O and d2H, indicative of evaporative conditions, of surface and active layer water from an ancient (2000- 5500 BP) DTLB that comprises a shallow basin with no outlets. Significantly higher Cl, Ca, Fe, Mg, Na, As, Mn and Sr concentrations were also found in pore waters collected immediately above the frost table at two locations. The first location is a small drainage leading from an area of polygonal terrain into an adjacent slough, while the second is upgradient of the estuarine terminus of a drainage sourced from a medium-aged DTLB (50- 300 BP). Higher concentrations at the frost table suggests a mechanism related to periodic freezing and thawing of the transition zone above permafrost or permafrost degradation. Alternative conceptual models, including the presence of a marine signal or the influence of cryopegs (brine layers within permafrost), will also be considered. Characterization of present day Arctic hydrology and chemistry at different scales is important for Earth Systems Models and for predicting hydrogeochemical change associated with landscape evolution due to future permafrost degradation.

Executive summary: Weldon Spring Site Environmental Report for calendar year 1992. Weldon Spring Site Remedial Action Project, Weldon Spring, Missouri

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1993-06-01

This report has been prepared to provide information about the public safety and environmental protection programs conducted by the Weldon Spring Site Remedial Action Project. The Weldon Spring site is located in southern St. Charles County, Missouri, approximately 48 km (30 mi) west of St. Louis. The site consists of two main areas, the Weldon Spring Chemical Plant and raffinate pits and the Weldon Spring Quarry. The objectives of the Site Environmental Report are to present a summary of data from the environmental monitoring program, to characterize trends and environmental conditions at the site, and to confirm compliance with environmentalmore » and health protection standards and requirements. The report also presents the status of remedial activities and the results of monitoring these activities to assess their impacts on the public and environment. The scope of the environmental monitoring program at the Weldon Spring site has changed since it was initiated. Previously, the program focused on investigations of the extent and level of contaminants in the groundwater, surface waters, buildings, and air at the site. In 1992, the level of remedial activities required monitoring for potential impacts of those activities, particularly on surface water runoff and airborne effluents. This report includes monitoring data from routine radiological and nonradiological sampling activities. These data include estimates of dose to the public from the Weldon Spring site; estimates of effluent releases; and trends in groundwater contaminant levels. Also, applicable compliance requirements, quality assurance programs, and special studies conducted in 1992 to support environmental protection programs are reviewed.« less

Stormwater runoff water quality evaluation and management program for hazardous chemical sites: Development issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, G.F.; Jones-Lee, A.

1998-12-31

The deficiencies in the typical stormwater runoff water quality monitoring from hazardous chemical sites and an alternative approach (Evaluation Monitoring) for monitoring that shifts the monitoring program from periodic sampling and analysis of stormwater runoff for a suite of chemical parameters to examining the receiving waters to determine what, if any, water quality use impairments are occurring due to the runoff-associated constituents is presented in this paper. Rather than measuring potentially toxic constituents such as heavy metals in runoff, the monitoring program determines whether there is aquatic life toxicity in the receiving waters associated with the stormwater runoff. If toxicitymore » is found, its cause is determined and the source of the constituents causing the toxicity is identified through forensic analysis. Based on this information, site-specific, technically valid stormwater runoff management programs can be developed that will control real water quality impacts caused by stormwater runoff-associated constituents.« less

All the catalytic active sites of MoS 2 for hydrogen evolution

DOE PAGES

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

2016-11-29

MoS 2 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 MoS 2, 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 tomore » 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 MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.

PubMed

Chen, Zhi-Wei; Datta, Saumen; Dubois, Jennifer L; Klinman, Judith P; Mathews, F Scott

2010-08-31

The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

SITE CHARACTERIZATION TO SUPPORT DEVELOPMENT OF CONCEPTUAL SITE MODELS AND TRANSPORT MODELS FOR MONITORING CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

Classroom Activities about Water and Climate Change

NASA Astrophysics Data System (ADS)

Rodriguez, M.

2012-04-01

The purpose of this activity is to demonstrate practical work and experiments in the classroom, with students on Water: Water is the most neccesary Earth's resource, although it is decreasing because many human activities are changing its quality and its availability. The activity is designed in order to recreate experiments, simulations, and determine the aspects of the problematic environment currently plaguing our planet, especially those related to water and climate change. The selected activities have to be easy to make, and easy to understand. Each activity will be illustrated, explained and described using pictures and short texts, so teachers could replay them in their classroom. 1. Simulation of the Ocean Water Currents Convection to understand the heat distribution in our planet. 2. Ocean Water Stratification According to Water Salinity. We can understand the behaviour of water when we mix water from different densities 3. Melting of the Arctic and Antarctic Polar Caps. In this experiment, we can see the consequences of changing environment and climate conditions as it pertains to ice and our polar ice caps. We want to show the different behaviours of continental and floating ice and to evaluate the consequences of their melting. 4. Detecting water pollution. Here, we can analyse some water patterns and get to know the existence or absence of pollutants in the water, as well as learning how to determine its pH level, hardness, nitrogen composition, bacteria content and more. 5. Creating a home treatment. We show the necessity to preserve the water quality through a suitable treatment.

Ground-water contamination by crude oil at the Bemidji, Minnesota, research site- An introduction: Chapter A in Ground-water contamination by crude oil at the Bemidji, Minnesota, research site; US Geological Survey Toxic Waste--ground-water contamination study

USGS Publications Warehouse

1984-01-01

The U.S. Geological Survey has begun a research project to improve understanding of the mobilization, transport, and fate of petroleum contaminants in the shallow subsurface and to use this understanding to develop predictive models of contaminant behavior. The project site is near Bemidji in northern Minnesota where an accidental spill of 10,500 barrels of crude oil occurred when a pipeline broke on August 20, 1979. Regulatory and remedial actions have been completed. The site is in a remote area with neither man-made hydraulic stresses nor other anthropogenic sources of the compounds of interest. The spill is in the recharge area of a local flow system that discharges to a small closed lake approximately 1,000 feet down the hydraulic gradient. The aquifer is pitted outwash dissected by younger glacial channels and is underlain by poorly permeable till at a depth of about 80 feet. Ground water dissolves oil floating on the water table under the spill site and moves toward the lake. At the water table, ground water enters the lake through lacustrine sediments; at depth, flow may be underneath the lake through the outwash. Contaminant transport has been as rapid as 4 feet per day based on the rate of movement of contaminants monitored through wells installed within a few days of the spill, but average rates are undoubtedly much less. 

WATER: Water Activities Teaching Environmental Responsibility: Teacher Resource, Environmental Science.

ERIC Educational Resources Information Center

Kramer, Ed, Ed.; And Others

This activity book was developed as part of an effort to protect water quality of the Stillwater River, Ohio, through a Watershed Protection Project. It is designed to raise teachers' and students' awareness and trigger a sense of stewardship towards the preservation of water resources. The activities are generally appropriate for elementary age…

GEO Water Cycle Activities and Plans

NASA Astrophysics Data System (ADS)

Lawford, R.; Koike, T.; Ishida, C.; Grabs, W.

2008-12-01

The Group on Earth Observations (GEO) consists of more than 70 countries and 40 international organizations which are working together to develop the Global Earth Observation System of Systems (GEOSS). Since its launch in 2004, GEO has stimulated a wide range of activities related to data systems and their architecture, the development of science and technology to support observational programs, user interactions and interfaces, and capacity building. GEO tasks directed at Water Resources Management, one of the nine GEO Societal Benefit areas, are an integral part of these developments. They draw heavily upon the activities of the Integrated Global Water Cycle Observations (IGWCO) theme and on the activities and infrastructure provided through GEO and its committees. Within the GEO framework the water related activities have been focused on four specific tasks namely integrated data set development; information for floods, droughts and water management; water quality, and capacity building. Currently these efforts are being facilitated by the IGWCO theme that was formed under the former Integrated Global Observing Strategy Partnership (IGOS-P). With the dissolution of this partnership, other mechanisms, including the GEO Water Cycle Community of Practice, are being considered as new opportunitites for coordinating the work of the theme and the water-related GEO tasks. This talk provides a description of the GEO water tasks and reviews the progress that has been made in addressing them. It also provides a perspective on new opportunities and briefly describes some of the mechanisms, such as the Water Cycle Community of Practice, that could be expanded to coordinate a more comprehensive set of water tasks and greater community involvement.

Screening of multiple hormonal activities in surface water and sediment from the Pearl River system, South China, using effect-directed in vitro bioassays.

PubMed

Zhao, Jian-Liang; Ying, Guang-Guo; Yang, Bin; Liu, Shan; Zhou, Li-Jun; Chen, Zhi-Feng; Lai, Hua-Jie

2011-10-01

This paper reports screening of multiple hormonal activities (estrogenic and androgenic activities, antiestrogenic and antiandrogenic activities) for surface water and sediment from the Pearl River system (Liuxi, Zhujiang, and Shijing rivers) in South China, using in vitro recombinant yeast bioassays. The detection frequencies for estrogenic and antiandrogenic activities were both 100% in surface water and 81 and 93% in sediment, respectively. The levels of estrogenic activity were 0.23 to 324 ng 17β-estradiol equivalent concentration (EEQ)/L in surface water and 0 to 101 ng EEQ/g in sediment. Antiandrogenic activities were in the range of 20.4 to 935 × 10(3) ng flutamide equivalent concentration (FEQ)/L in surface water and 0 to 154 × 10(3) ng FEQ/g in sediment. Moreover, estrogenic activity and antiandrogenic activity in sediment showed good correlation (R(2) = 0.7187), suggesting that the agonists of estrogen receptor and the antagonists of androgen receptor co-occurred in sediment. The detection frequencies for androgenic and antiestrogenic activities were 41 and 29% in surface water and 61 and 4% in sediment, respectively. The levels of androgenic activities were 0 to 45.4 ng dihydrotestosterone equivalent concentration (DEQ)/L in surface water, and the potency was very weak in the only detected sediment site. The levels of antiestrogenic activity were 0 to 1,296 × 10(3) ng tamoxifen equivalent concentration (TEQ)/L in surface water and 0 to 89.5 × 10(3) ng TEQ/g in sediment. The Shijing River displayed higher levels of hormonal activities than the Zhujiang and Liuxi rivers, indicating that the Shijing River had been suffering from heavy contamination with endocrine-disrupting chemicals. The equivalent concentrations of hormonal activities in some sites were greater than the lowest-observed-effect concentrations reported in the literature, suggesting potential adverse effects on aquatic organisms. Copyright © 2011 SETAC.

Water-quality and hydrologic conditions at a site of ground-water contamination by volatile organic compounds, South Grafton, Massachusetts, September and October 1994

USGS Publications Warehouse

DiSimone, L.A.; Barlow, P.M.

1995-01-01

Ground-water quality and hydrologic data were collected at a site contaminated by volatile organic compounds (VOCs) in South Grafton, Massachusetts, during September and October 1994. The VOCs have formed a plume of contaminated ground water at an abandoned textile mill adjacent to the Blackstone River. Concentrations of total VOCs in the plume ranged from less than 1 to more than 40,000 micrograms per liter. Trichloroethylene (TCE) was the primary chlorinated contaminant, comprising as much as 98 percent of the total VOCs. The highest concentration, 43,000 micrograms per liter, was higher than any previously measured concentration at the site; however, the maximum extent and distribution of concentrations in the VOC plume in September 1994 was similar to that found in July 1993 and in earlier rounds of sampling. In addition to TCE, 1,2-dichloroethene (1,2-DCE) and vinyl chloride were detected at most sites. Spatial and temporal changes in concentrations of TCE, 1,2-DCE, and vinyl chloride are consistent with the hypothesis that TCE biodegradation was the source of 1,2-DCE and vinyl chloride. Ground water at the site contained low to moderately high concentrations of dissolved solids (44 to 406 milligrams per liter), had a moderately high specific conductance (155 to 670 microsiemens per centimeter at 25 degrees Celsius), and was slightly acidic (pH=5.9 to 7.0). Concentrations of the major ions-calcium, sodium, chloride, and sulfate-were not related to VOC concentrations. Dissolved-oxygen concentrations were low (0 to 2 milligrams per liter) throughout most of the aquifer. Distribution of nitrogen species, iron, and manganese indicates that zones of varying oxidation-reduction potential were present in the aquifer. Concentrations of trace metals other than iron or manganese, including arsenic, cadmium, chromium, and copper, generally were less than analytical detection limits. Stream stage in the Blackstone River at the site during September and October 1994

Very Tiny Rocks: Site-Specific, Size-Dependent Reaction Kinetics at Nanoparticle-Water Interfaces

NASA Astrophysics Data System (ADS)

Rustad, J. R.

2008-12-01

One of the most fundamental challenges in geochemistry is to be able to understand the rates and mechanisms of elementary reactions that describe chemical processes occurring at mineral-water interfaces. One of the reasons for the primitive conceptual state of reaction kinetics in solid earth geochemistry is that it is very difficult to identify defensible elementary reactions where theoretical predictions can be made and the results can tested experimentally at the same length and time scale of the prediction. For example, the most fundamental predictor of complexation kinetics in aqueous solution is the characteristic water exchange rate, which are well known for the aquo ions and vary by 20 orders of magnitude even for simple trivalent ions. In contrast, for interfacial reactions, it was not even known whether water exchange rates were faster or slower than equivalent metal sites in solution, prohibiting any quantitive understanding of mineral reaction kinetics at the molecular level. Recent advances in synthesis and characterization of materials at nanometer length scales has been able to bridge the gap in scale, and nanometer-sized minerals have given us our first quantitative understanding of elementary reaction rates for fundamental processes involving water and hydroxide exchange reactions. I describe the results of molecular dynamics calculation and experimental measurement of the rates of water, hydroxide, and proton exchange reactions on nanoparticle surfaces. The calculations already show that transition state theory is completely inadequate to understand the rates of even the simplest elementary reactions. Furthermore, the mechanistic implications of rate parameters such as activation volume and activation enthalpy may be different in moving from aquo ions to interfaces. Is a molecular understanding of geochemical processes really needed? One might have asked a biologist at the turn of the century whether studying the structure of proteins would ever

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Water-Quality Characteristics for Selected Sites Within the Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, February 2004-September 2005

USGS Publications Warehouse

Thomas, Judith C.; Lutz, Michelle A.; Bruce, Jennifer L.; Graczyk, David J.; Richards, Kevin D.; Krabbenhoft, David P.; Westenbroek, Stephen M.; Scudder, Barbara C.; Sullivan, Daniel J.; Bell, Amanda H.

2007-01-01

The Milwaukee Metropolitan Sewerage District (MMSD) Corridor Study is a three-phase project designed to improve the understanding of water resources in the MMSD planning area to assist managers and policy makers in their decisions. Phase I of the Study involved the compilation of existing data from multiple agencies into a single database. These data were analyzed to identify spatial, temporal, and technological gaps in the planning area, and were used to develop Phase II of the Study. Phase II, the subject of this report, involved an intensive data-collection effort by the U.S. Geological Survey (USGS) in cooperation with MMSD (from February, 2004, through September, 2005). This phase addressed the data gaps identified in Phase I and completed a baseline assessment of water quality for selected stream and harbor sites in the MMSD planning area. This baseline assessment included evaluations of surface-water chemistry and microbial concentrations in the streams and harbor sites; additionally, stream sites were evaluated for discharge, sediment chemistry, fish-tissue chemistry, habitat, and the quality of biological communities (including fish, macroinvertebrates, and algae). In all, data were collected at 15 stream and 6 harbor sites within the MMSD planning area, including manual sampling and analysis for more than 220 water-quality properties and constituents at all 21 sites, stream-discharge data for 14 stream sites, and automated water-quality sampling at 4 stream sites. A bioassessment during autumn 2004 included collection of biologic-community data and stream-habitat data at wadeable streams. Quartiles of Phase II aggregate bioassessment rankings were used to divide the 14 wadeable stream sites into four groups to investigate relations between bioassessment data and site characteristic and water-quality data. Quartile numbers reflect relative water quality: quartile 1 contained sites where the bioassessment data indicated the least-degraded water quality

Chapter 12: Daily Patterns of Marbled Murrelet Activity at Inland Sites

Treesearch

Nancy L. Naslund; Brian P. O’Donnell

1995-01-01

Patterns in the daily activity of Marbled Murrelets (Brachyramphus marmoratus) at inland sites has been studied throughout their range from California to Alaska. Murrelets are most active at inland sites around dawn, and to a lesser degree, at dusk. Throughout their range, peak levels of activity (detections) occur in the hour around dawn, but...

Monitoring the Dynamics of Water Flow at a High-Mountain Permafrost Site Using Electrical Self-Potential Measurements

NASA Astrophysics Data System (ADS)

Kemna, A.; Weigand, M.; Wagner, F.; Hilbich, C.; Hauck, C.

2016-12-01

Flow of (liquid) water plays a crucial role in the dynamics of coupled thermo-hydro-mechanical processes in terrestrial permafrost systems. To better understand these processes in the active layer of permafrost regions, with the ultimate goal of adequately incorporating them in numerical models for improved scenario prediction, monitoring approaches offering high spatial and temporal resolution, areal coverage, and especially sensitivity to subsurface water flow, are highly desired. This particularly holds for high-mountain slopes, where strong variability in topography, precipitation, and snow cover, along with significant subsurface soil/rock heterogeneity, gives rise to complex spatio-temporal patterns of water flow during seasonal thawing and freezing periods. The electrical self-potential (SP) method is well known to, in theory, meeting the above monitoring demands by measuring the electrical streaming potential which is generated at the microscopic scale when water flows along electrically non-neutral interfaces. Despite its inherent sensitivity to subsurface water flow, the SP method has not yet been used for the monitoring of high-mountain permafrost sites. We here present first results from an SP monitoring survey conducted at the Schilthorn (2970 m asl) in the Bernese Alps, Switzerland, where SP data have been collected since September 2013 at a sampling rate of 10 min on a permanently installed array of 12 non-polarizing electrodes covering an area of 35 m by 15 m. While the SP time series exhibit systematic daily variations, with part of the signal clearly correlated with temperature, in particular in the snow-free periods, the largest temporal changes in the SP signal occur in spring, when the snow cover melts and thawing sets on in the active layer. The period of higher temporal SP variations continues until autumn, when the signal gradually returns to relatively low variations, coinciding with the freezing of the ground. Our results suggest that the

Geohydrology and ground-water quality at selected sites in Meade County, Kentucky, 1987-88

USGS Publications Warehouse

Mull, D.S.; Alexander, A.G.; Schultz, P.E.

1989-01-01

Meade County in north-central Kentucky is about 305 sq mi in size, and is underlain by thick beds of limestone and dolomite which are the principal sources of drinking water for about 8 ,500 residents. About half the area contains mature, karst terrain with abundant sinkholes, springs, and caves. Because of this karst terrain, groundwater is susceptible to rapid changes in water quality and contamination from human sources. Thirty-seven wells and 12 springs were selected as sampling points to characterize groundwater quality in the area. Water was analyzed for major anions and cations, nitrates, trace elements, and organic compounds. Water from selected sites was also analyzed for fecal species of coliform streptococci bacteria and total coliform content. Except for fluoride and lead, the water quality was within the range expected for carbonate aquifers.The fluoride content was significantly higher in water from wells than in water from springs. Concentrations of detectable lead ranged from 10 to 50 micrograms/L and had a median value of 7.5 microg/L. Dissolved solids ranged from 100 to 2,200 mg/L and the median value was 512 mg/L. Hardness ranged from 20 to 1,100 mg/L and the median value was 290 mg/L. Organic compounds detected by the gas chromatographic/flame ionization detection scans, did not indicate evidence of concentrations in excess of the current Federal drinking water standards. Analysis for specific organic compounds indicated that the presence of these compounds was associated with agricultural chemicals, usually pesticides. Total coliform content exceeded drinking water standards in water from all 12 springs and in 18 wells. Statistical analysis of the groundwater quality data indicates that the variance of the concentrations of fluoride and chloride may be attributed to the site type. There was strong correlation between hardness and dissolved solids, hardness and sulfate, and sulfate and dissolved solids. No apparent relations were detected

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

PubMed

Gerogiokas, G; Southey, M W Y; Mazanetz, M P; Heifetz, A; Hefeitz, A; Bodkin, M; Law, R J; Michel, J

2015-04-07

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. Protocols that vary in their use of restraints on protein and ligand atoms were compared to determine the influence of protein-ligand flexibility on computed water structure and energetics, and to assess protocols for routine analyses of protein-ligand complexes. The GCT-derived binding affinities correctly reproduce experimental trends, but the magnitude of the predicted changes in binding affinities is exaggerated with respect to results from a previous Monte Carlo Free Energy Perturbation study. Breakdown of the GCT water free energies into enthalpic and entropic components indicates that enthalpy changes dominate the observed variations in energetics. In EGFR kinase GCT analyses revealed that replacement of a pyrimidine by a cyanopyridine perturbs water energetics up three hydration shells away from the ligand.

Water-quality, biological, and physical-habitat conditions at fixed sites in the Cook Inlet Basin, Alaska, National Water-Quality Assessment Study Unit, October 1998-September 2001

USGS Publications Warehouse

Brabets, Timothy P.; Whitman, Matthew S.

2004-01-01

, nutrients, and dissolved organic carbon are transported in the spring from the melting snowpack. The urbanized stream, Chester Creek, had the highest concentrations of calcium, magnesium, chloride, and sodium, most likely because of the application of de-icing materials during the winter. Several volatile organic compounds and pesticides also were detected in samples from this stream. Aquatic communities in the Cook Inlet Basin are naturally different than similar sites in the contiguous United States because of the unique conditions of the northern latitudes where the Cook Inlet Basin is located, such as extreme diurnal cycles and long periods of ice cover. Blue-green algae was the dominant algae found at all sites although in some years green algae was the most dominant algae. Macroinvertebrate communities consist primarily of Diptera (true flies), Ephemeroptera (mayflies), and Plecoptera (stoneflies). Lowland areas have higher abundance of aquatic communities than glacier-fed basins. However, samples from the urbanized stream, Chester Creek, were dominated by oligochaetes, a class of worms. Most of the functional feeding groups were collector-gatherers. The number of taxa for both algae and macroinvertebrates were highest in water year 2001, which may be due to the relative mild winter of 2000?2001 and the above average air temperatures for this water year. The streams in the Cook Inlet Basin typically are low gradient. Bank substrates consist of silt, clay, or sand, and bed substrate consists of coarse gravel or cobbles. Vegetation is primarily shrubs and woodlands with spruce or cottonwood trees. Canopy angles vary with the size of the stream or river and are relatively low at the smaller streams and high at the larger streams. Suitable fish habitat, such as woody debris, pools, cobble substrate, and overhanging vegetation, is found at most sites. Of the human activities occurring in the fixed site basins ? high recreational use, logging, and urbanizat

SITE CHARACTERIZATION TO SUPPORT MODEL DEVELOPMENT FOR CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

PubMed Central

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Ground-water age and atmospheric tracers: Simulation studies and analysis of field data from the Mirror Lake site, New Hampshire

USGS Publications Warehouse

Goode, Daniel J.

1998-01-01

The use of environmental tracers in characterization of ground-water systems is investigated through mathematical modeling of ground-water age and atmospheric tracer transport, and by a field study at the Mirror Lake site, New Hampshire. Theory is presented for modeling ground-water age using the advective-dispersive transport equation. The transport equation includes a zero-order source of unit strength, corresponding to the rate of aging, and can accommodate matrix diffusion and other exchange processes. The effect of temperature fluctuations and layered soils on transport of atmospheric gases to the water table is investigated using a one-dimensional numerical model of chlorofluorocarbon (CFC-11) transport. The nonlinear relation between temperature and Henry's Law coefficient (reflecting air/water phase partitioning) can cause the apparent recharge temperature to be elevated above the annual mean temperature where the water table is shallow. In addition, fine-grained soils can isolate the air phase in the unsaturated zone from the atmosphere. At the USGS' Mirror Lake, New Hampshire fractured-rock research site CFC concentrations near the water table are depleted where dissolved oxygen is low. CFC-11 and CFC-113 are completely absent under anaerobic conditions, while CFC-12 is as low as one-third of modern concentrations. Anaerobic biodegradation apparently consumes CFC's near the water table at this site. One area of active degradation appears to be associated with streamflow loss to ground water. Soil gas concentrations are generally close to atmospheric levels, although some spatial correlation is observed between depleted concentrations of CFC-11 and CFC-113 in soil gas and water-table samples. Results of unsaturated-zone monitoring indicate that recharge occurs throughout the year in the watershed, even during summer evapotranspiration periods, and that seasonal temperature fluctuations occur as much as 5 meters below land surface. Application of ground-water

Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme.

PubMed

Wilson, R Hunter; Zamfir, Serban; Sumner, Isaiah

2017-09-01

The role of a highly conserved active site asparagine (N79) in the ubiquitin conjugating enzyme, Ubc13, is probed using molecular dynamics simulations. Both wild type and mutant enzymes (N79A and N79D) are studied. Contrary to a popular hypothesis, we show that it is unlikely that N79 stabilizes a reaction intermediate, but instead preferentially hydrogen bonds to a loop near the active site. This keeps the sidechain carboxylate of an aspartate in the loop (D119) near the sidechain amine of the substrate lysine. Our simulations show that this distance increases in the mutants. D119 has been hypothesized to play a variety of roles in the enzyme, including deprotonating the substrate lysine, so changing this distance can have an effect on the enzyme's efficiency. Finally, we show that it is possible for the aspartate to deprotonate the substrate even across long distances if short water wires form that connect the proton donor and acceptor. Short water wires form with greater probability in the wild type than in mutant enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

Lithologic and ground-water data for monitoring sites in the Mojave River and Warren Valley basins, San Bernardino County, California, 1992-1998

USGS Publications Warehouse

Huff, Julia A.; Clark, Dennis A.; Martin, Peter

2002-01-01

Lithologic and ground-water data were collected at 85 monitoring sites constructed in the Mojave Water Agency Management area in San Bernardino County, California, as part of a series of cooperative studies between the U.S. Geological Survey and the Mojave Water Agency. The data are being used to evaluate and address water-supply and water-quality issues. This report presents a compilation of the data collected at these sites from 1992 through 1998, including location and design of the monitoring sites, lithologic data, geophysical logs, ground-water-level measurements, and water-quality analyses.One to five small (generally 2-inch) diameter wells were installed at each of the 85 monitoring sites to collect depth-dependent hydrologic data. Lithologic logs were compiled from descriptions of drill cuttings collected at each site and from observations recorded during the drilling of the borehole. Generalized stratigraphic columns were compiled by grouping similar lithologic units. Geophysical logs provide information on the character of the lithologic units and on the presence of ground water and the chemical characteristics of that water. Water-level and water-quality data were collected periodically from the sites during 1992 through 1998.

Treatment of Produced Water from Carbon Sequestration Sites for Water Reuse and Mineral Recovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renew, Jay; Jenkins, Kristen; Bhagavatula, Abhijit

Southern Research along with Advanced Resources International, Inc. (ARI), Heartland Technology Partners, LLC (Heartland), New Logic Research, Inc. (New Logic), and Mr. Michael N. DiFilippo, Consultant developed a concept for an on-site strategy and design for management of produced water from CO 2 sequestration sites for maximum water reuse. When CO 2 is injected into deep saline aquifers, it may be necessary to produce water from the reservoir to reduce reservoir pressure. The New Logic Research, vibratory shear enhanced process (VSEP) membrane technology, and Heartland Technology Partners, low momentum-high turbulence (LM-HT) evaporation technology was selected for evaluation for treating thismore » produced water from a 530 MW natural gas combined cycle (NGCC) power plant by utilizing waste heat from the plant to drive the evaporation process. The technology was also evaluated for application to a coal-fired power plant in lieu of the NGCC power plant. The results from the project show that the application of the proposed technology to the 530 MW NGCC power plant scenario could be feasible. The results indicate that formation water TDS has a very large impact on the technical and economic feasibility of the process. One advantage of formations with low TDS water is that the VSEP membrane can be utilized to pre-concentrate the produced water upstream of the LM-HT. The results indicate that a significant portion of the exhaust gas from the NGCC power plant will have to be utilized to provide waste heat for the LM-HT evaporator; however, less will be required with low-TDS formation water. The CAPEX costs for LM-HT for all three formations (97.8USD to 122.7USD MM/year) and VSEP plus LM-HT (106.6USD MM/year) for the Keg River formation is high in cost but lower than all technology compared including crystallization, VSEP plus crystallization, FO plus LM-HT, VCE plus LM-HT, and VCE plus crystallization. The OPEX for the LM-HT for all three formations (6.33USD to 7

Water movement in the unsaturated zone at a low-level radioactive-waste burial site near Barnwell, South Carolina

USGS Publications Warehouse

Dennehy, K.F.; McMahon, P.B.

1987-01-01

Four unsaturated zone monitoring sites and a meteorologic station were installed at the low level radioactive waste burial site near Barnwell, South Carolina, to investigate the geohydrologic and climatologic factors affecting water movement in the unsaturated zone. The study site is located in the Atlantic Coastal Plain. The unsaturated zone consists of a few centimeters to > 1 m of surface sand, underlain by up to 15 m of clayey sand. Two monitoring sites were installed in experimental trenches and two were installed in radioactive waste trenches. Two different trench designs were evaluated at the monitoring sites. A meteorologic station was used to measure precipitation and to calculate actual evapotranspiration using the Bowen ratio method. Soil-moisture tensiometers, soil-moisture conductance probes, and temperature sensors were used to monitor soil-water movement in and adjacent to the trenches. Tracer tests using sodium chloride were conducted at each monitoring site. Data collection at the monitoring sites began in January 1982 and continued until early May 1984. Tensiometer data show that the unsaturated materials had their highest percent saturations in the winter and spring. Saturations in the backfill sand varied from 20 to 100%. They varied from about 75 to 100% in the adjacent undisturbed and overlying compacted clayey sand. Additionally, because tensiometer data indicate negligible water storage changes in the unsaturated zone, it is estimated that approximately 43 cm of recharge reached the water table. During 1984, the rise and fall of ponded water in an experimental trench was continuously monitored with a digital recorder. A cross-sectional finite element model of variably saturated flow was used to test the conceptual model of water movement in the unsaturated zone and to illustrate the effect of trench design on water movement into the experimental trenches. Monitoring and model results show that precipitation on trenches infiltrated the trench