bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of rat cathepsin E and mutants with changed active‐site residues and lacking propeptides and N‐glycosylation, expressed in human embryonic kidney 293T cells
Authors: Tsukuba Takayuki , Ikeda Shinobu , Okamoto Kuniaki , Yasuda Yoshiyuki , Sakai Eiko , Kadowaki Tomoko , Sakai Hideaki , Yamamoto Kenji
Published: December 2005

To study the roles of the catalytic activity, propeptide, and N‐glycosylation of the intracellular aspartic proteinase cathepsin E in biosynthesis, processing, and intracellular trafficking, we constructed various rat cathepsin E mutants in which active‐site Asp residues were changed to Ala or which lacked propeptides and N‐glycosylation. Wild‐type cathepsin E expressed in human embryonic kidney 293T cells was mainly found in the LAMP‐1‐positive endosomal organelles, as determined by immunofluorescence microscopy. Consistently, pulse–chase analysis revealed that the initially synthesized pro‐cathepsin E was processed to the mature enzyme within a 24 h chase. This process was completely inhibited by brefeldin A and bafilomycin A, indicating its transport from the endoplasmic reticulum (ER) to the endosomal acidic compartment. Mutants with Asp residues in the two active‐site consensus motifs changed to Ala and lacking the propeptide (Leu23‐Phe58) and the putative ER‐retention sequence (Ser59‐Asp98) were neither processed nor transported to the endosomal compartment. The mutant lacking the ER‐retention sequence was rapidly degraded in the ER, indicating the importance of this sequence in correct folding. The single (N92Q or N324D) and double (N92Q/N324D) N‐glycosylation‐deficient mutants were neither processed into a mature form nor transported to the endosomal compartment, but were stably retained in the ER without degradation. These data indicate that the catalytic activity, propeptides, and N‐glycosylation of this protein are all essential for its processing, maturation, and trafficking.
Contribution of Base Flow to Nonpoint Source Pollution Loads in an Agricultural Watershed
Authors: Schilling Keith E. , Wolter Calvin F.
Published: December 2005

Nonpoint source pollution of surface water from overland flow, drainage tiles, and ground water discharge is a major cause of water quality impairment in Iowa. Nonpoint source pollution from base flow ground water was estimated in the Walnut Creek watershed by measuirng chemical loads of atrazine, nitrate, chloride, and sulfate at 18 tributary creeks and 19 tiles. Loads were measured during a stable base flow period at creeks and tiles that discharged into Walnut Creek between two stream gauges. Chemical concentrations of atrazine (< 0.1−12 μg/L), nitrate (0.1 to 15 mg/L, and chloride (1.5 to 26 mg/L) in water were similar for creek and tile samples. Water draining predominantly agricultrural row crop areas had much higher concentrations than water draining restored prairie areas. Three methods were used to estimate base flow discharge in the watershed: (1) Darcy flux; (2) watershed discharge budget; and (3) discharge‐drainage area; each yielded similar results (31.2 L/s to 62.3 L/s). Base flow loads to the main channel were esteimated by subtracting the loads from the upstream gauge; creeks and tiles, from the total load measured at the downstream gauge station. Base flow concentration for atrazine ranged from 0.15 to 0.29 μg/L and sulfate concentration ranged from 32 to 64 mg/L, whereas concentrations for nitrate and chloride were negative (−1 to −4 mg/L). Calcultaed base flow concentrations of atrazine and sulfate appeared to be reasonable estimates, but negative concentrations of nitrate and chloride imply either loss of chemical mass in the stream from upstream to downstream sampling points or measurment error. Load data suggest little contribution from base flow pollutants to Walnut Creek water quality, with most of the pollutant load derived from major tributary creeks. Results from this study have implication for dtermining total maximum daily loads in agricultural watersheds where contributions from point sources (creeks and tiles) can be used to estimate loads from nonpoint source ground water inputs.
A Model of Cells as Practical Approach to Simulate Spring Flow in the Itxina Karstic Aquifer, Basque Country, Spain
Authors: Soliz J. Gárfias , Acebo H. Llanos
Published: December 2005

The aim of this study is to apply a parsimonious hydrologic model to the Itxina karstic aquifer that can predict changes in discharge resulting from variable inputs (recharge). The Itxina Aquifer was divided into four cells corresponding to different recharge areas. Each cell was treated as a tank to characterize the conditions within the cell. In the model, when the reservoir boundaries coincide with the position of the siphons, the signal simulated is sensitive to input pulses of the recharge. This supports the hypothesis that the siphons are the controlling mechanism in the flow system of the aquifer. The good agreement between predicted and measured discharges demonstrates the ability of the model to simulate the flow in the Itxina Aquifer. These results demonstrated that the hydraulic conductivity increases downstream within the aquifer. The hydraulic conductivities obtained by calibration varied between 4.2 × 10–3 m/s upstream of the aquifer, 6.0 × 10–2 m/s in the central region, and 9.5 × 10–1 m/s in the lower region of the aquifer. These values seem reasonable because the underground features in the principal caves show that the density of caves increases downstream in the Itxina Aquifer. The simple representation of the system produced results comparable to traditional ground water models with fewer data requirements and calibration parameters.
Modeling Preferential Flow in Reactive Barriers: Implications for Performance and Design
Authors: Benner S.G. , Blowes D.W. , Molson J.W.H.
Published: December 2005

Reactive barriers are passive and in situ ground water treatment systems. Heterogeneities in hydraulic conductivity (K) within the aquifer‐reactive barrier system will result in higher flux rates, and reduced residence times, through portions of the barrier. These spatial variations in residence time will affect the treatment capacity of the barrier. A numerical flow model was used to evaluate the effects of spatial variations in K on preferential flow through barriers. The simulations indicate that the impact of heterogeneities in K will be a function of their location and distribution; the more localized the high K zone, the greater the preferential flow. The geometry of the reactive barrier will also strongly influence flow distribution. Aquifer heterogeneities will produce greater preferential flow in thinner barriers compared to thicker barriers. If the barrier K is heterogeneous, greater preferential flow will occur in thicker barriers. The K of the barrier will affect the flow distribution; decreasing the K of the barrier can result in more even distribution of flow. Results indicate that less variable flow will be attained utilizing thicker, homogeneous barriers. The addition of homogeneous zones to thinner barriers will be effective at redistributing flow only if installed immediately adjacent to both the up‐ and downgradient faces of the barrier.
Modeling of a Deep‐Seated Geothermal System Near Tianjin, China
Authors: Xun Zhou , Mingyou Chen , Weiming Zhao , Minglang Li
Published: December 2005

A geothermal field is located in deep‐seated basement aquifers in the northeastern part of the North China Plain near Tianjin, China. Carbonate rocks of Ordovician and Middle and Upper Proterozoic age on the Cangxian Uplift are capable of yielding 960 to 4200 m3/d of 57°C to 96°C water to wells from a depth of more than 1000 m. A three‐dimensional nonisothermal numerical model was used to simulate and predict the spatial and temporal evolution of pressure and temperature in the geothermal system. The density of the geothermal water, which appears in the governing equations, can be expressed as a linear function of pressure, temperature, and total dissolved solids. A term describing the exchange of heat between water and rock is incorporated in the governing heat transport equation. Conductive heat flow from surrounding formations can be considered among the boundary conditions. Recent data of geothermal water production from the system were used for a first calibration of the numerical model. The calibrated model was used to predict the future changes in pressure and temperature of the geothermal water caused by two pumping schemes. The modeling results indicate that both pressure and temperature have a tendency to decrease with time and pumping. The current withdrawal rates and a pumping period of five months followed by a shut‐off period of seven months are helpful in minimizing the degradation of the geothermal resource potential in the area.
Exercises Illustrating Flow in Porous Media
Authors: Massmann Joel , Johnson Lisa
Published: December 2005

A set of physically based exercises is described for illustrating concepts and processes related to fluid movement in porous media. These exercises revolve around a permeameter that costs several dollars to construct and requires no external equipment and no electrical power to operate. The exercises can be used to illustrate concepts related to pressure and fluid statics, Darcy's equation for both gases and liquids, infiltration, and flow in layered media. Although the permeameter was originally developed as a teaching aid, it may also be useful in field applications as a tool to estimate air and hydraulic conductivity. Additional testing is recommended to further assess the accuracy of the results for field applications.
Fluorescence of Dissolved Organic Matter as a Natural Tracer of Ground Water
Authors: Baker Andy , Lamont‐BIack John
Published: December 2005

The fluorescence properties of dissolved organic matter (DOM) in ground water in the Permian limestone of northeast England is determined from six monitoring boreholes, a private water supply well and from a natural resurgence in a flooded collapse doline in the environs of Darlington, County Durham, northeast England. Measurements of both protein and “fulvic‐like” fluorescence was undertaken from January to December 1999. The wavelengths of fulvic‐like fluorescence excitation and emission and of protein fluorescence emission were all determined to be sensitive fingerprints of organic matter fluxes through the ground water, with water within the till and within both gypsum and limestone strata deep inside the Magnesian Limestone being differentiated by these parameters. Previous research has suggested that proteins in waters are “young” in age, hence our seasonal variations suggest that we are sampling recently formed DOM. The rapid response of all deep borehole samples suggests relatively rapid ground water flow, probably through karstic cave systems developed in the gypsum and solution widened features in the dolomitic limestone. Our results suggest that use of both protein and fulvic‐like fluorescence wavelength variations provides a DOM signature that can be used as a natural tracer.
Fate of the Herbicides 2,4,5‐T, Atrazine, and DNOC in a Shallow, Anaerobic Aquifer Investigated by In Situ Passive Diffusive Emitters and Laboratory Batch Experiments
Authors: Arildskov N.P. , Pedersen P.G. , Albrechtsen H.‐J.
Published: December 2005

The fate of the three herbicides 2,4,5‐T (2,4,5‐trichlorophenoxyacetic acid), atrazine (6‐chloro‐N‐ethyl‐N′‐[l‐methyl‐ethyl]‐l,3,5‐triazine‐2,4‐diamine), and DNOC (4,6‐dinitro‐2‐methylphenol) in an anaerobic sandy aquifer was investigated. In the field, each of the herbicides was released simultaneously with tritiated water (HTO) as tracer in the depth interval 3 to 4 mbs (meters below surface) by use of passive diffusive emitters. Atrazine and 2,4,5‐T were persistent during the approximately 18 days residence time in the aquifer. In contrast, DNOC was rapidly removed from the water phase following first‐order kinetics. The removal mechanism was likely an abiotic reduction. At day 25, the first‐order rate constant was 1.47 d−1, but it decreased with time and seemed to stabilize at 0.35 d−1 after 150 to 200 days.

In the laboratory, batch experiments were conducted with sediments from 3 to 4 mbs and from 8 to 9 mbs. In these incubations, formation of Fe2+ and depletion of sulfate showed iron and sulfate reduction in sediment from 3 to 3.5 mbs and sulfate reduction in 3.5 to 4 mbs sediment. In sediment from 8 to 9 mbs, the dominant redox process was methane formation. In sediment from 3 to 3.5 mbs, only 27% to 52% of the 2,4,5‐T remained after 196 days. 2,4,5‐trichlorophenol was identified as the major metabolite. A lag period of at least 50 days was observed, and no degradation occurred in HgCl2 amended controls, verifying that the process was microbially mediated. In the other 2,4,5‐T incubations and all the atrazine incubations, concentrations decreased linearly, but less than 25 % was removed within 200 to 250 days. No degradation products could be detected, and slow sorption was the likely explanation. In all the laboratory incubations DNOC was degraded, following first‐order kinetics, and when normalized to the sediment/water‐ratio, the field and laboratory derived rate constants compared well. The DNOC degradation in the methanogenic incubations (8 to 9 mbs) was up to 50 times faster than in the sediments from 3 to 4 mbs, likely due to the low redox potential.
Estimate of Recharge of a Rising Water Table in Semiarid Niger from 3H and 14C Modeling
Authors: Favreau Guillaume , Leduc Christian , Marlin Christelle , Dray Martial , Taupin Jean‐Denis , Massault Marc , Le Gal La Salle Corinne , Babic Milanka
Published: December 2005

A hydrodynamic survey carried out in semiarid southwest Niger revealed an increase in the unconfined ground water reserves of approximately 10% over the last 50 years due to the clearing of native vegetation. Isotopic samplings (3H, 18O,2H for water and 14C, 13C for the dissolved inorganic carbon) were performed on about 3500 km2 of this silty aquifer to characterize recharge. Stable isotope analyses confirmed the indirect recharge process that had already been shown by hydrodynamic surveys and suggested the tracers are exclusively of atmospheric origin. An analytical model that takes into account the long‐term rise in the water table was used to interpret 3H and 14C contents in ground water. The natural, preclearing median annual renewal rate (i.e., recharge as a fraction of the saturated aquifer volume) lies between 0.04% and 0.06%. For representative characteristics of the aquifer (30 m of saturated thickness, porosity between 10% and 25%), this implies a recharge of between 1 and 5 mm/year, which is much lower than the estimates of 20 to 50 mm/year for recent years, obtained using hydrological and hydrodynamic methods and the same aquifer parameters. Our study, therefore, reveals that land clearing in semiarid Niger increased ground water recharge by about one order of magnitude.
Flow Depletion in a Small Stream Caused by Ground Water Abstraction from Wells
Authors: Nyholm Thomas , Christensen Steen , Rasmussen Keld R.
Published: December 2005

The interaction between a gaining stream and a water‐table aquifer is studied at an outwash plain. The aquifer is hydraulically well connected to the stream. Pumping tests were carried out in 1997 and 1998 in two wells 60 m from the stream, screening different depths of the aquifer. Drawdown was measured on both sides of the stream. Hydraulic head, drawdown, and stream depletion data were analyzed using numerical flow models. Similar models were fitted to each of two different data sets: Model A was fitted to steady‐state hydraulic head and streamflow gain data not influenced by pumping; and model B was fitted to drawdown data measured during the 1998 pumping test. Each calibrated model closely fits its calibration data; however, predictions were biased if model A was used to predict the calibration data of model B, and vice versa. To further test the models, they were used to predict streamflow depletion during the two pumping tests as well as the drawdown during the 1997 test. Neither of these data were used for calibration. Model A predicted the measured depletions fairly accurately during both tests, whereas the predicted drawdowns in 1997 were significantly larger than actually measured. Contrary to this, the 1997 drawdowns predicted by model B were nearly unbiased; the predicted depletions deviate significantly from the measured depletions in 1997, but they compare well with the observations in 1998. Thus, although field work and analyses were extensive and done carefully to develop a ground water flow model that could predict both drawdown and streamflow depletion, the model predictions are biased. Analyses indicate that the deviations between model and data may be because of error in the models' representations of either the release of water from storage or of the hydrology in the riparian zone.
Permeability Changes in Layered Sediments: Impact of Particle Release
Authors: Blume Theresa , Weisbrod Noam , Selker John S.
Published: December 2005

One of the mechanisms of sudden particle release from grain surfaces in natural porous media is a decrease in salt concentration of the permeating fluid to below the critical salt concentration. Particle release can cause a change in hydraulic conductivity of the matrix, either by washing out the fines and thus increasing the pore sizes or by the plugging of pore constrictions. The phenomenon of permeability changes as a result of particle detachment was investigated in a series of column experiments. Coarse and fine sediments from the Hanford Formation in southeast Washington were tested. Columns were subject to a pulse of highly saline solution (NaNO3) followed by a fresh water shock causing particle release. Outflow rates and changes in hydraulic head as well as electric conductivity and pH were monitored over time. No permeability decrease occurred within the coarse matrix alone. However, when a thin layer of fine sediment was embedded within the coarse material (mimicking field conditions at the Hanford site), permeability irreversibly decreased to 10% to 20% of the initial value. Evidence suggests that most of this permeability decrease was a result of particles detached within the fine layer and its subsequent clogging. An additional observation was a sudden increase in pH in the outflow solution, generated in situ during the fresh water shock. Because layered systems are common in natural settings, our results suggest that alteration between sodium solution and fresh water can lead to particle release and subsequently reduce the overall permeability of the matrix.
Dynamic Optimal Ground Water Remediation Including Fixed and Operation Costs
Authors: Chang Liang‐Cheng , Hsiao Chin‐Tsai
Published: December 2005

In time‐varying ground water remediation, the lack of an optimal control algorithm to simultaneously consider fixed costs and time‐varying operating costs makes it nearly impossible to obtain an optimal solution. This study presents a novel algorithm that integrates a genetic algorithm (GA) and constrained differential dynamic programming (CDDP) to solve this time‐varying ground water remediation problem. A GA can easily incorporate the fixed costs associated with the installation of wells. However, using a GA to solve for time‐varying policies would dramatically increase the computational resources required. Therefore, the CDDP is used to handle the subproblems associated with time‐varying operating costs. A hypothetical case study that incorporates fixed and time‐varying operating costs is presented to demonstrate the effectiveness of the proposed algorithm. Simulation results indicate that the fixed costs can significantly influence the number and locations of wells, and a notable total cost savings can be realized by applying the novel algorithm herein.
Origin of Shallow Ground Water in an Alluvial Aquifer as Determined by Isotopic and Chemical Procedures
Authors: Rains Mark Cable , Mount Jeffrey F.
Published: December 2005

In this study, we identify the origin of shallow ground water that supports regionally unique plant and wildlife habitats in a riparian and reservoir‐fringe system using isotopic and chemical procedures. This study was conducted where Little Stony Creek flows into East Park Reservoir on the east front of the Coast Range, northern California. Little Stony Creek water, Hyphus Creek water, Franciscan Complex regional ground water, Great Valley Group regional ground water, and local shallow ground water were collected during wet and dry seasons and were analyzed for deuterium, oxygen‐18, temperature, pH, redox potential, conductivity, and major cation and anion concentrations. Turnover in the local flow system is rapid indicating that local shallow ground water is dependent on recent recharge. Local shallow ground water is recharged primarily by Little Stony Creek water and Franciscan Complex ground water. In the wet season, Little Stony Creek is the more prominent source of local shallow ground water, and the ratio of Little Stony Creek water to Franciscan Complex ground water decreases with distance from the channel. In the dry season, Franciscan Complex ground water is the more prominent source of local shallow ground water, and the ratio of Little Stony Creek water to Franciscan Complex ground water decreases with distance down the valley. Franciscan Complex ground water discharges to local shallow ground water throughout the year, primarily because the local flow system is a regional low that lies perpendicular to the Franciscan Complex ground water flowpath. Little Stony Creek is a more prominent source of ground water in the wet season than in the dry season because Little Stony Creek flows continuously through the alluvial reach in the wet season and intermittently through the alluvial reach in the dry season. Extensive ground water withdrawals from the Franciscan Complex flow system could reduce the amount of water available to the local flow system, particularly during the dry season, and could substantially reduce the geographic extent of the regionally unique plant and wildlife habitats.
Comparison of an Algebraic Multigrid Algorithm to Two Iterative Solvers Used for Modeling Ground Water Flow and Transport
Authors: Detwiler Russell L. , Mehl Steffen , Rajaram Harihar , Cheung Wendy W.
Published: December 2005

Numerical solution of large‐scale ground water flow and transport problems is often constrained by the convergence behavior of the iterative solvers used to solve the resulting systems of equations. We demonstrate the ability of an algebraic multigrid algorithm (AMG) to efficiently solve the large, sparse systems of equations that result from computational models of ground water flow and transport in large and complex domains. Unlike geometric multigrid methods, this algorithm is applicable to problems in complex flow geometries, such as those encountered in pore‐scale modeling of two‐phase flow and transport. We integrated AMG into MODFLOW 2000 to compare two‐ and three‐dimensional flow simulations using AMG to simulations using PCG2, a preconditioned conjugate gradient solver that uses the modified incomplete Cholesky preconditioner and is included with MODFLOW 2000. CPU times required for convergence with AMG were up to 140 times faster than those for PCG2. The cost of this increased speed was up to a nine‐fold increase in required random access memory (RAM) for the three‐dimensional problems and up to a four‐fold increase in required RAM for the two‐dimensional problems. We also compared two‐dimensional numerical simulations of steady‐state transport using AMG and the generalized minimum residual method with an incomplete LU‐decomposition preconditioner. For these transport simulations, AMG yielded increased speeds of up to 17 times with only a 20% increase in required RAM. The ability of AMG to solve flow and transport problems in large, complex flow systems and its ready availability make it an ideal solver for use in both field‐scale and pore‐scale modeling.
Effects of Land Use on Ground Water Quality in the Anoka Sand Plain Aquifer of Minnesota
Authors: Trojan Michael D. , Maloney Jennifer S. , Stockinger James M. , Eid Erin P. , Lahtinen Mark J.
Published: December 2005

We began a study, in 1996, to compare ground water quality under irrigated and nonirrigated agriculture, sewered and nonsewered residential developments, industrial, and nondeveloped land uses. Twenty‐three monitoring wells were completed in the upper meter of an unconfined sand aquifer. Between 1997 and 2000, sampling occurred quarterly for major ions, trace inorganic chemicals, volatile organic compounds (VOCs), herbicides, and herbicide degradates. On single occasions, we collected samples for polynuclear aromatic hydrocarbons (PAHs), perchlorate, and coliform bacteria. We observed significant differences in water chemistry beneath different land uses. Concentrations of several trace inorganic chemicals were greatest under sewered urban areas. VOC detection frequencies were 100% in commercial areas, 52% in sewered residential areas, and <10% for other land uses. Median nitrate concentrations were greatest under irrigated agriculture (15,350 μg/L) and nonsewered residential areas (6080 μg/L). Herbicides and degradates of acetanilide and triazine herbicides were detected in 86% of samples from irrigated agricultural areas, 68% of samples from nonirrigated areas, and <10% of samples from other land uses. Degradates accounted for 96% of the reported herbicide mass. We did not observe seasonal differences in water chemistry, but observed trends in water chemistry when land use changes occurred. Our results show land use is the dominant factor affecting shallow ground water quality. Trend monitoring programs should focus on areas where land use is changing, while resource managers and planners must consider potential impacts of land use changes on ground water quality.
Retracted: A Single Recovery Type Curve from Theis' Exact Solution
Authors: Samani Nozar , Pasandi M.
Published: December 2005

The following article from Ground Water Volume 41, Issue 5, September 2003, “A Single Recovery Type Curve from Theis' Exact Solution” by Nozar Samani and M. Pasandi, published online on December 13, 2005, in Wiley InterScience (http://www.interscience.wiley.com), has been retracted by the journal Editor‐in‐Chief, Mary P. Anderson, and Wiley‐Blackwell following discovery that the article was plagiarized. This retraction supersedes the Notice of Plagiarism, which was published in Ground Water Volume 42, Issue 1, January 2004.
Using Temperature to Test Models of Flow Near Yucca Mountain, Nevada
Authors: Painter Scott , Winterle James , Armstrong Amit
Published: December 2005

Ground water temperatures in the fractured volcanic aquifer near Yucca Mountain, Nevada, have previously been shown to have significant spatial variability with regions of elevated temperatures coinciding roughly with near‐vertical north‐south trending faults. Using insights gained from one‐dimensional models, previous investigators have suggested upwelling along faults from an underlying aquifer as a likely explanation for this ground water temperature pattern. Using a three‐dimensional coupled flow and heat‐transport model, we show that the thermal high coinciding with the Paintbrush fault zone can be explained without significant upwelling from the underlying aquifer. Instead, the thermal anomaly is consistent with thermal conduction enhanced slightly by vertical ground water movement within the volcanic aquifer sequence. If more than ‐400 m3/day of water enters the volcanic aquifer from below along a 10 km fault zone, the calculated temperatures at the water table are significantly greater than the measured temperatures. These results illustrate the potential limitations in using one‐dimensional models to interpret ground water temperature data, and underscore the value in combining temperature data with fully coupled three‐dimensional simulations.
The Effect of Critical pH on Virus Fate and Transport in Saturated Porous Medium
Authors: Guan Huade , Schulze‐Makuch Dirk , Schaffer Steve , Pillai Suresh D.
Published: December 2005

Several viral transport experiments were conducted in a model aquifer l m long, using bacteriophages MS2 and φX174 at various pH (4.6 to 8.3) conditions, to increase our understanding of virus behavior in ground water. The results indicate the existence of a critical pH at which the virus behavior changes abruptly. This is supported by data from field and batch experiments. The critical pH is determined to be 0.5 unit below the highest isoelectric point of the virus and porous medium. When water pH is below the critical pH, the virus has an opposite charge to at least one component of the porous medium, and is almost completely and irreversibly removed from the water. This suggests that electrostatic attraction at a subcritical water pH condition is an important factor controlling virus attenuation in ground water. The concept of critical pH can assist in the design of geologic barriers for preventing viral contamination in ground water.
Influence of Aquifer Properties on Phytoremediation Effectiveness
Authors: Matthews Daniel W. , Massmann Joel , Strand Stuart E.
Published: December 2005

Recent research has shown that planting deep‐rooted trees, such as poplar, can take up and degrade important ground water pollutants such as trichloroethylene (TCE) as they transpire water from the capillary fringe of shallow contaminated aquifers. The effect of hydrogeologic factors on the minimum plantation area needed to prevent downgradient migration of contaminated ground water is not well known. Accordingly, the objective of this research was to identify the hydrogeologic parameters that control phytoremediation effectiveness. We used a numerical ground water flow model to evaluate the effect that natural variations in hydrogeologic parameters and growing season duration have on the minimum plantation area required for capture. We found that the plantation area that was needed to completely capture a ground water contamination plume was directly proportional to aquifer horizontal hydraulic conductivity, saturated thickness, and ground water gradient. The plantation area needed for capture increased non‐linearly with increasing plume width, aquifer anisotropy, and decreasing growing season duration. The plantation area needed for capture was generally insensitive to aquifer‐specific yield and storativity. Steady‐state simulations can be used to predict the plantation area needed for capture in many applications. A particularly important finding of this work is that evapotranspiration fluxes through plantations appropriately sized to contain the plume substantially exceeded the ground water flux through the plume itself.
Aquifer Parameter Estimation from Surface Resistivity Data
Authors: Niwas Sri , de Lima Olivar A.L
Published: December 2005

This paper is devoted to the additional use, other than ground water exploration, of surface geoelectrical sounding data for aquifer hydraulic parameter estimation. In a mesoscopic framework, approximated analytical equations are developed separately for saline and for fresh water saturations. A few existing useful aquifer models, both for clean and shaley sandstones, are discussed in terms of their electrical and hydraulic effects, along with the linkage between the two. These equations are derived for insight and physical understanding of the phenomenon. In a macroscopic scale, a general aquifer model is proposed and analytical relations are derived for meaningful estimation, with a higher level of confidence, of hydraulic parameter from electrical parameters. The physical reasons for two different equations at the macroscopic level are explicitly explained to avoid confusion. Numerical examples from existing literature are reproduced to buttress our viewpoint.
Transport of Three Herbicides in Ground Water at Twin Lake Test Site, Chalk River, Ontario, Canada
Authors: Maloszewski P. , Zuber A. , Bedbur E. , Matthess G.
Published: December 2005

A field tracer test performed under natural flow conditions at the Twin Lake test site, Chalk River Laboratories of the Atomic Energy of Canada Ltd. in Chalk River, Ontario, Canada, using tritium and three herbicides (Chlor‐toluron, Terbuthylazine, and Pendimethalin) was interpreted using the dispersion equation with a combined reaction model. The reaction model couples an instantaneous equilibrium reaction governed by a linear adsorption isotherm with a reversible or irreversible kinetic reaction of the first order, and decay. An improved interpretation method consists of a simultaneous fitting of theoretical concentration and mass‐recovery curves to the experimental data, which leads to a more reliable determining of reaction models and improves the accuracy of fitting. Tritium served as the reference tracer to determine the flow velocity, dispersivity, and the recovery of the herbicides. Chlortoluron was slightly delayed by equilibrium exchange with strongly reduced concentration due to an irreversible kinetic reaction and/or decay. Terbuthilazine was slightly delayed by equilibrium exchange, with strongly reduced concentration due to a reversible kinetic reaction with some influence of decay. A strong equilibrium reaction and a strong reversible kinetic reaction without degradation governed the transport of Pendimethalin, reducing considerably its concentration. The results obtained show that simulations based only on Kd and decay constant, especially if these parameters are found in the laboratory, may considerably differ from those performed with reaction parameters determined in properly performed field tests. The dominant reaction types, and the values of parameters found in the study, supply useful information on the transport of the investigated herbicides in sandy aquifers under natural flow conditions.
Ground Water Discharge and Nitrate Flux to the Gulf of Mexico
Authors: Dowling Carolyn B. , Poreda Robert J. , Hunt Andrew G. , Carey Anne E.
Published: December 2005

Ground water samples (37 to 186 m depth) from Baldwin County, Alabama, are used to define the hydrogeology of Gulf coastal aquifers and calculate the subsurface discharge of nutrients to the Gulf of Mexico. The ground water flow and nitrate flux have been determined by linking ground water concentrations to 3H/3He and 4He age dates. The middle aquifer (A2) is an active flow system characterized by postnuclear tritium levels, moderate vertical velocities, and high nitrate concentrations. Ground water discharge could be an unaccounted source for nutrients in the coastal oceans. The aquifers annually discharge 1.1 ± 0.01 × 108 moles of nitrate to the Gulf of Mexico, or 50% and 0.8% of the annual contributions from the Mobile‐Alabama River System and the Mississippi River System, respectively.

In southern Baldwin County, south of Loxley, increasing reliance on ground water in the deeper A3 aquifer requires accurate estimates of safe ground water withdrawal. This aquifer, partially confined by Pliocene clay above and Pensacola Clay below, is tritium dead and contains elevated 4He concentrations with no nitrate and estimated ground water ages from 100 to 7000 years. The isotopic composition and concentration of natural gas diffusing from the Pensacola Clay into the A3 aquifer aids in defining the deep ground water discharge. The highest 4He and CH4 concentrations are found only in the deepest sample (Gulf State Park), indicating that ground water flow into the Gulf of Mexico suppresses the natural gas plume. Using the shape of the CH4‐He plume and the accumulation of 4He rate (2.2 ± 0.8 μcc/kg/1000 years), we estimate the natural submarine discharge and the replenishment rate for the A3 aquifer.
Assembly of CS1 Pili: the Role of Specific Residues of the Major Pilin, CooA
Authors: Starks Angela M. , Froehlich Barbara J. , Jones Tamara N. , Scott June R.
Published: December 2005

CS1 pili are important virulence factors of enterotoxigenic
Escherichia coli
strains associated with human diarrheal disease. They are the prototype for a family of pili that share extensive sequence similarity among their structural and assembly proteins. Only four linked genes,
cooB
,
cooA
,
cooC
, and
cooD
, are required to produce CS1 pili in
E. coli
K-12. To identify amino acids important for the function of the major pilin CooA, we used alanine substitution mutagenesis targeting conserved residues in the N and C termini of the protein. To test function, we examined
cooA
mutants for the ability to agglutinate bovine erythrocytes. Each hemagglutination-negative (HA
−
)
cooA
mutant was examined to identify its assembly pathway defect. CooA has been shown to be degraded in the absence of CooB (K. Voegele, H. Sakellaris, and J. R. Scott, Proc. Natl. Acad. Sci. USA
94:
13257-13261, 1997). We found several HA
−
cooA
mutants that produced no detectable CooA, suggesting that recognition by CooB is mediated by residues in both the N and C termini of CooA. In addition, we found that alanine substitution for some of the conserved residues in the C-terminal motif “AGxYxG(x
6
)T,” which is found in all subunits of this pilus family, had no effect on pilus formation. However, alanine substitution for some of the alternating hydrophobic residues within this motif prevented CooA from interacting with CooD, which serves as both the tip adhesin and nucleation protein for pilus formation. Thus, it appears that some, but not all, of the residues in both the N and C termini of CooA play a critical role in the intermolecular interactions of the major pilin with the other structural and assembly proteins. We anticipate that the results obtained here for CS1 pili in enterotoxigenic
E. coli
will help develop an understanding of the pilus assembly pathway used by CS1 family members in several important human pathogens.
Generation of DNA-Free
Escherichia coli
Cells by 2-Aminopurine Requires Mismatch Repair and Nonmethylated DNA
Authors: Matic Ivan , Ekiert Damian , Radman Miroslav , Kohiyama Masamichi
Published: December 2005

Undirected mismatch repair initiated by the incorporation of the base analog 2-aminopurine kills DNA-methylation-deficient
Escherichia coli dam
cells by DNA double-strand breakage. Subsequently, the chromosomal DNA is totally degraded, resulting in DNA-free cells.
Isolation of RNA Polymerase from
Clostridium difficile
and Characterization of Glutamate Dehydrogenase and rRNA Gene Promoters In Vitro and In Vivo
Authors: Mani Nagraj , Dupuy Bruno , Sonenshein Abraham L.
Published: December 2005

Clostridium difficile
is the primary causative agent of antibiotic-associated diarrheal disease. To facilitate molecular genetic analysis of gene expression in this organism, methods were developed to study transcriptional regulation in vitro and in vivo. That is,
C. difficile
RNA polymerase was partially purified and shown to bind to and initiate transcription in vitro from bona fide
C. difficile
promoters for rRNA and glutamate dehydrogenase genes. In addition, primer extension analyses and a β-glucuronidase reporter system were used to quantitate transcription from these promoters in vivo. With these tools in hand, it is now possible to characterize the behavior of any
C. difficile
gene in vivo and to study the regulation of its expression in detail.
Human T-Cell Leukemia Virus Open Reading Frame II Encodes a Posttranscriptional Repressor That Is Recruited at the Level of Transcription
Authors: Younis Ihab , Boris-Lawrie Kathleen , Green Patrick L.
Published: December 2005

Human T-cell leukemia virus (HTLV) infection is a chronic, lifelong infection that is associated with the development of leukemia and neurological disease after a long latency period, and the mechanism by which the virus is able to evade host immune surveillance is elusive. Besides the structural and enzymatic proteins, HTLV encodes regulatory (Tax and Rex) and accessory (open reading frame I [ORF I] and ORF II) proteins. Tax activates viral and cellular transcription and promotes T-cell growth and malignant transformation. Rex acts posttranscriptionally to facilitate cytoplasmic expression of incompletely spliced viral mRNAs. Recently, we reported that the accessory gene products of HTLV-1 and HTLV-2 ORF II (p30
II
and p28
II
, respectively) are able to restrict viral replication. These proteins act as negative regulators of both Tax and Rex by binding to and retaining their mRNA in the nucleus, leading to reduced protein expression and virion production. Here, we show that p28
II
is recruited to the viral promoter in a Tax-dependent manner. After recruitment to the promoter, p28
II
or p30
II
then travels with the transcription elongation machinery until its target mRNA is synthesized. Experiments artificially directing these proteins to the promoter indicate that p28
II
, unlike HTLV-1 p30
II
, displays no transcriptional activity. Furthermore, the tethering of p28
II
directly to
tax/rex
mRNA resulted in repression of Tax function, which could be attributed to the ability of p28
II
to block TAP/p15-mediated enhancement of Tax expression. p28
II
-mediated reduction of viral replication in infected cells may permit survival of the cells by allowing escape from immune recognition, which is consistent with the critical role of HTLV accessory proteins in viral persistence in vivo.
Regulatable Gutless Adenovirus Vectors Sustain Inducible Transgene Expression in the Brain in the Presence of an Immune Response against Adenoviruses
Authors: Xiong Weidong , Goverdhana Shyam , Sciascia Sandra A. , Candolfi Marianela , Zirger Jeffrey M. , Barcia Carlos , Curtin James F. , King Gwendalyn D. , Jaita Gabriela , Liu Chunyan , Kroeger Kurt , Agadjanian Hasmik , Medina-Kauwe Lali , Palmer Donna , Ng Philip , Lowenstein Pedro R. , Castro Maria G.
Published: December 2005

In view of recent serious adverse events and advances in gene therapy technologies, the use of regulatable expression systems is becoming recognized as indispensable adjuncts to successful clinical gene therapy. In the present work we optimized high-capacity adenoviral (HC-Ad) vectors encoding the novel tetracycline-dependent (TetOn)-regulatory elements for efficient and regulatable gene expression in the rat brain in vivo. We constructed two HC-Ad vectors encoding β-galactosidase (β-gal) driven by a TetOn system containing the rtTAS
s
M2 transactivator and the tTS
Kid
repressor under the control of the murine cytomegalovirus (mCMV) (HC-Ad-mTetON-β-Gal) or the human CMV (hCMV) promoter (HC-Ad-hTetON-β-Gal). Expression was tightly regulatable by doxycycline (Dox), reaching maximum expression in vivo at 6 days and returning to basal levels at 10 days following the addition or removal of Dox, respectively. Both vectors achieved higher transgene expression levels compared to the expression from vectors encoding the constitutive mCMV or hCMV promoter. HC-Ad-mTetON-β-Gal yielded the highest transgene expression levels and expressed in both neurons and astrocytes. Antivector immune responses continue to limit the clinical use of vectors. We thus tested the inducibility and longevity of HC-Ad-mediated transgene expression in the brain of rats immunized against adenovirus by prior intradermal injections of RAds. Regulated transgene expression from HC-Ad-mTetON-β-Gal remained active even in the presence of a significant systemic immune response. Therefore, these vectors display two coveted characteristics of clinically useful vectors, namely their regulation and effectiveness even in the presence of prior immunization against adenovirus.
Characterization of Mimivirus DNA Topoisomerase IB Suggests Horizontal Gene Transfer between Eukaryal Viruses and Bacteria
Authors: Benarroch Delphine , Claverie Jean-Michel , Raoult Didier , Shuman Stewart
Published: December 2005

Mimivirus, a parasite of
Acanthamoeba polyphaga
, is the largest DNA virus known; it encodes dozens of proteins with imputed functions in nucleic acid transactions. Here we produced, purified, and characterized mimivirus DNA topoisomerase IB (TopIB), which we find to be a structural and functional homolog of poxvirus TopIB and the poxvirus-like topoisomerases discovered recently in bacteria. Arginine, histidine, and tyrosine side chains responsible for TopIB transesterification are conserved and essential in mimivirus TopIB. Moreover, mimivirus TopIB is capable of incising duplex DNA at the 5′-CCCTT cleavage site recognized by all poxvirus topoisomerases. Based on the available data, mimivirus TopIB appears functionally more akin to poxvirus TopIB than bacterial TopIB, despite its greater primary structure similarity to the bacterial TopIB group. We speculate that the ancestral bacterial/viral TopIB was disseminated by horizontal gene transfer within amoebae, which are permissive hosts for either intracellular growth or persistence of many present-day bacterial species that have a type IB topoisomerase.
Inactivation of Prions by Acidic Sodium Dodecyl Sulfate
Authors: Peretz David , Supattapone Surachai , Giles Kurt , Vergara Julie , Freyman Yevgeniy , Lessard Pierre , Safar Jiri G. , Glidden David V. , McCulloch Charles , Nguyen Hoang-Oanh B. , Scott Michael , DeArmond Stephen J. , Prusiner Stanley B.
Published: December 2005

Prompted by the discovery that prions become protease-sensitive after exposure to branched polyamine dendrimers in acetic acid (AcOH) (S. Supattapone, H. Wille, L. Uyechi, J. Safar, P. Tremblay, F. C. Szoka, F. E. Cohen, S. B. Prusiner, and M. R. Scott, J. Virol.75:3453-3461, 2001), we investigated the inactivation of prions by sodium dodecyl sulfate (SDS) in weak acid. As judged by sensitivity to proteolytic digestion, the disease-causing prion protein (PrPSc) was denatured at room temperature by SDS at pH values of ≤4.5 or ≥10. Exposure of Sc237 prions in Syrian hamster brain homogenates to 1% SDS and 0.5% AcOH at room temperature resulted in a reduction of prion titer by a factor of ca. 107; however, all of the bioassay hamsters eventually developed prion disease. When various concentrations of SDS and AcOH were tested, the duration and temperature of exposure acted synergistically to inactivate both hamster Sc237 prions and human sporadic Creutzfeldt-Jakob disease (sCJD) prions. The inactivation of prions in brain homogenates and those bound to stainless steel wires was evaluated by using bioassays in transgenic mice. sCJD prions were more than 100,000 times more resistant to inactivation than Sc237 prions, demonstrating that inactivation procedures validated on rodent prions cannot be extrapolated to inactivation of human prions. Some procedures that significantly reduced prion titers in brain homogenates had a limited effect on prions bound to the surface of stainless steel wires. Using acidic SDS combined with autoclaving for 15 min, human sCJD prions bound to stainless steel wires were eliminated. Our findings form the basis for a noncorrosive system that is suitable for inactivating prions on surgical instruments, as well as on other medical and dental equipment.
Gamma Interferon Primes Productive Human Immunodeficiency Virus Infection in Astrocytes
Authors: Carroll-Anzinger Deborah , Al-Harthi Lena
Published: December 2005

Considerable controversy exists over whether astrocytes can support human immunodeficiency virus (HIV) infection. We evaluated the impact of three cytokines critical to the development of HIV neuropathogenesis, gamma interferon (IFN-γ), granulocyte-macrophage colony-stimulating factor, and tumor necrosis factor alpha, on priming astrocytes for HIV infection. We demonstrate that IFN-γ was the most potent in its ability to facilitate substantial productive HIV infection of an astroglioma cell line (U87MG) and human fetal astrocytes (HFA). The mechanism of IFN-γ-mediated priming of HIV in HFA is unlikely to be at the level of up-regulation of receptors and coreceptors relevant to HIV entry. These data demonstrate that cytokine priming can alter HIV replication in astrocytes.