bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of the Vadose Zone in Analyses of Unconfined Aquifer Tests
Authors: Moench Allen F. 
Published: December 2005

AbstractAnalytical models commonly used to interpret unconfined aquifer tests have been based on upper‐boundary (water table) conditions that do not adequately address effects of time‐varying drainage from the vadose zone. As a result, measured and simulated drawdown data may not agree and hydraulic parameters may be inaccurately estimated. A 72‐hour aquifer test conducted in Cape Cod, Massachusetts, in a slightly heterogeneous, coarse‐grained, glacial outwash deposit was found to be a good candidate for testing models with different upper‐boundary conditions. In general, under the commonly invoked assumption of instantaneous drainage, measured and simulated drawdowns were found to agree with one another only at late time and early time. In the intermediate‐time range, because of delayed drainage, measured drawdowns always exceeded simulated values, most noticeably in piezometers located near the water table. To reduce these discrepancies, an analytical model was developed that can fully account for time‐varying drainage given that the aquifer is not strongly heterogeneous. The approach is flexible as the model, which makes use of empirical relations, does not constrain drainage to follow any particular functional relation. By this approach, measured and simulated drawdowns agree over the complete time range, and the estimated parameters are consistent with prior studies and with what is known about the aquifer geometry, stratigraphy, and composition. By properly accounting for vadose zone drainage, it was found that realistic estimates of all hydraulic parameters, including specific yield, could be obtained with or without the use of late‐time data.
Delineating and Quantifying Ground Water Discharge Zones Using Streambed Temperatures
Authors: Conant Brewster 
Published: December 2005

AbstractStreambed temperature mapping, hydraulic testing using minipiezometers, and geochemical analyses of interstitial water of the streambed were used to delineate the pattern of ground water discharge in a sandy streambed and to develop a flux‐based conceptual model for ground water/surface water interactions. A new and simple empirical method was used to relate fluxes obtained from minipiezometer data to streambed temperatures. The relationship allowed flux to be calculated at locations where only streambed temperature measurements were made. Slug testing and potentiomanometer measurements at 34 piezometers indicated ground water discharge ranged from 0.03 to 446 L/m2/day (and possibly as high as 7060 L/m2/day) along a 60 m long by 11 to 14 m wide reach of river. Complex but similar plan‐view patterns of flux were calculated for both summer and winter using hundreds of streambed temperatures measured on a 1 by 2 m grid. The reach was dominated by ground water discharge and 5% to 7% of the area accounted for ∼20% to 24% of the total discharge. < 12% of the total area consisted of recharge zones or no‐discharge zones. A conceptual model for ground water/surface water interactions consisting of five different behaviors was developed based on the magnitude and direction of flux across the surface of the streambed. The behaviors include short‐circuit discharge (e.g., high‐flow springs), high discharge (e.g., preferential flowpaths), low to moderate discharge, no discharge (e.g., horizontal hyporheic or ground water flow), and recharge. Geological variations at depth played a key role in determining which type of flow behavior occurred in the streambed.
Validation of Numerical Ground Water Models Used to Guide Decision Making
Authors: Hassan Ahmed E. 
Published: December 2005

AbstractMany sites of ground water contamination rely heavily on complex numerical models of flow and transport to develop closure plans. This complexity has created a need for tools and approaches that can build confidence in model predictions and provide evidence that these predictions are sufficient for decision making. Confidence building is a long‐term, iterative process and the author believes that this process should be termed model validation. Model validation is a process, not an end result. That is, the process of model validation cannot ensure acceptable prediction or quality of the model. Rather, it provides an important safeguard against faulty models or inadequately developed and tested models. If model results become the basis for decision making, then the validation process provides evidence that the model is valid for making decisions (not necessarily a true representation of reality). Validation, verification, and confirmation are concepts associated with ground water numerical models that not only do not represent established and generally accepted practices, but there is not even widespread agreement on the meaning of the terms as applied to models. This paper presents a review of model validation studies that pertain to ground water flow and transport modeling. Definitions, literature debates, previously proposed validation strategies, and conferences and symposia that focused on subsurface model validation are reviewed and discussed. The review is general and focuses on site‐specific, predictive ground water models used for making decisions regarding remediation activities and site closure. The aim is to provide a reasonable starting point for hydrogeologists facing model validation for ground water systems, thus saving a significant amount of time, effort, and cost. This review is also aimed at reviving the issue of model validation in the hydrogeologic community and stimulating the thinking of researchers and practitioners to develop practical and efficient tools for evaluating and refining ground water predictive models.
Conduit Properties and Karstification in the Unconfined Floridan Aquifer
Authors: Screaton Elizabeth , Martin Jonathan B. , Ginn Brian , Smith Lauren 
Published: December 2005

AbstractExchange of water between conduits and matrix is an important control on regional chemical compositions, karstification, and quality of ground water resources in karst aquifers. A sinking stream (Santa Fe River Sink) and its resurgence (River Rise) in the unconfined portion of the Floridan Aquifer provide the opportunity to monitor conduit inflow and outflow. The use of temperature as a tracer allows determination of residence times and velocities through the conduit system. Based on temperature records from two high water events, flow is reasonably represented as pipe flow with a cross‐sectional area of 380 m2, although this model may be complicated by losses of water from the conduit system at higher discharge rates. Over the course of the study year, the River Rise discharged a total of 1.9 × 107 m3 more water than entered the River Sink, reflecting net contribution of ground water from the matrix into the conduit system. However, as River Sink discharge rates peaked following three rainfall events during the study period, the conduit system lost water, presumably into the matrix. Surface water in high flow events is typically undersatu‐rated with respect to calcite and thus may lead to dissolution, depending on its residence time in the matrix. A calculation of local denudation is larger than other regional estimates, perhaps reflecting return of water to conduits before calcite equilibrium is reached. The exchange of matrix and conduit water is an important variable in karst hydrology that should be considered in management of these water resources.
Spatial Variability of In Situ Microbial Activity: Biotracer Tests
Authors: Sandrin Susannah K. , Brusseau Mark L. , Piatt Joseph J. , Bodour Adria A. , Blanford William J. , Nelson Nicole T. 
Published: December 2005

AbstractBiotracer tests have been proposed as a means by which to characterize the in situ biodegradation potential for field‐scale systems. In this study, field experiments were conducted at two sites to evaluate the utility of the biotracer method for characterizing the spatial variability of microbial activity. The first site is a mixed waste‐contaminated sur‐ficial aquifer in Utah, and the second site is a chlorinated solvent‐contaminated regional aquifer in Tucson, Arizona. Mass recovery of the biotracer decreased approximately linearly with increasing residence time for the Tucson site. Similar behavior was observed at the Utah site, except in the region adjacent to the injection zone, where percent recoveries were much lower than those predicted using a correlation determined using data collected downgradient of the injection zone. First‐order biodegradation rate coefficients obtained from model calibration of the tracer data varied between 0.2 and 0.5/day for the Tucson site. For the Utah site, the values varied between 0.1 and 0.6/day downgradient of the injection wells, and between 0.7 and 2.6/day near the injection wells. Considering the large range over which biodegradation rate coefficients can vary, the rate coefficient exhibited relatively minimal spatial variability (factor of 2.5) for the Tucson site. Conversely, the spatial variability of the rate coefficient was an order of magnitude greater for the Utah site. These differences in variability are consistent with conditions associated with the respective sites. For example, the greater microbial activity observed in the vicinity of the injection wells for the Utah site is consistent with the biomass distribution determined from analysis of core samples, which shows larger bacterial cell densities for the region near the injection wells. These results illustrate the utility of biotracer tests for in situ characterization of microbial activity (e.g., biodegradation potential), including evaluation of potential spatial variability.
Estrogen in a Karstic Aquifer
Authors: Wicks Carol , Kelley Cheryl , Peterson Eric 
Published: December 2005

AbstractAdverse impacts on the health of some fish populations, such as skewed sex distributions, have been noted in surface waters and in laboratory experiments with relatively low concentrations (above 25 ng/L) of natural estrogen (17 β‐estradiol—E2). Sources of E2 to surface and ground waters can include avian, human, and mammalian waste products. The Ozark Plateau Aquifer (OPA) is a karstic basin that receives a significant portion of its water through losing reaches of rivers. Thus, there is a direct connection between surface water and ground water. The OPA was targeted for an E2 study to assess the potential for adverse health effects to aquatic organisms living in the system. Eight springs, which drain the aquifer, were sampled quarterly. The concentrations of E2 in the OPA ranged from 13 to 80 ng/L. For any one sampling event, the concentrations of E2 at the spring waters were statistically similar; however, the concentrations of E2 at all springs varied throughout the year. At Maramec Spring, one of the larger springs, the E2 concentration, was correlated with discharge. Based on the correlation between discharge and E2 concentration, aquatic organisms living in the plateau or in its discharged waters, including the threatened southern cavefish T. subterraneus, are exposed to concentration of E2 above 25 ng/L ∼60% of the time. This implies that organisms living in karst basins throughout the OPA are likely exposed to E2 concentrations that may adversely impact their reproductive success for a significant portion of each year.
Mutations in the Central Cavity and Periplasmic Domain Affect Efflux Activity of the Resistance-Nodulation-Division Pump EmhB from
Pseudomonas fluorescens
cLP6a
Authors: Hearn Elizabeth M. , Gray Murray R. , Foght Julia M. 
Published: December 2005

ABSTRACT

The EmhABC efflux system in
Pseudomonas fluorescens
cLP6a is homologous to the multidrug and solvent efflux systems belonging to the resistance-nodulation-division (RND) family and is responsible for polycyclic aromatic hydrocarbon transport, antibiotic resistance, and toluene efflux. To gain a better understanding of substrate transport in RND efflux pumps, the EmhB pump was subjected to mutational analysis. Mutagenesis of amino acids within the central cavity of the predicted three-dimensional structure of EmhB showed selective activity towards antibiotic substrates. An A384P/A385Y double mutant showed increased susceptibility toward rhodamine 6G compared to the wild type, and F386A and N99A single mutants showed increased susceptibility to dequalinium compared to the wild type. As well, the carboxylic acid side chain of D101, located in the central cavity region, was found to be essential for polycyclic aromatic hydrocarbon transport and resistance to all antibiotic substrates of EmhB. Phenylalanine residues located within the periplasmic pore domain were also targeted for mutagenesis, and the F325A and F281A mutations significantly impaired efflux activity for all EmhB substrates. One mutation (A206S) in the outer membrane protein docking domain increased antibiotic resistance and toluene tolerance, demonstrating the important role of this domain in transport activity. These data demonstrate the roles of the central cavity and periplasmic domains in the function of the RND efflux pump EmhB.
Hfq Is a Regulator of F-Plasmid TraJ and TraM Synthesis inEscherichia coli
Authors: Will William R. , Frost Laura S. 
Published: December 2005

ABSTRACTThe F plasmid ofEscherichia coliallows horizontal DNA transfer between an F+donor cell and an F−recipient. Expression of the transfer genes is tightly controlled by a number of factors, including the following plasmid-encoded regulatory proteins: TraJ, the primary activator of the 33-kbtraoperon, and the autoregulators TraM and TraY. Here, we demonstrate that the host RNA binding protein, Hfq, represses TraJ and TraM synthesis by destabilizing their respective mRNAs. Mating assays and immunoblot analyses for TraM and TraJ showed that transfer efficiency and protein levels increased in host cells containing a disruption inhfqcompared to wild-type cells in stationary phase. The stability of transcripts containing a putative Hfq binding site located in the intergenic untranslated region betweentraMandtraJwas increased inhfqmutant donor cells, suggesting that Hfq destabilizes these transcripts. Electrophoretic mobility shift assays demonstrated that Hfq specifically binds this region but not the antisense RNA, FinP, encoded on the opposite strand. Together, these findings indicate that Hfq regulatestraMandtraJtranscript stability by a mechanism separate from FinOP-mediated repression.
The
Pseudomonas aeruginosa
Ribbon-Helix-Helix DNA-Binding Protein AlgZ (AmrZ) Controls Twitching Motility and Biogenesis of Type IV Pili
Authors: Baynham Patricia J. , Ramsey Deborah M. , Gvozdyev Borys V. , Cordonnier Ellen M. , Wozniak Daniel J. 
Published: December 2005

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that is commonly found in water and soil. In order to colonize surfaces with low water content,
P. aeruginosa
utilizes a flagellum-independent form of locomotion called twitching motility, which is dependent upon the extension and retraction of type IV pili. This study demonstrates that AlgZ, previously identified as a DNA-binding protein absolutely required for transcription of the alginate biosynthetic operon, is required for twitching motility. AlgZ may be required for the biogenesis or function of type IV pili in twitching motility. Transmission electron microscopy analysis of an
algZ
deletion in nonmucoid PAO1 failed to detect surface pili. To examine expression and localization of PilA (the major pilin subunit), whole-cell extracts and cell surface pilin preparations were analyzed by Western blotting. While the PilA levels present in whole-cell extracts were similar for wild-type
P. aeruginosa
and
P. aeruginosa
with the
algZ
deletion, the amount of PilA on the surface of the cells was drastically reduced in the
algZ
mutant. Analysis of
algZ
and
algD
mutants indicates that the DNA-binding activity of AlgZ is essential for the regulation of twitching motility and that this is independent of the role of AlgZ in alginate expression. These data show that AlgZ DNA-binding activity is required for twitching motility independently of its role in alginate production and that this involves the surface localization of type IV pili. Given this new role in twitching motility, we propose that
algZ
(PA3385) be designated
amrZ
(
a
lginate and
m
otility
r
egulator
Z
).
Role of
Salmonella enterica
Serovar Typhimurium Two-Component System PreA/PreB in Modulating PmrA-Regulated Gene Transcription
Authors: Merighi Massimo , Carroll-Portillo Amanda , Septer Alecia N. , Bhatiya Aditi , Gunn John S. 
Published: December 2005

ABSTRACT

The
PmrA/PmrB two-component system encoded by the
pmrCAB
operon regulates the modification of
Salmonella
enterica
serovar Typhimurium lipopolysaccharide leading to
polymyxin B resistance. PmrA and PhoP are the only known activators of
pmrCAB
. A transposon mutagenesis screen for additional
regulators of a
pmrC
::MudJ fusion led to
the identification of a two-component system, termed PreA/PreB
(
pmrCAB
regulators A and B), that controls the transcription
of the
pmrCAB
operon in response to unknown signals. The
initial observations indicated that insertions in, or a deletion of,
the
preB
sensor, but not the
preA
response regulator,
caused upregulation of
pmrCAB
. Interestingly, the
expression of
pmrCAB
was not upregulated in a
preAB
mutant grown in LB broth, implicating PreA in the increased expression
of
pmrCAB
in the
preB
strain. This was confirmed by
overexpression of
preA

+

in
preAB
or
preB
backgrounds, which resulted in
significant upregulation or further upregulation of
pmrCAB
. No
such effect was observed in any tested
preB

+

backgrounds. Additionally,
an ectopic construct expressing a
preA
[D51A] allele also
failed to upregulate
pmrC
in any of the
pre
backgrounds tested, which implies that there is a need for
phosphorylation in the activation of the target genes. The observed
upregulation of
pmrCAB
occurred independently of the response
regulators PmrA and PhoP. Although a
preB
mutation led to
increased transcription of
pmrCAB
, this did not result in a
measurable effect on polymyxin B resistance. Our genetic data support a
model of regulation whereby, in response to unknown signals, the PreB
sensor activates PreA, which in turn indirectly upregulates
pmrCAB
transcription.
The
Mycobacterium tuberculosis
TrcR Response Regulator Represses Transcription of the Intracellularly Expressed Rv1057 Gene, Encoding a Seven-Bladed β-Propeller
Authors: Haydel Shelley E. , Clark-Curtiss Josephine E. 
Published: December 2005

ABSTRACT

The
Mycobacterium tuberculosis
TrcR response regulator binds and regulates its own promoter via an AT-rich sequence. Sequences within this AT-rich region determined to be important for TrcR binding were used to search the
M. tuberculosis
H37Rv genome to identify additional related TrcR binding sites. A similar AT-rich sequence was identified within the intergenic region located upstream of the Rv1057 gene. In the present work, we demonstrate that TrcR binds to a 69-bp AT-rich sequence within the Rv1057 intergenic region and generates specific contacts on the same side of the DNA helix. An
M. tuberculosis trcRS
deletion mutant, designated STS10, was constructed and used to determine that TrcR functions as a repressor of Rv1057 expression. Additionally, identification of the Rv1057 transcriptional start site suggests that a SigE-regulated promoter also mediates control of Rv1057 expression. Using selective capture of transcribed sequences (SCOTS) analysis as an evaluation of intracellular expression, Rv1057 was shown to be expressed during early
M. tuberculosis
growth in human macrophages, and the Rv1057 expression profile correlated with a gene that would be repressed by TrcR. Based on structural predictions, motif analyses, and molecular modeling, Rv1057 consists of a series of antiparallel β-strands which adopt a β-propeller fold, and it was determined to be the only seven-bladed β-propeller encoded in the
M. tuberculosis
genome. These results provide evidence of TrcR response regulator repression of the Rv1057 β-propeller gene that is expressed during growth of
M. tuberculosis
within human macrophages.
Reconstruction and Regulation of the Central Catabolic Pathway in the Thermophilic Propionate-Oxidizing SyntrophPelotomaculum thermopropionicum
Authors: Kosaka Tomoyuki , Uchiyama Taku , Ishii Shun-ichi , Enoki Miho , Imachi Hiroyuki , Kamagata Yoichi , Ohashi Akiyoshi , Harada Hideki , Ikenaga Hiroshi , Watanabe Kazuya 
Published: December 2005

ABSTRACTObligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with methanogenic archaea share the intermediate bottleneck step in organic-matter decomposition. These organisms (called syntrophs) are biologically significant in terms of their growth at the thermodynamic limit and are considered to be the ideal model to address bioenergetic concepts. We conducted genomic and proteomic analyses of the thermophilic propionate-oxidizing syntrophPelotomaculum thermopropionicumto obtain the genetic basis for its central catabolic pathway. Draft sequencing and subsequent targeted gap closing identified all genes necessary for reconstructing its propionate-oxidizing pathway (i.e., methylmalonyl coenzyme A pathway). Characteristics of this pathway include the following. (i) The initial two steps are linked to later steps via transferases. (ii) Each of the last three steps can be catalyzed by two different types of enzymes. It was also revealed that many genes for the propionate-oxidizing pathway, except for those for propionate coenzyme A transferase and succinate dehydrogenase, were present in an operon-like cluster and accompanied by multiple promoter sequences and a putative gene for a transcriptional regulator. Proteomic analysis showed that enzymes in this pathway were up-regulated when grown on propionate; of these enzymes, regulation of fumarase was the most stringent. We discuss this tendency of expression regulation based on the genetic organization of the open reading frame cluster. Results suggest that fumarase is the central metabolic switch controlling the metabolic flow and energy conservation in this syntroph.