bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrogeology of the Gallup Sandstone, San Juan Basin, Northwest New Mexico
Authors: Stone William J. 
Published: July 2006

ABSTRACTComparison of the hydrologic and geologic characteristics of the Gallup Sandstone (Late Cretaceous) has shown that its aquifer properties, the movement of its ground water, and the variation in its water quality are subject to considerable geologic control. This control is imposed mainly by the distribution of seven progradational sandstone bodies which make up the Gallup. These fluvial and marine sandstone bodies were deposited along the shore of a northeast‐regressing sea. The two transmissivity zones recognized have the same trend as that of the upper marine sandstone bodies (northwest‐southeast), and transmissivity decreases northeast of the pinch‐out of the lower marine sandstone bodies. Ground‐water flow is variously controlled by geologic structure, the geometry and orientation of the marine sandstones, and the position of the northeast limit of the Gallup Sandstone. Concentration of dissolved solids, as reflected by specific conductance, is controlled in part by distance from recharge area and in part by the distribution of transmissivity. The types of geologic control determined for the Gallup should apply to other Cretaceous, marine‐sandstone aquifers in the San Juan Basin, and, in a general way, to ancient shorezone deposits elsewhere.
Fault Controlled Ground‐Water Circulation Under the Colorado River, Marble Canyon, Arizona
Authors: Huntoon Peter W. 
Published: July 2006

ABSTRACTSprings with observed yields totalling about 10,000 gal/min discharge along both sides of the Colorado River in Marble Canyon, Arizona, between river miles 30 and 34.5. The waters originate from the plateaus on the respective sides of the canyon and are conducted to the floor of the canyon along the Fence fault zone or associated fractures. Chemical quality and temperature data demonstrate that some of the water discharging from springs on the west bank actually originates east of the river. This water flows under the Colorado River in the Fence fault zone, where it mixes with water from the west side before discharging from springs along the west bank. This is an unusual occurrence for the area and results because the heads at the springs along the west bank are the lowest in the circulation system associated with the fault.
DIGITAL RECORDER FOR AQUIFER TESTS
Authors: Getzen Rufus T. 
Published: July 2006

AbstractData loggers, in combination with appropriate electronic measuring devices, can improve pumping‐test data by reducing cost and by increasing accuracy, precision, speed, and computational convenience. The data logger (digital recorder) described herein was tested and found to work well. Sensitivity to blowing sand and freezing temperatures, excessive power consumption, and poor display legibility in bright sunlight are minor design deficiencies that slightly restrict the usefulness of this data logger. These problems can be easily corrected.
Geoelectric Soundings for Predicting Aquifer Properties
Authors: Kosinski Walter K. , Kelly William E. 
Published: July 2006

ABSTRACTTwo bedrock valleys, filled with glacial outwash material, were investigated with Schlumberger resistivity soundings. Aquifer electrical resistivities were determined for 16 vertical electrical soundings at seven sites in southern Rhode Island where pumping tests had been run previously. Resistivities for the different aquifer materials were derived with boring log control. The auxiliary point methods were used to reduce the aquifer layering to a single representative resistivity value. Relationships between the representative aquifer resistivity and aquifer permeability and transmissivity were derived.
Kd's — Can They Be Used to Describe Reversible Ion Sorption Reactions in Contaminant Migration?
Authors: Reardon E. J. 
Published: July 2006

ABSTRACTIn considering reversible sorption processes in ground‐water flow systems, it is important to determine whether the ground water is in steady‐state or dynamic chemical evolution. In steady‐state chemical evolution, the sorbed site populations at any point along the flow path are in equilibrium with the way in which ground water will evolve chemically due to mineral dissolution/precipitation, redox reactions, etc., during flow when it reaches this point. In dynamic chemical evolution it is not. In the steady‐state case, a location in the flow system can be characterized by a constant distribution coefficient over time for an ionic species involved in reversible sorption reactions. In the dynamic case, the distribution coefficient can be expected to vary at a location in a flow system over time. Subsurface contaminant migration problems which confront hydrogeologists invariably are of the dynamic chemical evolution type and the notion of a constant distribution coefficient or Kd to describe reversible sorption processes cannot be entertained.
AN ALL‐TEFLON BAILER AND AN AIR‐DRIVEN PUMP FOR EVACUATING SMALL‐DIAMETER GROUND‐WATER WELLS
Authors: Buss Daniel F. , Bandt Keith E. 
Published: July 2006

Abstract.During the past decade, increasing concern has arisen over the potential contamination to ground‐water systems by chemical substances which could threaten human health or the environment. Assessment of the impact of toxic substances on ground‐water quality is only as good as the chemical data analyzed in ground‐water samples.Small‐diameter observation wells can be evacuated rapidly by an air‐driven pump. This air‐driven system has proven very effective when depth to water surface distances are greater than the suction lift height. The use of this device has greatly reduced well evacuation time in comparison to the conventional bailer. Following evacuation of several well volumes, an all‐teflon bailer can be used to collect the water sample for analysis. This material can be machined with some difficulty, but its inert properties render it a most desirable material for this purpose. Both of the devices discussed herein may be improved upon to fit different‐sized wells or different situations. The materials are easily accessible and except for machining of the teflon bailer parts, can be constructed with minimal effort. These devices were designed by Keith Bandt and Dan Buss of Camp Dresser & McKee, Inc., and used by the authors on various ground‐water monitoring projects to meet collection standards dictated by the U.S. EPA (1977) and the Wisconsin Department of Natural Resources (WDNR, 1977).
Analysis of Ground‐Water Hydrographs for Defining a Crystalline Hydrogeological Environment
Authors: Briz‐Kishore B. H. , Bhimasankaram V.L.S. 
Published: July 2006

ABSTRACTWater levels and gradients are a consequence of the nature of geological media and their study helps to define the hydrogeological environment. In this paper, water levels of wells in a typical weathered and fractured granitic environment of Shadnagar Basin, Andhra Pradesh were analyzed. These studies indicate the hydraulic continuity and unity of ground‐water flow systems in weathered and fractured granites contrary to the conclusions of earlier workers. Also, the long‐term behaviour of hydrographs reveals that the basin is not over‐developed and precipitation is the only source of recharge to the ground‐water system.
Environmental Isotopes as a Tool in Hydrogeological Research in an Arid Basin
Authors: Lssar Arie , Gat Joel 
Published: July 2006

ABSTRACTStable and radioactive isotopes (deuterium, tritium, 18O, 14C) were used as an aid for better understanding the regime of recharge and flow in ground water in the Wadi Feiran basin in the southern Sinai.The annual average precipitation in the Sinai basin is between 80 mm in its upper reaches and 15 mm in the lower regions.In the upper part, underlain by crystalline rocks, ground water was found in shallow and deep fractures as in shallow alluvial deposits. The quality of water in the shallow fractures showed little effect of evaporation in relation to precipitation, which shows that recharge occurs directly and quickly through the open fractures. In the middle part of the basin, water in the riverbed alluvium was found to be recharged mainly by flood water and discharged also through deep fractures. In the lower part of the basin, the ground water was found to flow into the alluvial plain at A‐Tor. Part of it mixes with paleo‐water and emerges as thermal springs.
Persistence and Growth of Fecal
Bacteroidales
Assessed by Bromodeoxyuridine Immunocapture
Authors: Walters Sarah P. , Field Katharine G. 
Published: July 2006

ABSTRACT

Extraintestinal growth of fecal bacteria can impair accurate assessment of watershed health. Anaerobic fecal bacteria belonging to the order
Bacteroidales
are attractive candidates for fecal source tracking because they have host-specific distributions and do not grow well in the presence of high oxygen concentrations. Growth of general and human-specific fecal
Bacteroidales
marker organisms in environmental samples (sewage) and persistence of the corresponding genetic markers were investigated using bromodeoxyuridine (BrdU) DNA labeling and immunocapture, followed by PCR detection. Background amplification of unlabeled controls occasionally occurred when a high number of PCR cycles was used. By using fluorescent detection of PCR products obtained after 15 cycles, which was determined to be quantitative, we enriched for BrdU-labeled DNA and did not detect unlabeled DNA. By using pure cultures of
Bacteroides vulgatus
, the ability of
Bacteroidales
bacteria to take up and incorporate BrdU into nascent DNA was confirmed. Fecal
Bacteroidales
organisms took up and incorporated BrdU into DNA during growth. In sewage incubated aerobically at the in situ temperature,
Bacteroidales
genetic marker sequences persisted for at least 24 h and
Bacteroidales
fecal bacteria grew for up to 24 h as well. Detection by PCR using a low, quantitative cycle number decreased the sensitivity of the assay such that we were unable to detect fecal
Bacteroidales
human-specific marker sequences in unlabeled or BrdU-labeled fractions, even when fluorescent detection was used. Using 30 PCR cycles with unlabeled fractions, human-specific
Bacteroidales
sequences were detected, and they persisted for up to 24 h in sewage. These data support the utility of BrdU labeling and immunocapture followed by length heterogeneity PCR or fluorescent detection using low numbers of PCR cycles. However, this method may not be sensitive enough to identify cells that are present at low densities in aquatic environments.
Biodesulfurization in Biphasic Systems Containing Organic Solvents
Authors: Tao Fei , Yu Bo , Xu Ping , Ma Cui Qing 
Published: July 2006

ABSTRACT

Biphasic systems can overcome the problem of low productivity in conventional media and have been exploited for biocatalysis. Solvent-tolerant microorganisms are useful in biotransformation with whole cells in biphasic reactions. A solvent-tolerant desulfurizing bacterium,
Pseudomonas putida
A4, was constructed by introducing the biodesulfurizing gene cluster
dszABCD
, which was from
Rhodococcus erythropolis
XP, into the solvent-tolerant strain
P. putida
Idaho. Biphasic reactions were performed to investigate the desulfurization of various sulfur-containing heterocyclic compounds in the presence of various organic solvents.
P. putida
A4 had the same substrate range as
R. erythropolis
XP and could degrade dibenzothiophene at a specific rate of 1.29 mM g (dry weight) of cells
−1
h
−1
for the first 2 h in the presence of 10% (vol/vol)
p
-xylene.
P. putida
A4 was also able to degrade dibenzothiophene in the presence of many other organic solvents at a concentration of 10% (vol/vol). This study is a significant step in the exploration of the biotechnological potential of novel biocatalysts for developing an efficient biodesulfurization process in biphasic reaction mixtures containing toxic organic solvents.
Weakening Effect of Cell Permeabilizers on Gram-Negative Bacteria Causing Biodeterioration
Authors: Alakomi H.-L. , Paananen A. , Suihko M.-L. , Helander I. M. , Saarela M. 
Published: July 2006

ABSTRACTGram-negative bacteria play an important role in the formation and stabilization of biofilm structures on stone surfaces. Therefore, the control of growth of gram-negative bacteria offers a way to diminish biodeterioration of stone materials. The effect of potential permeabilizers on the outer membrane (OM) properties of gram-negative bacteria was investigated and further characterized. In addition, efficacy of the agents in enhancing the activity of a biocide (benzalkonium chloride) was assessed. EDTA, polyethylenimine (PEI), and succimer (meso-2,3-dimercaptosuccinic) were shown to be efficient permeabilizers of the members ofPseudomonasandStenotrophomonasgenera, as indicated by an increase in the uptake of a hydrophobic probe (1-N-phenylnaphthylamine) and sensitization to hydrophobic antibiotics. Visualization ofPseudomonascells treated with EDTA or PEI by atomic force microscopy revealed damage in the outer membrane structure. PEI especially increased the surface area and bulges of the cells. Topographic images of EDTA-treated cells were compatible with events assigned for the effect of EDTA on outer membranes, i.e., release of lipopolysaccharide and disintegration of OM structure. In addition, the effect of EDTA treatment was visualized in phase-contrast images as large areas with varying hydrophilicity on cell surfaces. In liquid culture tests, EDTA and PEI supplementation enhanced the activity of benzalkonium chloride toward the target strains. Use of permeabilizers in biocide formulations would enable the use of decreased concentrations of the active biocide ingredient, thereby providing environmentally friendlier products.
In Vivo Transduction of an Stx-Encoding Phage in Ruminants
Authors: Cornick Nancy A. , Helgerson Amy F. , Mai Volker , Ritchie Jennifer M. , Acheson David W. K. 
Published: July 2006

ABSTRACTWe assessed the ability of a kanamycin-marked Stx phage to move into a commensal, ovineEscherichia colistrain in the ruminant gastrointestinal tract. Transduction was detected in 19/24 sheep tested, resulting in the recovery of 47 transductants. Subtherapeutic doses of the quinolone antibiotic enrofloxacin did not increase the rate of transduction.
Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique
Authors: Wu Mingming , Roberts John W. , Kim Sue , Koch Donald L. , DeLisa Matthew P. 
Published: July 2006

ABSTRACT

An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming
Escherichia coli
cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type
Escherichia coli
strain RP437 as well as for isogenic derivatives that display smooth swimming due to a
cheA
deletion (strain RP9535) or incessant tumbling behavior due to a
cheZ
deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria.
Anaerobic Sulfide Oxidation with Nitrate by a Freshwater
Beggiatoa
Enrichment Culture
Authors: Kamp Anja , Stief Peter , Schulz-Vogt Heide N. 
Published: July 2006

ABSTRACT

A lithotrophic freshwater
Beggiatoa
strain was enriched in O
2
-H
2
S gradient tubes to investigate its ability to oxidize sulfide with NO
3
−
as an alternative electron acceptor. The gradient tubes contained different NO
3
−
concentrations, and the chemotactic response of the
Beggiatoa
mats was observed. The effects of the
Beggiatoa
sp. on vertical gradients of O
2
, H
2
S, pH, and NO
3
−
were determined with microsensors. The more NO
3
−
that was added to the agar, the deeper the
Beggiatoa
filaments glided into anoxic agar layers, suggesting that the
Beggiatoa
sp. used NO
3
−
to oxidize sulfide at depths below the depth that O
2
penetrated. In the presence of NO
3
−
Beggiatoa
formed thick mats (>8 mm), compared to the thin mats (ca. 0.4 mm) that were formed when no NO
3
−
was added. These thick mats spatially separated O
2
and sulfide but not NO
3
−
and sulfide, and therefore NO
3
−
must have served as the electron acceptor for sulfide oxidation. This interpretation is consistent with a fourfold-lower O
2
flux and a twofold-higher sulfide flux into the NO
3
−
-exposed mats compared to the fluxes for controls without NO
3
−
. Additionally, a pronounced pH maximum was observed within the
Beggiatoa
mat; such a pH maximum is known to occur when sulfide is oxidized to S
0
with NO
3
−
as the electron acceptor.
Excisable Cassettes: New Tools for Functional Analysis of
Streptomyces
Genomes
Authors: Raynal Alain , Karray Fatma , Tuphile Karine , Darbon-Rongère Emmanuelle , Pernodet Jean-Luc 
Published: July 2006

ABSTRACT

The functional analysis of microbial genomes often requires gene
inactivation. We constructed a set of cassettes consisting of single
antibiotic resistance genes flanked by the
attL
and
attR
sites resulting from site-specific integration of the
Streptomyces
pSAM2 element. These cassettes can easily be used
to inactivate genes by in-frame deletion in
Streptomyces
by a
three-step strategy. In the first step, in
Escherichia coli
,
the cassette is inserted into a cloned copy of the gene to be
inactivated. In the second step, the gene is replaced by homologous
recombination in
Streptomyces
, allowing substitution of the
wild-type target gene with its inactivated counterpart. In the third
step, the cassette can be removed by expression of the pSAM2 genes
xis
and
int
. The resulting strains are marker-free
and contain an “
attB
-like” sequence of 33, 34,
or 35 bp with no stop codon if the cassette is correctly chosen. Thus,
a gene can be disrupted by creating an in-frame deletion, avoiding
polar effects if downstream genes are cotranscribed with the target
gene. A set of cassettes was constructed to contain a hygromycin or
gentamicin resistance gene flanked by the
attL
and
attR
sites. The initial constructions carrying convenient
cloning sites allow the insertion of any other marker gene. We tested
insertion and excision by inserting a cassette into
orf3
, the
third gene of an operon involved in spiramycin biosynthesis. We
verified that the cassette exerted a polar effect on the transcription
of downstream genes but that, after excision, complementation with
orf3
alone restored spiramycin
production.
Seasonal Variations in Virus-Host Populations in Norwegian Coastal Waters: Focusing on the Cyanophage Community Infecting Marine
Synechococcus
spp
Authors: Sandaa Ruth-Anne , Larsen Aud 
Published: July 2006

ABSTRACT

Viruses are ubiquitous components of the marine ecosystem. In the current study we investigated seasonal variations in the viral community in Norwegian coastal waters by pulsed-field gel electrophoresis (PFGE). The results demonstrated that the viral community was diverse, displaying dynamic seasonal variation, and that viral populations of 29 different sizes in the range from 26 to 500 kb were present. Virus populations from 260 to 500 kb and dominating autotrophic pico- and nanoeukaryotes showed similar dynamic variations. Using flow cytometry and real-time PCR, we focused in particular on one host-virus system:
Synechococcus
spp. and cyanophages. The two groups covaried throughout the year and were found in the highest amounts in fall with concentrations of 7.3 × 10
4
Synechococcus
cells ml
−1
and 7.2 × 10
3
cyanophage ml
−1
. By using primers targeting the g20 gene in PCRs on DNA extracted from PFGE bands, we demonstrated that cyanophages were found in a genomic size range of 26 to 380 kb. The genetic richness of the cyanophage community, determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified g20 gene fragments, revealed seasonal shifts in the populations, with one community dominating in spring and summer and a different one dominating in fall. Phylogenetic analysis of the sequences originating from PFGE and DGGE bands grouped the sequences into three groups, all with homology to cyanomyoviruses present in cultures. Our results show that the cyanophage community in Norwegian coastal waters is dynamic and genetically diverse and has a surprisingly wide genomic size range.
Okadaic Acid, an Apoptogenic Toxin for Symbiotic/Parasitic Annelids in the Demosponge
Suberites domuncula
Authors: Schröder Heinz C. , Breter Hans J. , Fattorusso Ernesto , Ushijima Hiroshi , Wiens Matthias , Steffen Renate , Batel Renato , Müller Werner E. G. 
Published: July 2006

ABSTRACT

The role of okadaic acid (OA) in the defense system of the marine demosponge
Suberites domuncula
against symbiotic/parasitic annelids was examined. Bacteria within the mesohyl produced okadaic acid at concentrations between 32 ng/g and 58 ng/g of tissue (wet weight). By immunocytochemical methods and by use of antibodies against OA, we showed that the toxin was intracellularly stored in vesicles. Western blotting experiments demonstrated that OA also existed bound to a protein with a molecular weight of 35,000 which was tentatively identified as a galectin (by application of antigalectin antibodies). Annelids that are found in
S. domuncula
undergo apoptotic cell death. OA is one candidate inducer molecule of this process, since this toxin accumulated in these symbionts/parasites. Furthermore, we identified the cDNA encoding the multifunctional prosurvival molecule BAG-1 in
S. domuncula
; it undergoes strong expression in the presence of the annelid. Our data suggest that sponges use toxins (here, OA) produced from bacteria to eliminate metazoan symbionts/parasites by apoptosis.
Differential Adsorption of Occluded and Nonoccluded Insect-Pathogenic Viruses to Soil-Forming Minerals
Authors: Christian Peter D. , Richards Andrew R. , Williams Trevor 
Published: July 2006

ABSTRACT

Soil represents the principal environmental reservoir of many insect-pathogenic viruses. We compared the adsorption and infectivity of one occluded and two nonoccluded viruses,
Helicoverpa armigera single nucleopolyhedrovirus
(HaSNPV) (
Baculoviridae
),
Cricket paralysis virus
(CrPV) (
Dicistroviridae
), and
Invertebrate iridescent virus 6
(IIV-6) (
Iridoviridae
), respectively, in mixtures with a selection of soil-forming minerals. The relative infective titers of HaSNPV and CrPV were unchanged or slightly reduced in the presence of different minerals compared to their titers in the absence of the mineral. In contrast, the infective titer of IIV-6 varied according to the mineral being tested. In adsorption studies, over 98% of HaSNPV occlusion bodies were adsorbed by all the minerals, and a particularly high affinity was observed with ferric oxide, attapulgite, and kaolinite. In contrast, the adsorption of CrPV and IIV-6 differed markedly with mineral type, with low affinity to bentonites and high affinity to ferric oxide and kaolinite. We conclude that interactions between soil-forming minerals and insect viruses appear to be most important in nucleopolyhedroviruses, followed by invertebrate iridescent viruses, and least important in CrPV, which may reflect the ecology of these pathogens. Moreover, soils with a high content of iron oxides or kaolinite would likely represent highly effective reservoirs for insect-pathogenic viruses.