bluuebunny/crossref_metadata_2025_split huggingface dataset:
Borehole Siting in Crystalline Basement Areas of Nigeria with a Microprocessor‐Controlled Resistivity Traversing System
Authors: Olayinka Abel , Barker Ron 
Published: August 2005

AbstractA Microprocessor‐controlled Resistivity Traversing (MRT) System using the Wenner configuration has been developed to measure the distribution of resistivity in the subsurface down to depths of 200 m. The data are presented as a contoured apparent resistivity cross section, a type of electrical image, from which useful information about the structure of the subsurface can be obtained. Quantitative interpretation consists of iterative computer modeling using a two‐dimensional finite‐difference method.Measurements conducted in Kwara State, Nigeria, in borehole siting surveys show that MRT surveys are an important aid in locating areas of deep weathering and fissure zones in structurally complex basement areas. The resistivity information obtained allows an appreciation of the subsurface structure which cannot be obtained easily with other geophysical techniques.
An Analytical Solution for Steady‐State Flow Between Aquifers Through an Open Well
Authors: Silliman Stephen , Higgins David 
Published: August 2005

AbstractVertical communication between aquifers via open wells may cause migration of a chemical plume from a contaminated aquifer into a water‐supply aquifer. Hence, quantifying the rate of flow through such wells may aid either in identifying likely transport paths or in designing a migration monitoring system. In this study, a steady‐state solution was developed which allows quantification of the volumetric flow rate which will occur within an inactive well which fully penetrates two confined aquifers. The solution is an adaptation of the Thiem solution and includes a well‐loss term based on the square of the flow rate. The solution for flow between a confined aquifer and an unconfined aquifer is also presented. Based on three examples concerning hypothetical flow problems, it was shown that the well‐loss term is insignificant unless both aquifers have high transmissivities and the well‐loss coefficient is large. Limitations of the solution are also presented.
Characterization of Transmissive Fractures by Simple Tracing of In‐Well Flow
Authors: Michalski Andrew , Klepp George M. 
Published: August 2005

AbstractUnder‐exploration of complex hydrogeologic settings may lead to the occurrence of short‐circuiting internal flows in monitoring wells. Susceptible settings include fractured formations with large thickness and monotonous lithology. The occurrence of internal flow may distort flow pattern and induce contaminant migration. Monitoring data from the affected wells may be misinterpreted if the flow is unaccounted for. In order to identify and measure well bore flow in several deep monitoring wells at a site, a technique of in‐well tracing was used. The vertical movement, dispersion, and dilution of an injected saline slug was tracked by periodic electrical conductivity logging.Combining internal flow measurements with baseline conductivity and temperature logs provided estimates of the quality and origin of water entering well bores from major transmissive fractures. Identified locations of these fractures coincided with locations of larger fractures seen on video logs; only a few fractures were significant for the flow. Relative distributions of heads and fracture permeabilities in a well with internal flow could be evaluated easily, but determination of their absolute values would require measurement of static heads. In data quality, cost, and feasibility, the in‐well slug tracking compares favorably with conventional fracture characterization methods, such as coring, packer permeability testing, flowmeter and other specialized geophysical logging.
OASIS: A Graphical Decision Support System for Ground‐Water Contaminant Modeling
Authors: Newell Charles J. , Haasbeek John F. , Bedient Philip B. 
Published: August 2005

AbstractThree new software technologies were applied to develop an efficient and easy to use decision support system for ground‐water contaminant modeling. Graphical interfaces create a more intuitive and effective form of communication with the computer compared to text‐based interfaces. Concepts from the field of hypertext were applied to design the extensive electronic documentation and databases. Finally, object oriented programming permitted scientists with little programming experience to develop the system by manipulating preexisting software objects instead of writing computer code, greatly increasing the productivity of the project team.A decision support system is a class of software with different origins and characteristics than conventional programs or expert systems. Decision support systems are designed to help users with broad, semistructured problems, with the user directing the problem‐solving process. The decision support software described in this paper, the OASIS system, provides ground‐water modelers with a ground‐water biodegradation model, model documentation, background information, data from chemical and hydrogeologic databases, and data management tools. The system was developed using HyperCard software on a Macintosh personal computer. It currently has over 1700 different computer screens of information and occupies approximately 10 megabytes of hard disk storage.OASIS is a new type of modeling software where ground‐water models, data, and knowledge are integrated together using a graphical interface and an easily modified software architecture. Two groups of users can benefit from the system: current modelers who need more efficient interfaces and data management tools, and people who are not using models now because the modeling process is too involved and requires specialized knowledge.
Sampling Radius of a Porous Cup Sampler: Experimental Results
Authors: Morrison R. D. , Lowery B. 
Published: August 2005

AbstractLaboratory experiments were conducted to examine the radius of soil (sand) sampled (Sr) by a porous cup sampler. Sr was defined by the detection of potassium bromide (KBr) in a sample when KBr was injected at horizontal distances of 5, 10, 15, 30, and 45 cm from the sampler. For quasi‐static soil moisture conditions, the relation between Sr as defined by the arrival time of KBr (t) at the sampler (evacuated with a constant vacuum of 70kPa) after it was injected at a distance (x) was described by t = 1.4x2.3.As expected, desaturation occurred most rapidly near the sampler (0‐5 cm). The amount of KBr collected on a mass balance basis was greatest when KBr was injected near the sampler and decreased with injection distance. The injection of KBr into the soil at a prescribed distance from the sampler was a better method for predicting Sr for a given time than change in matric potential of the soil.
Characterization of the Exosporium Basal Layer Protein BxpB of
Bacillus anthracis
Authors: Steichen Christopher T. , Kearney John F. , Turnbough Charles L. 
Published: August 2005

ABSTRACT

Bacillus anthracis
spores, the cause of anthrax, are enclosed by a prominent loose-fitting structure called the exosporium. The exosporium is composed of a basal layer and an external hair-like nap. The filaments of the hair-like nap are apparently formed by a single collagen-like glycoprotein called BclA, whereas several different proteins form or are tightly associated with the basal layer. In this study, we used immunogold electron microscopy to demonstrate that BxpB (also called ExsF) is a component of the exosporium basal layer. Binding to the basal layer by an anti-BxpB monoclonal antibody was greatly increased by the loss of BclA. We found that BxpB and BclA are part of a stable complex that appears to include the putative basal layer protein ExsY and possibly other proteins. Previous results suggested that BxpB was glycosylated; however, our results indicate that it is not a glycoprotein. We showed that
ΔbxpB
spores, which lack BxpB, contain an exosporium devoid of hair-like nap even though the
ΔbxpB
strain produces normal levels of BclA. These results indicated that BxpB is required for the attachment of BclA to the exosporium. Finally, we found that the efficiency of production of
ΔbxpB
spores and their resistance properties were similar to those of wild-type spores. However,
ΔbxpB
spores germinate faster than wild-type spores, indicating that BxpB suppresses germination. This effect did not appear to be related to the absence from
ΔbxpB
spores of a hair-like nap or of enzymes that degrade germinants.
A Novel β-Peptidyl Aminopeptidase (BapA) from Strain 3-2W4 Cleaves Peptide Bonds of Synthetic β-Tri- and β-Dipeptides
Authors: Geueke Birgit , Namoto Kenji , Seebach Dieter , Kohler Hans-Peter E. 
Published: August 2005

ABSTRACTA novel bacterial strain that was capable of growing on the β-tripeptide H-βhVal-βhAla-βhLeu-OH as the sole carbon and nitrogen source was isolated from an enrichment culture. On the basis of physiological characterization, partial 16S rRNA sequencing, and fatty acid analysis, strain 3-2W4 was identified as a member of the familySphingomonadaceae. Growth on the β-tripeptide and the β-dipeptide H-βhAla-βhLeu-OH was observed, and emerging metabolites were characterized. Small amounts of a persisting metabolite, the N-acetylated β-dipeptide, were identified in both media. According to dissolved organic carbon measurements, 74 to 80% of the available carbon was dissimilated. The β-peptide-degrading enzyme was purified from the crude cell extract of cells from strain 3-2W4 grown on complex medium. The enzyme was composed of two subunits, and the N-terminal sequences of both were determined. With this information, it was possible to identify the complete nucleotide sequence and to deduce the primary structure of the genebapA. The gene encoded a β-peptidyl aminopeptidase (BapA) of 402 amino acids that was synthesized as preprotein with a signal sequence of 29 amino acids. The enzyme was cleaved into two subunits (residues 30 to 278 and 279 to 402). It belonged to the N-terminal nucleophile (Ntn) hydrolase superfamily.
Identification of Residues Responsible for the Defective Virulence Gene Regulator Mga Produced by a Natural Mutant ofStreptococcus pyogenes
Authors: Vahling Cheryl M. , McIver Kevin S. 
Published: August 2005

ABSTRACTMga is a transcriptional regulator in the pathogenStreptococcus pyogenesthat positively activates several important virulence genes involved in colonization and immune evasion in the human host. A naturally occurring mutant of Mga that is defective in its ability to activate transcription has been identified in the serotype M50 strain B514-Sm. Sequence alignment of the defective M50 Mga with the fully functional Mga from serotypes M4 and M49 revealed only three amino acid changes that might result in a defective protein. Electrophoretic mobility shift assays using purified M50 and M4 maltose binding protein-Mga found that both exhibited DNA-binding activity towards regulated promoters. Thus, the significance of each residue for the functionality of M50 Mga was explored through introduction of “gain-of-function” mutations based on M4 Mga. Transcriptional studies of the mutant alleles under both constitutive (PrpsL) and autoactivated (Pmga4) promoters illustrated that an arginine-to-methionine change at position 461 of M50 Mga protein fully restored activation of downstream genes. Western blot analyses of steady-state Mga levels suggest that the M461 residue may play a role in overall conformation and protein stability of Mga. However, despite the conservation of the M461 protein among all other Mga proteins, it does not appear to be necessary for activity in a divergent M6 Mga. These studies highlight the potential differences that exist between divergent Mga proteins in this important human pathogen.
Regulation of the
Bacillus subtilis ytmI
Operon, Involved in Sulfur Metabolism
Authors: Burguière Pierre , Fert Juliette , Guillouard Isabelle , Auger Sandrine , Danchin Antoine , Martin-Verstraete Isabelle 
Published: August 2005

ABSTRACT

The YtlI regulator of
Bacillus subtilis
activates the transcription of the
ytmI
operon encoding an
l
-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of the
ytlI
gene and the
ytmI
operon was high with methionine and reduced with sulfate. Using deletions and site-directed mutagenesis, a
cis
-acting DNA sequence important for YtlI-dependent regulation was identified upstream from the −35 box of
ytmI
. Gel mobility shift assays confirmed that YtlI specifically interacted with this sequence. The replacement of the sulfur-regulated
ytlI
promoter by the
xylA
promoter led to constitutive expression of a
ytmI
′
-lacZ
fusion in a
ytlI
mutant, suggesting that the repression of
ytmI
expression by sulfate was mainly at the level of YtlI synthesis. We further showed that the YrzC regulator negatively controlled
ytlI
expression while this repressor also acted on
ytmI
expression via YtlI. The cascade of regulation observed in
B. subtilis
is conserved in
Listeria
spp. Both a YtlI-like regulator and a
ytmI
-type operon are present in
Listeria
spp. Indeed, the Lmo2352 protein from
Listeria monocytogenes
was able to replace YtlI for the activation of
ytmI
expression and a lmo2352′
-lacZ
fusion was repressed in the presence of sulfate via YrzC in
B. subtilis
. A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the
ytlI
and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in
ytlI
regulation.
ExploringLactobacillus plantarumGenome Diversity by Using Microarrays
Authors: Molenaar Douwe , Bringel Françoise , Schuren Frank H. , de Vos Willem M. , Siezen Roland J. , Kleerebezem Michiel 
Published: August 2005

ABSTRACTLactobacillus plantarumis a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments ofL. plantarumstrain WCFS1 were used to perform stringent genotyping of 20 strains ofL. plantarumfrom various sources. The gene categories with the most genes conserved in all strains were those involved in biosynthesis or degradation of structural compounds like proteins, lipids, and DNA. Conversely, genes involved in sugar transport and catabolism were highly variable between strains. Moreover, besides the obvious regions of variance, like prophages, other regions varied between the strains, including regions encoding plantaricin biosynthesis, nonribosomal peptide biosynthesis, and exopolysaccharide biosynthesis. In many cases, these variable regions colocalized with regions of unusual base composition. Two large regions of flexibility were identified between 2.70 and 2.85 and 3.10 and 3.29 Mb of the WCFS1 chromosome, the latter being close to the origin of replication. The majority of genes encoded in these variable regions are involved in sugar metabolism. This functional overrepresentation and the unusual base composition of these regions led to the hypothesis that they represented lifestyle adaptation regions inL. plantarum. The present study consolidates this hypothesis by showing that there is a high degree of gene content variation amongL. plantarumstrains in genes located in these regions of the WCFS1 genome. Interestingly, based on our genotyping dataL. plantarumstrains clustered into two clearly distinguishable groups, which coincided with an earlier proposed subdivision of this species based on conventional methods.
Effects of Nitrogen and Carbon Sources on Transcription of Soluble Methyltransferases in
Methanosarcina mazei
Strain Gö1
Authors: Veit Katharina , Ehlers Claudia , Schmitz Ruth A. 
Published: August 2005

ABSTRACT

The methanogenic archaeon
Methanosarcina mazei
strain Gö1 uses versatile carbon sources and is able to fix molecular nitrogen with methanol as carbon and energy sources. Here, we demonstrate that when growing on trimethylamine (TMA), nitrogen fixation does not occur, indicating that ammonium released during TMA degradation is sufficient to serve as a nitrogen source and represses
nif
gene induction. We further report on the transcriptional regulation of soluble methyltransferases, which catalyze the initial step of methylamine consumption by methanogenesis, in response to different carbon and nitrogen sources. Unexpectedly, we obtained conclusive evidence that transcription of the

mtmB
2
C
2

operon, encoding a monomethylamine (MMA) methyltransferase and its corresponding corrinoid protein, is highly increased under nitrogen limitation when methanol serves as a carbon source. In contrast, transcription of the homologous

mtmB
1
C
1

operon is not affected by the nitrogen source but appears to be increased when TMA is the sole carbon and energy source. In general, transcription of operons encoding dimethylamine (DMA) and TMA methyltransferases and methylcobalamine:coenzyme M methyltransferases is not regulated in response to the nitrogen source. However, in all cases transcription of one of the homologous operons or genes is increased by TMA or its degradation products DMA and MMA.
The N-Terminal Domain of Enterococcal Surface Protein, Esp, Is Sufficient for Esp-Mediated Biofilm Enhancement inEnterococcus faecalis
Authors: Tendolkar Preeti M. , Baghdayan Arto S. , Shankar Nathan 
Published: August 2005

ABSTRACTEnterococci have emerged as one of the leading causes of nosocomial bloodstream, surgical site, and urinary tract infections. More recently, enterococci have been associated with biofilms, which are bacterial communities attached to a surface and encased in an extracellular polymeric matrix. The enterococcal cell surface-associated protein, Esp, enhances biofilm formation byEnterococcus faecalisin a glucose-dependent manner. Mature Esp consists of a nonrepeat N-terminal domain and a central region made up of two types of tandem repeats followed by a C-terminal membrane-spanning and anchor domain. This study was undertaken to localize the specific domain(s) of Esp that plays a role in Esp-mediated biofilm enhancement. To achieve this objective, we constructed in-frame deletion mutants expressing truncated forms of Esp in an isogenic background. By comparing strains expressing the mutant forms of Esp to those expressing wild-type Esp, we found that the strain expressing Esp lacking the N-terminal domain formed biofilms that were quantitatively less in biovolume than the strain expressing wild-type Esp. Furthermore, anE. faecalisstrain expressing only the N-terminal domain of Esp fused to a heterologous protein anchor formed biofilms that were quantitatively similar to those formed by a strain expressing full-length Esp. This suggested that the minimal region contributing to Esp-mediated biofilm enhancement inE. faecaliswas confined to the nonrepeat N-terminal domain. Expression of full-lengthE. faecalisEsp in heterologous host systems ofesp-deficientLactococcus lactisandEnterococcus faeciumdid not enhance biofilm formation as was observed forE. faecalis. These results suggest that Esp may require interaction with an additionalE. faecalis-specific factor(s) to result in biofilm enhancement.
Xanthomonas campestris
pv. campestris Possesses a Single Gluconeogenic Pathway That Is Required for Virulence
Authors: Tang Dong-Jie , He Yong-Qiang , Feng Jia-Xun , He Bao-Ren , Jiang Bo-Le , Lu Guang-Tao , Chen Baoshan , Tang Ji-Liang 
Published: August 2005

ABSTRACT

Disruption of
ppsA
, a key gene in gluconeogenesis, of
Xanthomonas campestris
pv. campestris resulted in the failure of the pathogen to grow in medium with pyruvate or C
4
-dicarboxylates as the sole carbon source and a significant reduction in virulence, indicating that
X. campestris
pv. campestris possesses only the malic enzyme-PpsA route in gluconeogenesis, which is required for virulence.
Acquisition of Insertion Sequences and the GBSi1 Intron by
Streptococcus agalactiae
Isolates Correlates with the Evolution of the Species
Authors: Héry-Arnaud Geneviève , Bruant Guillaume , Lanotte Philippe , Brun Stella , Rosenau Agnès , van der Mee-Marquet Nathalie , Quentin Roland , Mereghetti Laurent 
Published: August 2005

ABSTRACT

The prevalence of insertion sequences IS
1548
, IS
861
, IS
1381
, and ISSa4 and of the group II intron GBSi1 within
Streptococcus agalactiae
human isolates strongly correlates with the genetic lineages obtained by multilocus sequence typing. Our results yielded an evolutionary scheme for the acquisition of these genetic elements linked to the ecosystems from which the isolates were obtained.
A randomised controlled intervention study on prevention of work related skin problems among gut cleaners in swine slaughterhouses
Authors: Flyvholm M-A , Mygind K , Sell L , Jensen A , Jepsen K F 
Published: August 2005

Aims:To evaluate the effect of an intervention to reduce work related skin problems in gut cleaning departments in Danish swine slaughterhouses. The intervention consisted of an evidence based prevention programme and a documented method for implementation.Methods:Randomised controlled intervention study with a one year follow up. The intervention included educational activities and evidence based recommendations. The effect of the intervention was evaluated by telephone interviews using a standardised questionnaire based on the Nordic Occupational Skin Questionnaire (NOSQ-2002) with modified and additional questions on exposure, preventive measures, information, and discussions on prevention of skin problems, etc.Results:A total of 644 (87.5%) responded at the baseline interview and 622 (71.6%) at the one year follow up interview. A total of 495 participated in both interviews (67.3%). In the intervention departments the frequency of eczema on hands or forearms within the past three months at follow up was reduced significantly from 56.2% at baseline to 41.0% at follow up, while a slight non-significant increase was observed in the comparison departments (from 45.9% to 50.2%). The intervention activities resulted in more frequent use of protective gloves in general and the use of cotton gloves worn underneath rubber and plastic gloves. At follow up three times as many in the intervention departments used the recommended high fat skin care products introduced as part of the intervention activities. At follow up, discussion of skin problems was increased in the intervention group while no changes were observed in the comparison group.Conclusions:A significant 27% relative reduction of occupational eczema in a high risk group was feasible through implementation of an evidence based prevention programme.