bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic Resonance Sounding Applied to Aquifer Characterization
Authors: Legchenko Anatoly , Baltassat Jean‐Michel , Bobachev Alexey , Martin Charlotte , Robain Henri , Vouillamoz Jean‐Michel 
Published: December 2005

AbstractMagnetic resonance sounding (MRS) is distinguished from other geophysical tools used for ground water investigation by the fact that it measures a magnetic resonance signal generated directly from subsurface water molecules. An alternating current pulse energizes a wire loop on the ground surface and the MRS signal is generated; subsurface water is indicated, with a high degree of reliability, by nonzero amplitude readings. Measurements with varied pulse magnitudes then reveal the depth and thickness of water saturated layers. The hydraulic conductivity of aquifers can also be estimated using boreholes for calibration. MRS can be used for both predicting the yield of water supply wells and for interpolation between boreholes, thereby reducing the number of holes required for hydrogeological modeling. An example of the practical application of MRS combined with two‐dimensional electrical imaging, in the Ker‐bernez and Kerien catchments area of France, demonstrates the efficiency of the technique.
Effects of Model Sensitivity and Nonlinearity on Nonlinear Regression of Ground Water Flow
Authors: Yager Richard M. 
Published: December 2005

AbstractNonlinear regression is increasingly applied to the calibration of hydrologic models through the use of perturbation methods to compute the Jacobian or sensitivity matrix required by the Gauss‐Newton optimization method. Sensitivities obtained by perturbation methods can be less accurate than those obtained by direct differentiation, however, and concern has arisen that the optimal parameter values and the associated parameter covariance matrix computed by perturbation could also be less accurate.Sensitivities computed by both perturbation and direct differentiation were applied in nonlinear regression calibration of seven ground water flow models. The two methods gave virtually identical optimum parameter values and covariances for the three models that were relatively linear and two of the models that were relatively nonlinear, but gave widely differing results for two other nonlinear models. The perturbation method performed better than direct differentiation in some regressions with the nonlinear models, apparently because approximate sensitivities computed for an interval yielded better search directions than did more accurately computed sensitivities for a point. The method selected to avoid overshooting minima on the error surface when updating parameter values with the Gauss‐Newton procedure appears for nonlinear models to be more important than the method of sensitivity calculation in controlling regression convergence.
Temporal Changes in Water Quality at a Childhood Leukemia Cluster
Authors: Seller Ralph L. 
Published: December 2005

AbstractSince 1997, 15 cases of acute lymphocytic leukemia and one case of acute myelocytic leukemia have been diagnosed in children and teenagers who live, or have lived, in an area centered on the town of Fallon, Nevada. The expected rate for the population is about one case every five years. In 2001, 99 domestic and municipal wells and one industrial well were sampled in the Fallon area. Twenty‐nine of these wells had been sampled previously in 1989. Statistical comparison of concentrations of major ions and trace elements in those 29 wells between 1989 and 2001 using the nonparametric Wilcoxon signed‐rank test indicate water quality did not substantially change over that period; however, short‐term changes may have occurred that were not detected. Volatile organic compounds were seldom detected in ground water samples and those that are regulated were consistently found at concentrations less than the maximum contaminant level (MCL). The MCL for gross‐alpha radioactivity and arsenic, radon, and uranium concentrations were commonly exceeded, and sometimes were greatly exceeded. Statistical comparisons using the nonparametric Wilcoxon rank‐sum test indicate gross‐alpha and ‐beta radioactivity, arsenic, uranium, and radon concentrations in wells used by families having a child with leukemia did not statistically differ from the remainder of the domestic wells sampled during this investigation. Isotopic measurements indicate the uranium was natural and not the result of a 1963 underground nuclear bomb test near Fallon. In arid and semiarid areas where trace‐element concentrations can greatly exceed the MCL, household reverse‐osmosis units may not reduce their concentrations to safe levels. In parts of the world where radon concentrations are high, water consumed first thing in the morning may be appreciably more radioactive than water consumed a few minutes later after the pressure tank has been emptied because secular equilibrium between radon and its immediate daughter progeny is attained in pressure tanks overnight.
Genetic Transplantation:
Salmonella enterica
Serovar Typhimurium as a Host To Study Sigma Factor and Anti-Sigma Factor Interactions in GeneticallyIntractable Systems
Authors: Karlinsey Joyce E. , Hughes Kelly T. 
Published: December 2005

ABSTRACT

In
Salmonella enterica
serovar Typhimurium,σ
28
and anti-sigma factor FlgM are regulatory
proteins crucial for flagellar biogenesis and motility. In this study,
we used
S. enterica
serovar Typhimurium as an in vivo
heterologous system to study σ
28
and
anti-σ
28
interactions in organisms where genetic
manipulation poses a significant challenge due to special growth
requirements. The chromosomal copy of the
S. enterica
serovar
Typhimurium σ
28
structural gene
fliA
was
exchanged with homologs of
Aquifex aeolicus
(an extreme
thermophile) and
Chlamydia trachomatis
(an obligate
intracellular pathogen) by targeted replacement of a
tetRA
element in the
fliA
gene location using λ-Red-mediated
recombination. The
S. enterica
serovar Typhimurium hybrid
strains showed σ
28
-dependent gene expression,
suggesting that σ
28
activities from diverse species
are preserved in the heterologous host system.
A. aeolicus
mutants defective for σ
28
/FlgM interactions were
also isolated in
S. enterica
serovar Typhimurium. These
studies highlight a general strategy for analysis of protein function
in species that are otherwise genetically intractable and a
straightforward method of chromosome restructuring usingλ
-Red-mediated
recombination.
CcpC-Dependent Regulation ofcitBand lmo0847 inListeria monocytogenes
Authors: Kim Hyun-Jin , Mittal Meghna , Sonenshein Abraham L. 
Published: December 2005

ABSTRACTInBacillus subtilis, the catabolite control protein C (CcpC) plays a critical role in regulating the genes encoding the enzymes of the tricarboxylic acid branch of the Krebs citric acid cycle. A gene encoding a potential CcpC homolog and two potential target genes were identified in theListeria monocytogenesgenome. In vitro gel mobility shift assays and DNase I footprinting experiments showed thatL. monocytogenesCcpC (CcpCLm) interacts with the promoter regions ofcitBLm(the gene that is likely to encode aconitase) and lmo0847 (encoding a possible glutamine transporter) and that citrate is a specific inhibitor of this interaction. To study in vivo promoter activity, a newlacZreporter system was developed. This system allows stable integration into the chromosome of a promoter region transcriptionally fused to a promoterlesslacZgene at a nonessential, ectopic locus. Analysis of strains carrying acitBLm-lacZor lmo0847-lacZfusion revealed that CcpCLmrepressescitBLmand lmo0847 in media containing an excess of glucose and glutamine. In addition, regulation ofcitBLmexpression in rich medium was growth phase dependent; during exponential growth phase, expression was very low even in the absence of CcpCLm, but a higher level ofcitBLmexpression was induced in stationary phase, suggesting the involvement of another, as yet unidentified regulatory factor.
Transposon Disruption of the Complex I NADH Oxidoreductase Gene (
snoD
) in
Staphylococcus aureus
Is Associated with Reduced Susceptibility to the Microbicidal Activity of Thrombin-Induced Platelet Microbicidal Protein 1
Authors: Bayer Arnold S. , McNamara Peter , Yeaman Michael R. , Lucindo Natalie , Jones Tiffanny , Cheung Ambrose L. , Sahl Hans-Georg , Proctor Richard A. 
Published: December 2005

ABSTRACT

The cationic molecule thrombin-induced platelet microbicidal protein 1 (tPMP-1) exerts potent activity against
Staphylococcus aureus
. We previously reported that a Tn
551 S. aureus
transposon mutant, ISP479R, and two bacteriophage back-transductants, TxA and TxB, exhibit reduced in vitro susceptibility to tPMP-1 (tPMP-1
r
) compared to the parental strain, ISP479C (V. Dhawan, M. R. Yeaman, A. L. Cheung, E. Kim, P. M. Sullam, and A. S. Bayer, Infect. Immun.
65:
3293-3299, 1997). In the current study, the genetic basis for tPMP-1
r
in these mutants was identified. GenBank homology searches using sequence corresponding to chromosomal DNA flanking Tn
551
mutant strains showed that the fourth gene in the staphylococcal
mnh
operon (
mnhABCDEFG
) was insertionally inactivated. This operon was previously reported to encode a Na
+
/H
+
antiporter involved in pH tolerance and halotolerance. However, the capacity of ISP479R to grow at pH extremes and in high NaCl concentrations (1 to 3 M), coupled with its loss of transmembrane potential (ΔΨ) during postexponential growth, suggested that the
mnh
gene products are not functioning as a secondary (i.e., passive) Na
+
/H
+
antiporter. Moreover, we identified protein homologies between
mnhD
and the
nuo
genes of
Escherichia coli
that encode components of a complex I NADH:ubiquinone oxidoreductase. Consistent with these data, exposures of tPMP-1-susceptible (tPMP-1
s
) parental strains (both clinical and laboratory derived) with either CCCP (a proton ionophore which collapses the proton motive force) or pieracidin A (a specific complex I enzyme inhibitor) significantly reduced tPMP-induced killing to levels seen in the tPMP-1
r
mutants. To reflect the energization of the gene products encoded by the
mnh
operon, we have renamed the locus
sno
(
S. aureus nuo
orthologue). These novel findings indicate that disruption of a complex I enzyme locus can confer reduced in vitro susceptibility to tPMP-1 in
S. aureus
.
The AidB Component of the
Escherichia coli
Adaptive Response to Alkylating Agents Is a Flavin-Containing, DNA-Binding Protein
Authors: Rohankhedkar Mukta S. , Mulrooney Scott B. , Wedemeyer William J. , Hausinger Robert P. 
Published: December 2005

ABSTRACT

Upon exposure to alkylating agents,
Escherichia coli
increases expression of
aidB
along with three genes (
ada
,
alkA
, and
alkB
) that encode DNA repair proteins. In order to begin to identify the role of AidB in the cell, the protein was purified to homogeneity, shown to possess stoichiometric amounts of flavin adenine dinucleotide (FAD), and confirmed to have low levels of isovaleryl-coenzyme A (CoA) dehydrogenase activity. A homology model of an AidB homodimer was constructed based on the structure of a four-domain acyl-CoA oxidase. The predicted structure revealed a positively charged groove connecting the two active sites and a second canyon of positive charges in the C-terminal domain, both of which could potentially bind DNA. Three approaches were used to confirm that AidB binds to double-stranded DNA. On the basis of its ability to bind DNA and its possession of a redox-active flavin, AidB is predicted to catalyze the direct repair of alkylated DNA.
Cold-Induced Putative DEAD Box RNA Helicases CshA and CshB Are Essential for Cold Adaptation and Interact with Cold Shock Protein B in
Bacillus subtilis
Authors: Hunger Karen , Beckering Carsten L. , Wiegeshoff Frank , Graumann Peter L. , Marahiel Mohamed A. 
Published: December 2005

ABSTRACT

The nucleic acid binding cold shock proteins (CSPs) and the cold-induced DEAD box RNA helicases have been proposed separately to act as RNA chaperones, but no experimental evidence has been reported on a direct cooperation. To investigate the possible interaction of the putative RNA helicases CshA and CshB and the CSPs from
Bacillus subtilis
during cold shock, we performed genetic as well as fluorescence resonance energy transfer (FRET) experiments. Both
cshA
and
cshB
genes could be deleted only in the presence of a
cshB
copy in
trans
, showing that the presence of one
csh
gene is essential for viability. The combined gene deletion of
cshB
and
cspD
resulted in a cold-sensitive phenotype that was not observed for either helicase or
csp
single mutants. In addition to the colocalization of the putative helicases CshA and CshB with CspB and the ribosomes in areas surrounding the nucleoid, we detected a strong FRET interaction in vivo between CshB and CspB that depended on active transcription. In contrast, a FRET interaction was not observed for CshB and the ribosomal protein L1. Therefore, we propose a model in which the putative cold-induced helicases and the CSPs work in conjunction to rescue misfolded mRNA molecules and maintain proper initiation of translation at low temperatures in
B. subtilis
.
Genomic Changes during Chronic
Helicobacter pylori
Infection
Authors: Kraft Christian , Stack Allison , Josenhans Christine , Niehus Eike , Dietrich Guido , Correa Pelayo , Fox James G. , Falush Daniel , Suerbaum Sebastian 
Published: December 2005

ABSTRACT

The gastric pathogen
Helicobacter pylori
shows tremendous genetic variability within human populations, both in gene content and at the sequence level. We investigated how this variability arises by comparing the genome content of 21 closely related pairs of isolates taken from the same patient at different time points. The comparisons were performed by hybridization with whole-genome DNA microarrays. All loci where microarrays indicated a genomic change were sequenced to confirm the events. The number of genomic changes was compared to the number of homologous replacement events without loss or gain of genes that we had previously determined by multilocus sequence analysis and mathematical modeling based on the sequence data. Our analysis showed that the great majority of genetic changes were due to homologous recombination, with 1/650 events leading to a net gain or loss of genes. These results suggest that adaptation of
H. pylori
to the host individual may principally occur through sequence changes rather than loss or gain of genes.
Divergence and Mosaicism among Virulent Soil Phages of the
Burkholderia cepacia
Complex
Authors: Summer Elizabeth J. , Gonzalez Carlos F. , Bomer Morgan , Carlile Thomas , Embry Addie , Kucherka Amalie M. , Lee Jonte , Mebane Leslie , Morrison William C. , Mark Louise , King Maria D. , LiPuma John J. , Vidaver Anne K. , Young Ry 
Published: December 2005

ABSTRACT

We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A, and Bcep781, whose hosts are soil isolates of the
Burkholderia cepacia
complex. Despite temporal and spatial separations between initial isolations, three of the phages (Bcep1, Bcep43, and Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence identity to one another and most coding region differences are due to synonymous nucleotide substitutions, a hallmark of neutral genetic drift. Phage BcepB1A has a very different genome organization but is clearly a mosaic with respect to many of the genes of the Bcep781 group, as is a defective prophage element in
Photorhabdus luminescens
. Functions were assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded proteins were identified for their ability to support homotypic interactions. While head and tail morphogenesis genes have retained canonical gene order despite extreme sequence divergence, genes involved in DNA metabolism and host lysis are not organized as in other phages. This unusual genome arrangement may contribute to the ability of the Bcep781-like phages to maintain a unified genomic type. However, the Bcep781 group phages can also engage in lateral gene transfer events with otherwise unrelated phages, a process that contributes to the broader-scale genomic mosaicism prevalent among the tailed phages.
A Little Gene with Big Effects: a
serT
Mutant Is Defective in
flgM
Gene Translation
Authors: Chevance Fabienne F. V. , Karlinsey Joyce E. , Wozniak Christopher E. , Hughes Kelly T. 
Published: December 2005

ABSTRACT

A conditional-lethal mutant was isolated as having a flagellar regulatory phenotype at 30°C and being unable to grow at 42°C. Chromosomal mapping localized the mutation to the
serT
gene, which encodes an essential serine tRNA species (

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). DNA sequence analysis revealed the mutation to be a single base change in G:A at position 10 of the
serT
gene that lies within the D-stem of the essential

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathbf{tRNA}_{_{cmo}5}\mathbf{UGA}^{Ser}\) \end{document}

species.

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recognizes UCA, UCG, and UCU codons, but UCU is also recognized by

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathbf{tRNA_{GGA}^{Ser}}\) \end{document}

and UCG by

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathbf{tRNA_{CGA}^{Ser}}\) \end{document}

. No other tRNAs are known to read the UCA codon. Thus, the UCA codon is specifically recognized by

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathbf{tRNA}_{_{cmo}5}\mathbf{UGA}^{Ser}\) \end{document}

. We show that the anti-σ
28
activity of FlgM is defective in the
serT
mutant strain. The
serT
allele causes a 10-fold increase in σ
28
-dependent
fliC
promoter transcription, indicating a defect in FlgM anti-σ
28
activity in the presence of the
serT
mutation. The
flgM
gene contains only one UCA codon. Changing the UCA of
flgM
to ACG reversed the effect of the
serT
allele. Implications for context effects in regulation of gene expression are discussed.
Autoinducer 2 Controls Biofilm Formation in
Escherichia coli
through a Novel Motility Quorum-Sensing Regulator (MqsR, B3022)
Authors: González Barrios Andrés F. , Zuo Rongjun , Hashimoto Yoshifumi , Yang Li , Bentley William E. , Wood Thomas K. 
Published: December 2005

ABSTRACT

The cross-species bacterial communication signal autoinducer 2 (AI-2), produced by the purified enzymes Pfs (nucleosidase) and LuxS (terminal synthase) from
S-
adenosylhomocysteine, directly increased
Escherichia coli
biofilm mass 30-fold. Continuous-flow cells coupled with confocal microscopy corroborated these results by showing the addition of AI-2 significantly increased both biofilm mass and thickness and reduced the interstitial space between microcolonies. As expected, the addition of AI-2 to cells which lack the ability to transport AI-2 (
lsr
null mutant) failed to stimulate biofilm formation. Since the addition of AI-2 increased cell motility through enhanced transcription of five motility genes, we propose that AI-2 stimulates biofilm formation and alters its architecture by stimulating flagellar motion and motility. It was also found that the uncharacterized protein B3022 regulates this AI-2-mediated motility and biofilm phenotype through the two-component motility regulatory system QseBC. Deletion of b3022 abolished motility, which was restored by expressing b3022 in
trans
. Deletion of b3022 also decreased biofilm formation significantly, relative to the wild-type strain in three media (46 to 74%) in 96-well plates, as well as decreased biomass (8-fold) and substratum coverage (19-fold) in continuous-flow cells with minimal medium (growth rate not altered and biofilm restored by expressing b3022 in
trans
). Deleting b3022 changed the wild-type biofilm architecture from a thick (54-μm) complex structure to one that contained only a few microcolonies. B3022 positively regulates expression of
qseBC
,
flhD
,
fliA
, and
motA
, since deleting b3022 decreased their transcription by 61-, 25-, 2.4-, and 18-fold, respectively. Transcriptome analysis also revealed that B3022 induces
crl
(26-fold) and
flhCD
(8- to 27-fold). Adding AI-2 (6.4 μM) increased biofilm formation of wild-type K-12 MG1655 but not that of the isogenic b3022,
qseBC
,
fliA
, and
motA
mutants. Adding AI-2 also increased
motA
transcription for the wild-type strain but did not stimulate
motA
transcription for the b3022 and
qseB
mutants. Together, these results indicate AI-2 induces biofilm formation in
E. coli
through B3022, which then regulates QseBC and motility; hence, b3022 has been renamed the motility quorum-sensing regulator gene (the
mqsR
gene).
Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters
Authors: Rodionov Dmitry A. , Hebbeln Peter , Gelfand Mikhail S. , Eitinger Thomas 
Published: December 2005

ABSTRACT

The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B
12
riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B
12
biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the
Salmonella enterica
serovar Typhimurium transporter.
Mutations in
Flavobacterium johnsoniae secDF
Result in Defects in Gliding Motility and Chitin Utilization
Authors: Nelson Shawn S. , McBride Mark J. 
Published: December 2005

ABSTRACT

secDF
mutants of
Flavobacterium johnsoniae
were deficient in gliding motility and chitin utilization. Cells of the mutants had reduced levels of GldJ protein, which is required for both processes. SecDF is similar to
Escherichia coli
SecD and SecF, which are involved in protein secretion.