bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive Growth Rate-Dependent Regulation of the
pdxA
,
ksgA
, and
pdxB
Genes of
Escherichia coli
K-12
Authors: Pease Andrew J. , Roa Benjamin R. , Luo Wen , Winkler Malcolm E. 
Published: April 2009

ABSTRACT

We found that transcription of the
pdxA
and
pdxB
genes, which mediate steps in the biosynthesis of the essential coenzyme pyridoxal 5"-phosphate, and the
ksgA
gene, which encodes an rRNA modification enzyme and is partly cotranscribed with
pdxA
, is subject to positive growth rate regulation in
Escherichia coli
K-12. The amounts of the
pdxA-ksgA
cotranscript and
pdxB-
and
ksgA-
specific transcripts and expression from
pdxA-
and
pdxB
-
lacZ
fusions increased as the growth rate increased. The half-lives of
ksgA-
and
pdxB-
specific transcripts were not affected by the growth rate, whereas the half-life of the
pdxA-ksgA
cotranscript was too short to be measured accurately. A method of normalization was applied to determine the amount of mRNA synthesized per gene and the rate of protein accumulation per gene. Normalization removed an apparent anomaly at fast growth rates and demonstrated that positive regulation of
pdxB
occurs at the level of transcription initiation over the whole range of growth rates tested. RNA polymerase limitation and autoregulation could not account for the positive growth rate regulation of
pdxA
,
pdxB
, and
ksgA
transcription. On the other hand, growth rate regulation of the amount of the
pdxA-ksgA
cotranscript was abolished by a
fis
mutation, suggesting a role for the Fis protein. In contrast, the
fis
mutation had no effect on
pdxB-
or
ksgA
-specific transcript amounts. The amounts of the
pdxA-ksgA
cotranscript and
ksgA-
specific transcript were repressed in the presence of high intracellular concentrations of guanosine tetraphosphate; however, this effect was independent of
relA
function for the
pdxA-ksgA
cotranscript. Amounts of the
pdxB
-specific transcript remained unchanged during amino acid starvation in wild-type and
relA
mutant strains.
NorA Functions as a Multidrug Efflux Protein in both Cytoplasmic Membrane Vesicles and Reconstituted Proteoliposomes
Authors: Yu Jian-Lin , Grinius Leo , Hooper David C. 
Published: April 2009

ABSTRACTOverexpression of NorA, an endogenous efflux transporter ofStaphylococcus aureus, confers resistance to certain fluoroquinolone antimicrobials and diverse other substrates. ThenorAgene was amplified by PCR and cloned in the expression vector pTrcHis2. Histidine-tagged NorA (NorA-His) was overexpressed inEscherichia colicells to prepare two experimental systems, everted membrane vesicles enriched with NorA-His and proteoliposomes reconstituted with purified NorA-His. In membrane vesicles, NorA-His actively transported Hoechst 33342, a dye that is strongly fluorescent in the membrane but has low fluorescence in an aqueous environment. Transport was activated by the addition of ATP or lactate and reversed by the addition of nigericin, with the addition of K+-valinomycin having little effect. Transport of Hoechst 33342 was inhibited competitively by verapamil, a known inhibitor of NorA, and by other NorA substrates, including tetraphenyl phosphonium and the fluoroquinolones norfloxacin and ciprofloxacin. In contrast, sparfloxacin, a fluoroquinolone whose antimicrobial activity is not affected by NorA expression, exhibited noncompetitive inhibition. NorA induction and overexpression yielded 0.5 to 1 mg of a largely homogeneous 40- to 43-kDa protein per liter of culture. NorA-His incorporated into proteoliposomes retained the ability to transport Hoechst 33342 in response to an artificial proton gradient, and transport was blocked by nigericin and verapamil. These data provide the first experimental evidence of NorA functioning as a self-sufficient multidrug transporter.
Effects of a Squalene Epoxidase Inhibitor, Terbinafine, on Ether Lipid Biosyntheses in a Thermoacidophilic Archaeon,
Thermoplasma acidophilum
Authors: Kon Takahide , Nemoto Naoki , Oshima Tairo , Yamagishi Akihiko 
Published: April 2009

ABSTRACT

The archaeal plasma membrane consists mainly of diether lipids and tetraether lipids instead of the usual ester lipids found in other organisms. Although a molecule of tetraether lipid is thought to be synthesized from two molecules of diether lipids, there is no direct information about the biosynthetic pathway(s) or intermediates of tetraether lipid biosynthesis. In this study, we examined the effects of the fungal squalene epoxidase inhibitor terbinafine on the growth and ether lipid biosyntheses in the thermoacidophilic archaeon
Thermoplasma acidophilum
. Terbinafine was found to inhibit the growth of
T. acidophilum
in a concentration-dependent manner. When growing
T. acidophilum
cells were pulse-labeled with [2-
14
C]mevalonic acid in the presence of terbinafine, incorporation of radioactivity into the tetraether lipid fraction was strongly suppressed, while accumulation of radioactivity was noted at the position corresponding to diether lipids, depending on the concentration of terbinafine. After the cells were washed with fresh medium and incubated further without the radiolabeled substrate and the inhibitor, the accumulated radioactivity in the diether lipid fraction decreased quickly while that in the tetraether lipids increased simultaneously, without significant changes in the total radioactivity of ether lipids. These results strongly suggest that terbinafine inhibits the biosynthesis of tetraether lipids from a diether-type precursor lipid(s). The terbinafine treatment will be a tool for dissecting tetraether lipid biosynthesis in
T. acidophilum
.
Quantitative Assessment of Oxygen Availability: Perceived Aerobiosis and Its Effect on Flux Distribution in the Respiratory Chain of
Escherichia coli
Authors: Alexeeva Svetlana , Hellingwerf Klaas J. , Teixeira de Mattos M. Joost 
Published: April 2009

ABSTRACT

Despite a large number of studies on the role of oxygen in cellular processes, there is no consensus as to how oxygen availability to the cell should be defined, let alone how it should be quantified. Here, a quantitative definition for oxygen availability (perceived aerobiosis) is presented; the definition is based on a calibration with reference to the minimal oxygen supply rate needed for fully oxidative catabolism (i.e., complete conversion of the energy source to CO
2
and water for glucose-limited conditions). This quantitative method is used to show how steady-state electron fluxes through the alternative cytochrome oxidases of
Escherichia coli
are distributed as a function of the extent of aerobiosis of glucose-limited chemostat cultures. At low oxygen availability the electron flux is mainly via the high-affinity cytochrome
bd
oxidase, and, at higher oxygen availability, a similar phenomenon occurs but now via the low-affinity cytochrome
bo
oxidase. The main finding is that the catabolic activities of
E. coli
(and specifically its respiratory activity) are affected by the actual oxygen availability per unit of biomass rather than by the residual dissolved oxygen concentration of the culture.
Posttranscriptional Activation of the Transcriptional Activator Rob by Dipyridyl inEscherichia coli
Authors: Rosner Judah L. , Dangi Bindi , Gronenborn Angela M. , Martin Robert G. 
Published: April 2009

ABSTRACTThe transcriptional activator Rob consists of an N-terminal domain (NTD) of 120 amino acids responsible for DNA binding and promoter activation and a C-terminal domain (CTD) of 169 amino acids of unknown function. Although several thousand molecules of Rob are normally present perEscherichia colicell, they activate promoters of therobregulon poorly. We report here that in cells treated with either 2,2"- or 4,4"-dipyridyl (the latter is not a metal chelator), Rob-mediated transcription of variousrobregulon promoters was increased substantially. A small, growth-phase-dependent effect of dipyridyl on therobpromoter was observed. However, dipyridyl enhanced Rob's activity even whenrobwas regulated by a heterologous (lac) promoter showing that the action of dipyridyl is mainly posttranscriptional. Mutants lacking from 30 to 166 of the C-terminal amino acids of Rob had basal levels of activity similar to that of wild-type cells, but dipyridyl treatment did not enhance this activity. Thus, the CTD is not an inhibitor of Rob but is required for activation of Rob by dipyridyl. In contrast to its relatively low activity in vivo, Rob binding to cognate DNA and activation of transcription in vitro is similar to that of MarA, which has a homologous NTD but no CTD. In vitro nuclear magnetic resonance studies demonstrated that 2,2"-dipyridyl binds to Rob but not to the CTD-truncated Rob or to MarA, suggesting that the effect of dipyridyl on Rob is direct. Thus, it appears that Rob can be converted from a low activity state to a high-activity state by a CTD-mediated mechanism in vivo or by purification in vitro.
Directed Mutagenesis and Plasmid-Based Complementation in the Methanogenic Archaeon
Methanosarcina acetivorans
C2A Demonstrated by Genetic Analysis of Proline Biosynthesis
Authors: Zhang Jun Kai , White Andrea K. , Kuettner H. Craig , Boccazzi Paolo , Metcalf William W. 
Published: April 2009

ABSTRACT

We report here the first use of directed mutagenesis in
Methanosarcina acetivorans
C2A. The method employs homologous recombination-mediated gene replacement and was used to construct a variety of proline auxotrophs with mutations in the
proABC
locus. Each mutation was also complemented in
trans
with autonomously replicating
Methanosarcina
-
Escherichia
plasmid shuttle vectors.
Bypass of A- and B-Signaling Requirements for
Myxococcus xanthus
Development by Mutations in
spdR
Authors: Tse Hubert , Gill Ronald E. 
Published: April 2009

ABSTRACT

Mutations in
spdR
, previously reported to bypass the developmental requirement for B-signaling in
Myxococcus xanthu
s, also bypass the requirement for A-signaling but not C-, D-, or E-signaling. Mutations in
spdR
restored nearly wild-type levels of sporulation to representative A-signal-deficient mutants carrying
asgA476, asgB480
, and
asgC767
and improved the quality of fruiting body formation in the
asgB480
mutant. The defect in A-factor production by the
asgB480
mutant was not restored in the
spdR2134 asgB480
double mutant.
Mapping of
Myxococcus xanthus
Social Motility
dsp
Mutations to the
dif
Genes
Authors: Lancero Hope , Brofft Jennifer E. , Downard John , Birren Bruce W. , Nusbaum Chad , Naylor Jerome , Shi Wenyuan , Shimkets Lawrence J. 
Published: April 2009

ABSTRACT

Myxococcus xanthus dsp
and
dif
mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping, complementation with a cosmid clone, DNA sequencing, and gene disruption and found that 16 of the 18
dsp
alleles map to the
dif
genes. Another
dsp
allele contains a mutation in the
sglK
gene. About 36.6 kb around the
dsp-dif
locus was sequenced and annotated, and 50% of the genes are novel.
Monitoring Key Reactions in Degradation of Chloroaromatics by In Situ
1
H Nuclear Magnetic Resonance: Solution Structures of Metabolites Formed from
cis
-Dienelactone
Authors: Pieper Dietmar H. , Pollmann Katrin , Nikodem Patricia , Gonzalez Bernardo , Wray Victor 
Published: April 2009

ABSTRACT

A
1
H nuclear magnetic resonance (
1
H NMR) assay was used to study the enzymatic transformation of
cis
-dienelactone, a central intermediate in the degradation of chloroaromatics. It was shown that the product of the
cis
-dienelactone hydrolase reaction is maleylacetate, in which there is no evidence for the formation of 3-hydroxymuconate. Under acidic conditions, the product structure was 4-carboxymethyl-4-hydroxybut-2-en-4-olide. Maleylacetate was transformed by maleylacetate reductase into 3-oxoadipate, a reaction competing with spontaneous decarboxylation into
cis
-acetylacrylate. One-dimensional
1
H NMR in
1
H
2
O could thus be shown to be an excellent noninvasive tool for monitoring enzyme activities and assessing the solution structure of substrates and products.
Novel Group I Intron in the tRNA
Leu
(UAA) Gene of a γ-Proteobacterium Isolated from a Deep Subsurface Environment
Authors: Vepritskiy Alexey A. , Vitol Inna A. , Nierzwicki-Bauer Sandra A. 
Published: April 2009

ABSTRACT

A group I intron has been found to interrupt the anticodon loop of the tRNA
Leu
(UAA) gene in a bacterium belonging to the γ-subdivision of
Proteobacteria
and isolated from a deep subsurface environment. The subsurface isolate SMCC D0715 was identified as belonging to the genus
Pseudomonas
. The group I intron from this isolate is the first to be reported for γ-proteobacteria, and the first instance of a tRNA
Leu
(UAA) group I intron to be found in a group of bacteria other than cyanobacteria. The 231-nucleotide (nt) intron's sequence has group I conserved elements and folds into a bona fide group I secondary structure with canonical base-paired segments P1 to P9 and a paired region, P10. The D0715 intron possesses the 11-nt motif CCUACG … UAUGG in its P8 region, a feature not common in bacterial introns. To date, phylogenetic analysis has shown that bacterial introns form two distinct families, and their complex distribution suggests that both lateral transfer and common ancestry have taken part in the evolutionary history of these elements.
Endocarditis Due to
Neisseria bacilliformis
in a Patient with a Bicuspid Aortic Valve
Authors: Masliah-Planchon Julien , Breton Guillaume , Jarlier Vincent , Simon Anne , Benveniste Olivier , Herson Serge , Drieux Laurence 
Published: April 2009

ABSTRACT

We report a case of endocarditis due to the rod-shaped
Neisseria
species
Neisseria bacilliformis
. The phenotypic characterization of this recently characterized bacteria is difficult, and the identification requires the sequencing of the 16S rRNA gene. The resolution of the disease was complete after appropriate antibiotic therapy, and surgery was not required.
Evaluation of Impact of Serial Hepatitis B Virus DNA Levels on Development of Hepatocellular Carcinoma
Authors: Chan Henry Lik-Yuen , Wong Vincent Wai-Sun , Wong Grace Lai-Hung , Chim Angel Mei-Ling , Lai Larry Hin , Sung Joseph Jao-Yiu 
Published: April 2009

ABSTRACT

We aimed to investigate the impact of hepatitis B virus (HBV) DNA on the development of hepatocellular carcinoma (HCC). We conducted a case/control study based on 506 chronic HBV patients followed up since 1997. Forty-one patients developed HCC, and each of them was age and gender matched with two simultaneously recruited controls without HCC. HBV DNA was measured at the initial visit, at yearly intervals, and at the last visit. Patient age at the time of HCC development was 55 ± 9 years. Forty-nine (40%) patients experienced antiviral treatment. The median time from diagnosis to the development of HCC was 17 months, and the control patients were followed for 92 months. At the trough level (defined as lowest level among all studied visits), more (27 patients; 66%) HCC patients had HBV DNA levels of >10,000 copies/ml than the controls (17 patients; 21%). The area under the receiver operating characteristic curve of the trough log HBV DNA level for HCC was 0.79 (95% confidence interval [CI], 0.69 to 0.89). Trough log HBV DNA (odds ratio, 11.4; 95% CI, 3.6 to 37.6;
P
< 0.0001) and liver cirrhosis (odds ratio, 11.4; 95% CI, 3.6 to 36.2;
P
< 0.0001) levels were independently associated with HCC after an adjustment for age, gender, antiviral treatment, and HBV genotype. The difference in the trough HBV DNA level was more obvious among untreated patients (5.7 ± 1.4 log copies/ml in HCC patients versus 3.2 ± 1.3 log copies/ml in control patients;
P
< 0.0001) than among those who had received antiviral treatment (3.0 ± 1.4 log copies/ml in HCC patients versus 2.5 ± 0.9 log copies/ml in control patients;
P
= 0.38). A high trough HBV DNA level was associated with a higher risk of HCC. Whether antiviral treatment could prevent HCC was uncertain.
Feasibility of the GenoType MTBDR
sl
Assay for Fluoroquinolone, Amikacin-Capreomycin, and Ethambutol Resistance Testing of
Mycobacterium tuberculosis
Strains and Clinical Specimens
Authors: Hillemann Doris , Rüsch-Gerdes Sabine , Richter Elvira 
Published: April 2009

ABSTRACT

The new GenoType
Mycobacterium tuberculosis
drug resistance second line (MTBDR
sl
) assay (Hain Lifescience, Nehren, Germany) was tested on 106 clinical isolates and directly on 64 sputum specimens for the ability to detect resistance to fluoroquinolones, injectable drugs (amikacin or capreomycin), and ethambutol in
Mycobacterium tuberculosis
strains. A total of 63 strains harboring fluoroquinolone, amikacin/capreomycin, or ethambutol resistance and 43 fully susceptible strains were comparatively analyzed with the new MTBDR
sl
assay, by DNA sequencing, and by conventional drug susceptibility testing in liquid and solid media. No discrepancies were obtained in comparison with the DNA sequencing results. Fluoroquinolone resistance was detected in 29 (90.6%) of 32, amikacin/capreomycin resistance was detected in 39/39 (84.8%/86.7%) of 46/45, and ethambutol resistance was detected in 36 (69.2%) of 52 resistant strains. A total of 64 sputum specimens (42 smear positive, 12 scanty, and 10 smear negative) were tested with the new MTBDR
sl
assay, and the results were compared with those of conventional drug susceptibility testing. Fluoroquinolone resistance was detected in 8 (88.9%) of 9, amikacin/capreomycin resistance was detected in 6/7 (75.0%/87.5%) of 8, and ethambutol resistance was detected in 10 (38.5%) of 26 resistant strains. No mutation was detected in susceptible strains. The new GenoType MTBDR
sl
assay represents a reliable tool for the detection of fluoroquinolone and amikacin/capreomycin resistance and to a lesser extent also ethambutol resistance. In combination with a molecular test for detection of rifampin and isoniazid resistance, the potential for the detection of extensively resistant tuberculosis within 1 to 2 days can be postulated.
Outbreak of Nontuberculous Mycobacterial Subcutaneous Infections Related to Multiple Mesotherapy Injections
Authors: Carbonne Anne , Brossier Florence , Arnaud Isabelle , Bougmiza Iheb , Caumes Eric , Meningaud Jean-Paul , Dubrou Sylvie , Jarlier Vincent , Cambau Emmanuelle , Astagneau Pascal 
Published: April 2009

ABSTRACT

We describe an outbreak of severe subcutaneous infections due to nontuberculous mycobacteria following mesotherapy. Epidemiological studies and molecular comparisons of
Mycobacterium chelonae
strains from different patients and the environment suggested that contamination may be associated with inappropriate cleaning of the multiple-injection device with tap water.
PediatricHelicobacter pyloriIsolates Display Distinct Gene Coding Capacities and Virulence Gene Marker Profiles
Authors: Talarico Sarah , Gold Benjamin D. , Fero Jutta , Thompson Dexter T. , Guarner Jeannette , Czinn Steven , Salama Nina R. 
Published: April 2009

ABSTRACTHelicobacter pyloristrains display remarkable genetic diversity, and the presence of strains bearing the toxigenicvacAs1 allele, a completecagpathogenicity island (PAI),cagAalleles containing multiple EPIYA phosphorylation sites, and expressing the BabA adhesin correlates with development of gastroduodenal disease in adults. To better understand the genetic variability present among pediatric strains and its relationship to disease, we characterizedH. pyloristrains infecting 47 pediatric North American patients. Prevalence of mixed infection was assessed by random amplified polymorphic DNA analysis of multipleH. pyloriclones from each patient. Microarray-based comparative genomic hybridization was used to examine the genomic content of the pediatric strains. ThecagAandvacAalleles were further characterized by allele-specific PCR. A range of EPIYA motif configurations were observed for thecagAgene, which was present in strains from 22 patients (47%), but only 19 (41%) patients contained a completecagPAI. Thirty patients (64%) were infected with a strain having thevacAs1 allele, and 28 patients (60%) had thebabAgene. The presence of a functionalcagPAI was correlated with ulcer disease (P= 0.0095). In spite of declining rates ofH. pyloriinfection in North America, at least 11% of patients had mixed infection. Pediatric strains differ in their spectrum of strain-variable genes and percentage of absent genes in comparison to adult strains. Most children were infected withH. pyloristrains lacking thecagPAI, but the presence of a completecagPAI, in contrast to other virulence markers, was associated with more severe gastroduodenal disease.
Spontaneous Bacterial Pericarditis with Tamponade Due to
Ureaplasma
spp
Authors: Tarrant William P. , Gonzalez-Berjon Jose M. , Cernoch Patricia L. , Olsen Randall J. , Musser James M. 
Published: April 2009

ABSTRACT

Infectious pericardial effusion with tamponade is an uncommon but life-threatening disease. We report an unusual case of spontaneous
Ureaplasma
pericardial effusion with tamponade associated with pneumonia, pleural effusion, and urinary tract infection. All published cases of clinically invasive
Ureaplasma
infections in the adult population are also reviewed.
High Diversity ofMycobacterium tuberculosisGenotypes in South Africa and Preponderance of Mixed Infections among ST53 Isolates
Authors: Stavrum Ruth , Mphahlele Matsie , Øvreås Kristi , Muthivhi Tshilidzi , Fourie P. Bernard , Weyer Karin , Grewal Harleen M. S. 
Published: April 2009

ABSTRACTThe reemergence of tuberculosis (TB) has become a major health problem worldwide, especially in Asia and Africa. Failure to combat this disease due to nonadherence or inappropriate drug regimens has selected for the emergence of multiple-drug-resistant (MDR) TB. The development of new molecular genotyping techniques has revealed the presence of mixedMycobacterium tuberculosisinfections, which may accelerate the emergence of drug-resistant strains. There are some studies describing the local distribution of circulating strains in South Africa, but to date, reports describing the frequency and distribution ofM.tuberculosisgenotypes, and specifically MDR genotypes, across the different provinces are limited. Thus, 252 isolates (of which 109 were MDR) from eight of the nine provinces of South Africa were analyzed by spoligotyping. Spoligotyping showed 10 different lineages, and ST53 (11.1%) and ST1 (10.3%) were the most frequent genotypes. Of the 75 different spoligopatterns observed, 20 (7.9%) were previously unreported. Analysis of the mycobacterial interspersed repetitive units of variable-number tandem repeats of the ST53 and ST1 isolates revealed that ∼54% of the ST53 isolates were of mixedM.tuberculosissubpopulations. Drug resistance (defined as resistance to at least isoniazid and/or rifampin) could only be linked to a history of previous anti-TB treatment (adjusted odds ratio, 4.0; 95% confidence interval, 2.27 to 7.10;P= <0.0001). This study describes a high diversity of circulating genotypes in South Africa in addition to a high frequency of mixedM.tuberculosissubpopulations among the ST53 isolates. MDR TB in South Africa could not be attributed to the spread of any single lineage.