bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Hypercompetence in
Legionella pneumophila
Authors: Sexton Jessica A. , Vogel Joseph P. 
Published: June 2004

ABSTRACT

Although many bacteria are known to be naturally competent for DNA uptake, this ability varies dramatically between species and even within a single species, some isolates display high levels of competence while others seem to be completely nontransformable. Surprisingly, many nontransformable bacterial strains appear to encode components necessary for DNA uptake. We believe that many such strains are actually competent but that this ability has been overlooked because standard laboratory conditions are inappropriate for competence induction. For example, most strains of the gram-negative bacterium
Legionella pneumophila
are not competent under normal laboratory conditions of aerobic growth at 37°C. However, it was previously reported that microaerophilic growth at 37°C allows
L
.
pneumophila
serogroup 1 strain AA100 to be naturally transformed. Here we report that another
L
.
pneumophila
serogroup 1 strain, Lp02, can also be transformed under these conditions. Moreover, Lp02 can be induced to high levels of competence by a second set of conditions, aerobic growth at 30°C. In contrast to Lp02, AA100 is only minimally transformable at 30°C, indicating that Lp02 is hypercompetent under these conditions. To identify potential causes of hypercompetence, we isolated mutants of AA100 that exhibited enhanced DNA uptake. Characterization of these mutants revealed two genes,
proQ
and
comR
, that are involved in regulating competence in
L
.
pneumophila
. This approach, involving the isolation of hypercompetent mutants, shows great promise as a method for identifying natural transformation in bacterial species previously thought to be nontransformable.
Vibrio fischeri
LuxS and AinS: Comparative Study of Two Signal Synthases
Authors: Lupp Claudia , Ruby Edward G. 
Published: June 2004

ABSTRACT

Vibrio fischeri
possesses two acyl-homoserine lactone quorum-sensing systems,
ain
and
lux
, both of which are involved in the regulation of luminescence gene expression and are required for persistent colonization of the squid host,
Euprymna scolopes
. We have previously demonstrated that the
ain
system induces luminescence at cell densities that precede
lux
system activation. Our data suggested that the
ain
system both relieves repression and initially induces the
lux
system, thereby achieving sequential induction of gene expression by these two systems. Analysis of the
V. fischeri
genome revealed the presence of a putative third system based on the enzyme LuxS, which catalyzes the synthesis of the
Vibrio harveyi
autoinducer 2 (AI-2). In this study, we investigated the impact of
V. fischeri
LuxS on luminescence and colonization competence in comparison to that of the
ain
system. Similar to the
ain
system, inactivation of the AI-2 system decreased light production in culture, but not in the squid host. However, while an
ainS
mutant produces no detectable light in culture, a
luxS
mutant expressed approximately 70% of wild-type luminescence levels. A mutation in
luxS
alone did not compromise symbiotic competence of
V. fischeri
; however, levels of colonization of an
ainS luxS
double mutant were reduced to 50% of the already diminished level of
ainS
mutant colonization, suggesting that these two systems regulate colonization gene expression synergistically through a common pathway. Introduction of a
luxO
mutation into the
luxS
and
ainS luxS
background could relieve both luminescence and colonization defects, consistent with a model in which LuxS, like AinS, regulates gene expression through LuxO. Furthermore, while
luxS
transcription appeared to be constitutive and the AI-2 signal concentration did not change dramatically, our data suggest that
ainS
transcription is autoregulated, resulting in an over 2,000-fold increase in signal concentration as culture density increased. Taken together, these data indicate that
V. fischeri
LuxS affects both luminescence regulation and colonization competence; however, its quantitative contribution is small when compared to that of the AinS signal.
Control of Photosynthetic and High-Light-Responsive Genes by the Histidine Kinase DspA: Negative and Positive Regulation and Interactions between Signal Transduction Pathways
Authors: Hsiao Hui-Yi , He Qingfang , van Waasbergen Lorraine G. , Grossman Arthur R. 
Published: June 2004

ABSTRACT

We have deleted a gene for a sensor histidine kinase,
dspA
(or
hik33
), in the cyanobacterium
Synechocystis
sp. strain PCC6803. In low and moderate light, the mutant grew slowly under photoautotrophic conditions, with a doubling time of ∼40 h, and had severely reduced photosynthetic oxygen evolution. When the mutant was maintained in low or moderate light in the presence of glucose, its growth rate was only somewhat lower than that of wild-type cells. However, the mutant was light sensitive and rapidly died in high light. Furthermore, levels of many transcripts encoding genes associated with photosynthesis were altered in the mutant relative to wild-type
Synechocystis
sp. strain PCC6803 both in low light and following exposure to high light. There was constitutive expression of several high-light-inducible genes, including
hli
,
psbAIII
, and
gpx2
; there was little increased accumulation of
sodB
mRNA in high light; and the cells failed to accumulate
cpcBA
and
psaAB
mRNAs in low light in the presence of glucose, although a normal decline in the levels of these mRNAs was observed during exposure to high light. These results suggest that DspA is involved in controlling sets of photosynthetic and high-light-responsive genes, either directly or indirectly. These and other results, some of which are presented in a companion paper (C.-J. Tu, J. Shrager, R. Burnap, B. L. Postier, and A. R. Grossman, J. Bacteriol. 186:3889-3902, 2004), suggest that DspA acts as a global regulator that helps coordinate cellular metabolism with growth limitations imposed by environmental conditions.
Extensive Genomic Diversity in Pathogenic
Escherichia coli
and
Shigella
Strains Revealed by Comparative Genomic Hybridization Microarray
Authors: Fukiya Satoru , Mizoguchi Hiroshi , Tobe Toru , Mori Hideo 
Published: June 2004

ABSTRACT

Escherichia coli
, including the closely related genus
Shigella
, is a highly diverse species in terms of genome structure. Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of
E. coli
K-12 with the gene contents of pathogenic strains. Missing genes in a pathogen were detected on a microarray slide spotted with 4,071 open reading frames (ORFs) of W3110, a commonly used wild-type K-12 strain. For 22 strains subjected to the CGH microarray analyses 1,424 ORFs were found to be absent in at least one strain. The common backbone of the
E. coli
genome was estimated to contain about 2,800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions. Prophages, cell envelope genes, transporter genes, and regulator genes in the K-12 genome often were not present in pathogens. The gene contents of the strains tested were recognized as a matrix for a neighbor-joining analysis. The phylogenic tree obtained was consistent with the results of previous studies. However, unique relationships between enteroinvasive strains and
Shigella
, uropathogenic, and some enteropathogenic strains were suggested by the results of this study. The data demonstrated that the CGH microarray technique is useful not only for genomic comparisons but also for phylogenic analysis of
E. coli
at the strain level.
CovS Inactivates CovR and Is Required for Growth under Conditions of General Stress in
Streptococcus pyogenes
Authors: Dalton Tracy L. , Scott June R. 
Published: June 2004

ABSTRACT

The gram-positive human pathogen
Streptococcus pyogenes
(group A streptococcus [GAS]) causes diseases ranging from mild and often self-limiting infections of the skin or throat to invasive and life-threatening illnesses. To cause such diverse types of disease, the GAS must be able to sense adverse environments and regulate its gene expression accordingly. The CovR/S two-component signal transduction regulatory system in GAS represses about 15% of the GAS genome, including many genes involved in virulence, in response to the environment. We report that CovR is still able to repress transcription from several promoters in the absence of the putative histidine kinase sensor for this system, CovS. We also show that a phosphorylation site mutant (D53A) of CovR is unable to repress gene expression. In addition, we report that a strain with a nonpolar mutation in CovS does not grow at a low pH, elevated temperature, or high osmolarity. The stress-related phenotypes of the CovS mutant were complemented by expression of
covS
from a plasmid. Selection for growth of a CovS mutant under stress conditions resulted in isolation of second-site mutations that inactivated
covR
, indicating that CovR and CovS act in the same pathway. Also, at 40°C in the wild-type strain, CovR appeared to be less active on the promoter tested, which is consistent with the hypothesis that it was partially inactivated by CovS. We suggest that under mild stress conditions, CovS inactivates CovR, either directly or indirectly, and that this inactivation relieves repression of many GAS genes, including the genes needed for growth of GAS under stress conditions and some genes that are necessary for virulence. Growth of many gram-positive bacteria under multiple-stress conditions requires alteration of promoter recognition produced by RNA polymerase association with the general stress response sigma factor, σ
B
. We provide evidence that for GAS, which lacks a
sigB
ortholog, growth under stress conditions requires the CovR/S two-component regulatory system instead. This two-component system in GAS thus appears to perform a function for which other gram-positive bacteria utilize an alternative sigma factor.
Genomic Diversity of
Burkholderia pseudomallei
Clinical Isolates: Subtractive Hybridization Reveals a
Burkholderia mallei
-Specific Prophage in
B. pseudomallei
1026b
Authors: DeShazer David 
Published: June 2004

ABSTRACT

Burkholderia pseudomallei
is the etiologic agent of the disease melioidosis and is a category B biological threat agent. The genomic sequence of
B. pseudomallei
K96243 was recently determined, but little is known about the overall genetic diversity of this species. Suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of
B. pseudomallei
, 1026b and K96243. Numerous mobile genetic elements, including a temperate bacteriophage designated φ1026b, were identified among the 1026b-specific suppression subtractive hybridization products. Bacteriophage φ1026b was spontaneously produced by 1026b, and it had a restricted host range, infecting only
Burkholderia mallei
. It possessed a noncontractile tail, an isometric head, and a linear 54,865-bp genome. The mosaic nature of the φ1026b genome was revealed by comparison with bacteriophage φE125, a
B. mallei
-specific bacteriophage produced by
Burkholderia thailandensis
. The φ1026b genes for DNA packaging, tail morphogenesis, host lysis, integration, and DNA replication were nearly identical to the corresponding genes in φE125. On the other hand, φ1026b genes involved in head morphogenesis were similar to head morphogenesis genes encoded by
Pseudomonas putida
and
Pseudomonas aeruginosa
bacteriophages. Consistent with this observation, immunogold electron microscopy demonstrated that polyclonal antiserum against φE125 reacted with the tail of φ1026b but not with the head. The results presented here suggest that
B. pseudomallei
strains are genetically heterogeneous and that bacteriophages are major contributors to the genomic diversity of this species. The bacteriophage characterized in this study may be a useful diagnostic tool for differentiating
B. pseudomallei
and
B. mallei
, two closely related biological threat agents.
Effects of Perturbing Nucleoid Structure on Nucleoid Occlusion-Mediated Toporegulation of FtsZ Ring Assembly
Authors: Sun Qin , Margolin William 
Published: June 2004

ABSTRACT

In
Escherichia coli
, assembly of the FtsZ ring (Z ring) at the cell division site is negatively regulated by the nucleoid in a phenomenon called nucleoid occlusion (NO). Previous studies have indicated that chromosome packing plays a role in NO, as
mukB
mutants grown in rich medium often exhibit FtsZ rings on top of diffuse, unsegregated nucleoids. To address the potential role of overall nucleoid structure on NO, we investigated the effects of disrupting chromosome structure on Z-ring positioning. We found that NO was mostly normal in cells with inactivated DNA gyrase or in
mukB
-null mutants lacking
topA
, although some suppression of NO was evident in the latter case. Previous reports suggesting that transcription, translation, and membrane insertion of proteins (“transertion”) influence nucleoid structure prompted us to investigate whether disruption of these activities had effects on NO. Blocking transcription caused nucleoids to become diffuse, and FtsZ relocalized to multiple bands on top of these nucleoids, biased towards midcell. This suggested that these diffuse nucleoids were defective in NO. Blocking translation with chloramphenicol caused characteristic nucleoid compaction, but FtsZ rarely assembled on top of these centrally positioned nucleoids. This suggested that NO remained active upon translation inhibition. Blocking protein secretion by thermoinduction of a
secA
(Ts) strain caused a chromosome segregation defect similar to that in
parC
mutants, and NO was active. Although indirect effects are certainly possible with these experiments, the above data suggest that optimum NO activity may require specific organization and structure of the nucleoid.
Genes Involved in Formation of Structured Multicellular Communities byBacillus subtilis
Authors: Branda Steven S. , González-Pastor José Eduardo , Dervyn Etienne , Ehrlich S. Dusko , Losick Richard , Kolter Roberto 
Published: June 2004

ABSTRACTThe spore-forming bacteriumBacillus subtilisis capable of assembling multicellular communities (biofilms) that display a high degree of spatiotemporal organization. Wild strains that have not undergone domestication in the laboratory produce particularly robust biofilms with complex architectural features, such as fruiting-body-like aerial projections whose tips serve as preferential sites for sporulation. To discover genes involved in this multicellular behavior and to do so on a genome-wide basis, we took advantage of a large collection of mutants which have disruptions of most of the uncharacterized genes in theB. subtilisgenome. This collection, which was generated with a laboratory strain, was screened for mutants that were impaired in biofilm formation. This subset of mutated genes was then introduced into the wild strain NCIB 3610 to study their effects on biofilm formation in liquid and solid media. In this way we identified six genes that are involved in the development of multicellular communities. These areyhxB(encoding a putative phosphohexomutase that may mediate exopolysaccharide synthesis),sipW(encoding a signal peptidase),ecsB(encoding an ABC transporter subunit),yqeK(encoding a putative phosphatase),ylbF(encoding a regulatory protein), andymcA(a gene of unknown function). Further analysis revealed that these six genes play different roles inB. subtiliscommunity development.
Cross-Regulation in
Vibrio parahaemolyticus
: Compensatory Activation of Polar Flagellar Genes by the Lateral Flagellar Regulator LafK
Authors: Kim Yun-Kyeong , McCarter Linda L. 
Published: June 2004

ABSTRACT

Gene organization and hierarchical regulation of the polar flagellar genes of
Vibrio parahaemolyticus
,
Vibrio cholerae
, and
Pseudomonas aeruginosa
appear highly similar, with one puzzling difference. Two σ
54
-dependent regulators are required to direct different classes of intermediate flagellar gene expression in
V. cholerae
and
P. aeruginosa
, whereas the
V. parahaemolyticus
homolog of one of these regulators, FlaK, appears dispensable. Here we demonstrate that there is compensatory activation of polar flagellar genes by the lateral flagellar regulator LafK.
Resuscitation of a Defective Prophage in
Salmonella
Cocultures
Authors: Figueroa-Bossi Nara , Bossi Lionello 
Published: June 2004

ABSTRACT

Widely studied
Salmonella enterica
serovar Typhimurium strains ATCC 14028s and SL1344 harbor a cryptic ST64B prophage unable to produce infectious virions. We found that coculturing either strain with an isogenic sibling lacking the prophage leads to the appearance of active forms of the virus. Active phage originates from reversion of a +1 frameshift mutation at a monotonous G:C run in a presumptive tail assembly pseudogene.
MacA, a Diheme
c
-Type Cytochrome Involved in Fe(III) Reduction by
Geobacter sulfurreducens
Authors: Butler Jessica E. , Kaufmann Franz , Coppi Maddalena V. , Núñez Cinthia , Lovley Derek R. 
Published: June 2004

ABSTRACT

A 36-kDa diheme
c
-type cytochrome abundant in Fe(III)-respiring
Geobacter sulfurreducens
, designated MacA, was more highly expressed during growth with Fe(III) as the electron acceptor than with fumarate. Although MacA has homology to proteins with in vitro peroxidase activity, deletion of
macA
had no impact on response to oxidative stress. However, the capacity for Fe(III) reduction was greatly diminished, indicating that MacA, which is predicted to be localized in the periplasm, is a key intermediate in electron transfer to Fe(III).
Design of Ferromagnetic Shape Memory Alloy Composites
Authors: Kusaka Masahiro , Taya Minoru 
Published: May 2004

Ferromagnetic shape memory alloy (FSMA) composites composed of a ferromagnetic material and a shape memory alloy (SMA) are key material systems for fast-responsive and compact actuators. The function of ferromagnetic material is to induce magnetic force which is then used to induce the stress in the SMA, resulting in the stress-induced marten site transformation (SIM), i.e. change in the Young’s modulus, stiff (austenite) to soft (martensite). This SIM-induced phase change causes larger deformation in the SMA, which is often termed as “superelastic”. This paper discusses a simple model by which the stress and strain field in the FSMA composites subjected to bending and torsion loading are computed with the aim of identifying the optimum geometry of FSMA composites. The results of the present analytical study are utilized to design torque actuator (bending of FSMA composite plate) and spring actuator (torsion of helical FSMA composite spring).
Vascular viewpoint
Authors: Tran Huyen 
Published: May 2004

Question: Is a history of pre-existing atherothrombotic disease associated with an increased risk of subsequent ischemic events, and is it associated with a reduction in efficacy of clopidogrel? Population: Patients with recent ischemic stroke (IS), myocardial infarction (MI), or established peripheral arterial disease, and a history of pre-existing symptomatic atherothrombotic disease (IS and=or MI) were enrolled in the Clopidogrel versus Aspirin in Patients at Risk of Ischemic Events (CAPRIE) trial. CAPRIE was a randomized, blinded, clinical trial comparing the efficacy of clopidogrel with aspirin in patients at risk of ischemic events. Design and methods: Retrospective, subgroup analysis of 4496 patients with a prior history of symptomatic atherothrombotic disease from the CAPRIE study. Results: Compared with the overall population of CAPRIE, patients with pre-existing symptomatic atherothrombotic disease have elevated rates of IS, MI, or vascular death. The 3-year rates of IS, MI, or vascular death were 20.4% with clopidogrel and 23.8% with aspirin (absolute risk reduction: 3.4%; 95% CI: -0.2 to 7.0; number needed to treat: 29; relative risk reduction: 14.9% (95% CI: 0.3 to 27.3; p = 0.045)). Conclusion: Patients with a history of previous symptomatic atherothrombotic disease suffer a high rate of subsequent ischemic events. Among these patients, the absolute risk reduction of clopidogrel over aspirin is greater compared with patients without pre-existing atherothrombotic disease.
Pretest Probability Estimates: A Pitfall to the Clinical Utility of Evidence‐based Medicine?
Authors: Phelps Molly A. , Levitt M. Andrew 
Published: June 2004

Abstract Objectives: The Bayesian application of likelihood ratios has become incorporated into evidence‐based medicine (EBM). This approach uses clinicians' pretest estimates of disease along with the results of diagnostic tests to generate individualized posttest disease probabilities for a given patient. To date, there is minimum scientific validation for the clinical application of this approach. This study is designed to evaluate variability in the initial step of this process, clinicians' estimates of pretest probability of disease, to assess whether this approach can be expected to yield consistent posttest disease estimates. Methods:This cross‐sectional cohort study was conducted at an urban county teaching hospital by using a sample of emergency and internal medicine residents and faculty, as well as emergency department (ED) midlevel practitioners. Participants read clinical vignettes designed to raise consideration for common ED disorders and were asked to estimate the likelihood of the suggested diagnosis based on the history and physical examination findings alone. No information about laboratory results or imaging studies was provided. Results: Mean pretest probability estimates of disease ranged from 42% (95% confidence interval [95% CI] = 36.6% to 47.4%) to 77% (95% CI = 72.9% to 81.1%). The smallest difference in pretest probability magnitude for a single vignette was 70% (range 30–100%; interquartile range [IQR] 64–80%), whereas the largest was 95% (range 3–98%; IQR 30–60%). Conclusions: Wide variability in clinicians' pretest probability estimates of disease may present a possible concern about decision‐making models based on Bayes' theorem, because it may ultimately yield inconsistent posttest disease estimates.