bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Transcriptome Analysis of
Listeria monocytogenes
Strains of the Two Major Lineages Reveals Differences in Virulence, Cell Wall, and Stress Response
Authors: Severino Patricia , Dussurget Olivier , Vêncio Ricardo Z. N. , Dumas Emilie , Garrido Patricia , Padilla Gabriel , Piveteau Pascal , Lemaître Jean-Paul , Kunst Frank , Glaser Philippe , Buchrieser Carmen 
Published: August 2007

ABSTRACT

Listeria monocytogenes
is a food-borne, opportunistic, bacterial pathogen causing a wide spectrum of diseases, including meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13
L. monocytogenes
serovars described, human listeriosis is mostly associated with strains of serovars 4b, 1/2b, and 1/2a. Within the species
L. monocytogenes
, three phylogenetic lineages are described. Serovar 1/2a belongs to phylogenetic lineage I, while serovars 4b and 1/2b group in phylogenetic lineage II. To explore the role of gene expression in the adaptation of
L. monocytogenes
strains of these two major lineages to different environments, as well as in virulence, we performed whole-genome expression profiling of six
L. monocytogenes
isolates of serovars 4b, 1/2b, and 1/2a of distinct origins, using a newly constructed
Listeria
multigenome DNA array. Comparison of the global gene expression profiles revealed differences among strains. The expression profiles of two strains having distinct 50% lethal doses, as assessed in the mouse model, were further analyzed. Gene ontology term enrichment analysis of the differentially expressed genes identified differences in protein-, nucleic acid-, carbon metabolism-, and virulence-related gene expression. Comparison of the expression profiles of the core genomes of all strains revealed differences between the two lineages with respect to cell wall synthesis, the stress-related sigma B regulon and virulence-related genes. These findings suggest different patterns of interaction with host cells and the environment, key factors for host colonization and survival in the environment.
Changes in Nucleoid Morphology and Origin Localization upon Inhibition or Alteration of the Actin Homolog, MreB, ofVibrio cholerae
Authors: Srivastava Preeti , Demarre Gäelle , Karpova Tatiana S. , McNally James , Chattoraj Dhruba K. 
Published: August 2007

ABSTRACTMreB is an actin homolog required for the morphogenesis of most rod-shaped bacteria and for other functions, including chromosome segregation. InCaulobacter crescentusandEscherichia coli, the protein seems to play a role in the segregation of sister origins, but its role inBacillus subtilischromosome segregation is less clear. To help clarify its role in segregation, we have here studied the protein inVibrio cholerae, whose chromosome I segregates like the one inC. crescentusand whose chromosome II like the one inE. coliorB. subtilis. The properties ofVibrioMreB were similar to those of its homologs in other bacteria in that it formed dynamic helical filaments, was essential for viability, and was inhibited by the drug A22. Wild-type (WT) cells exposed to A22 became spherical and larger. The nucleoids enlarged correspondingly, and the origin positions for both the chromosomes no longer followed any fixed pattern. However, the sister origins separated, unlike the situation in other bacteria. In mutants isolated as A22 resistant, the nucleoids in some cases appeared compacted even when the cell shape was nearly normal. In these cells, the origins of chromosome I were at the distal edges of the nucleoid but not all the way to the poles where they normally reside. The sister origins of chromosome II also separated less. Thus, it appears that the inhibition or alteration ofVibrioMreB can affect both the nucleoid morphology and origin localization.
The NtcA-Regulated
amtB
Gene Is Necessary for Full Methylammonium Uptake Activity in the Cyanobacterium
Synechococcus elongatus
Authors: Paz-Yepes Javier , Herrero Antonia , Flores Enrique 
Published: August 2007

ABSTRACT

The Amt proteins constitute a ubiquitous family of transmembrane ammonia channels that permit the net uptake of ammonium by cells. In many organisms, there is more than one
amt
gene, and these genes are subjected to nitrogen control. The mature Amt protein is a homo- or heterooligomer of three Amt subunits. We previously characterized an
amt1
gene in the unicellular cyanobacterium
Synechococcus elongatus
strain PCC 7942. In this work, we describe the presence in this organism of a second
amt
gene,
amtB
, which encodes a protein more similar to the bacterial AmtB proteins than to any other characterized cyanobacterial Amt protein. The expression of
amtB
took place in response to nitrogen step-down, required the NtcA transcription factor, and occurred parallel to the expression of
amt1
. However, the transcript levels of
amtB
measured after 2 h of nitrogen deprivation were about 100-fold lower than those of
amt1
. An
S. elongatus amtB
insertional mutant exhibited an activity for uptake of [
14
C]methylammonium that was about 55% of that observed in the wild type, but inactivation of
amtB
had no noticeable effect on the uptake of ammonium when it was supplied at a concentration of 100 μM or more. Because an
S. elongatus amt1
mutant is essentially devoid of [
14
C]methylammonium uptake activity, the mature Amt transporter is functional in the absence of AmtB subunits but not in the absence of Amt1 subunits. However, the
S. elongatus amtB
mutant could not concentrate [
14
C]methylammonium within the cells to the same extent as the wild type. Therefore, AmtB is necessary for full methylammonium uptake activity in
S. elongatus
.
Diversity of Bacteriocins and Activity Spectrum inStreptococcus pneumoniae
Authors: Lux Thomas , Nuhn Michael , Hakenbeck Regine , Reichmann Peter 
Published: August 2007

ABSTRACTThe production of bacteriocins can be favorable for colonization of the host by eliminating other bacterial species that share the same environment. InStreptococcus pneumoniae, thepnc(blp) locus encoding putative bacteriocins, immunity, and export proteins is controlled by a two-component system similar to thecomCDEsystem required for the induction of genetic competence. A detailed comparison of thepncclusters of four genetically distinct isolates confirmed the great plasticity of this locus and documented several repeat sequences. Members of the multiple-antibiotic-resistant Spain23F-1 clone, one member of the Spain9V-3 clone, sensitive 23F strain 2306, and the TIGR4 strain produced bactericidal substances active against other gram-positive bacteria and in some cases againstS. pneumoniaeas well. However, other strains did not show activity against the indicator strains despite the presence of a bacteriocin cluster, indicating that other factors are required for bacteriocin activity. Analysis of strain 2306 and mutant derivatives of this strain confirmed that bacteriocin production was dependent on the two-component regulatory system and genes involved in bacteriocin transport and processing. At least one other bacteriocin gene,pncE, is located elsewhere on the chromosome and might contribute to the bacteriocin activity of this strain.
Induction of RpoS Degradation by the Two-Component System Regulator RstA in
Salmonella enterica
Authors: Cabeza María L. , Aguirre Andrés , Soncini Fernando C. , Véscovi Eleonora García 
Published: August 2007

ABSTRACT

Bacterial survival in diverse and changing environments relies on the accurate interplay between different regulatory pathways, which determine the design of an adequate adaptive response. The proper outcome depends on a precise gene expression profile generated from the finely tuned and concerted action of transcriptional factors of distinct regulatory hierarchies.
Salmonella enterica
serovar Typhimurium harbors multiple regulatory systems that are crucial for the bacterium to cope with harsh extra- and intracellular environments. In this work, we found that the expression of
Salmonella
RstA, a response regulator from the two-component system family, was able to downregulate the expression of three RpoS-controlled genes (
narZ
,
spvA
, and
bapA
). Furthermore, this downregulation was achieved by a reduction in RpoS cellular levels. The alternative sigma factor RpoS is critical for bacterial endurance under the most-stressful conditions, including stationary-phase entrance and host adaptation. Accordingly, RpoS cellular levels are tightly controlled by complex transcriptional, translational, and posttranslational mechanisms. The analysis of each regulatory step revealed that in
Salmonella
, RstA expression was able to promote RpoS degradation independently of the MviA-ClpXP proteolytic pathway. Additionally, we show that RstA is involved in modulating
Salmonella
biofilm formation. The fact that the RpoS-modulated genes affected by RstA expression have previously been demonstrated to contribute to
Salmonella
pathogenic traits, which include biofilm-forming capacity, suggests that under yet unknown conditions, RstA may function as a control point of RpoS-dependent pathways that govern
Salmonella
virulence.
The Circadian Clock-Related Gene
pex
Regulates a Negative
cis
Element in the
kaiA
Promoter Region
Authors: Kutsuna Shinsuke , Kondo Takao , Ikegami Haruki , Uzumaki Tatsuya , Katayama Mitsunori , Ishiura Masahiro 
Published: August 2007

ABSTRACT

In the cyanobacterium
Synechococcus
sp. strain PCC 7942, a circadian clock-related gene,
pex
, was identified as the gene prolonging the period of the clock. A PadR domain, which is a newly classified transcription factor domain, and the X-ray crystal structure of the Pex protein suggest a role for Pex in transcriptional regulation in the circadian system. However, the regulatory target of the Pex protein is unknown. To determine the role of Pex, we monitored bioluminescence rhythms that reported the expression activity of the
kaiA
gene or the
kaiBC
operon in
pex
deficiency,
pex
constitutive expression, and the wild-type genotype. The expression of
kaiA
in the
pex
-deficient or constitutive expression genotype was 7 or 1/7 times that of the wild type, respectively, suggesting that
kaiA
is the target of negative regulation by Pex. In contrast, the expression of the
kaiBC
gene in the two
pex
-related genotypes was the same as that in the wild type, suggesting that Pex specifically regulates
kaiA
expression. We used primer extension analysis to map the transcription start site for the
kaiA
gene 66 bp upstream of the translation start codon. Mapping with deletion and base pair substitution of the
kaiA
upstream region revealed that a 5-bp sequence in this region was essential for the regulation of
kaiA
. The repression or constitutive expression of the
kaiA
transgene caused the prolongation or shortening of the circadian period, respectively, suggesting that the Pex protein changes the period via the negative regulation of
kaiA
.
The Motors Powering A-Motility in
Myxococcus xanthus
Are Distributed along the Cell Body
Authors: Sliusarenko Oleksii , Zusman David R. , Oster George 
Published: August 2007

ABSTRACT

Two models have been proposed to explain the adventurous gliding motility of
Myxococcus xanthus
: (i) polar secretion of slime and (ii) an unknown motor that uses cell surface adhesion complexes that form periodic attachments along the cell length. Gliding movements of the leading poles of cephalexin-treated filamentous cells were observed but not equivalent movements of the lagging poles. This demonstrates that the adventurous-motility motors are not confined to the rear of the cell.
The Extension of the Fourth Transmembrane Helix of the Sensor Kinase KdpD ofEscherichia coliIs Involved in Sensing
Authors: Zimmann Petra , Steinbrügge Anne , Schniederberend Maren , Jung Kirsten , Altendorf Karlheinz 
Published: August 2007

ABSTRACTThe KdpD sensor kinase and the KdpE response regulator control expression of thekdpFABCoperon coding for the KdpFABC high-affinity K+transport system ofEscherichia coli. In search of a distinct part of the input domain of KdpD which is solely responsible for K+sensing, sequences ofkdpDencoding the transmembrane region and adjacent N-terminal and C-terminal extensions were subjected to random mutagenesis. Nine KdpD derivatives were identified that had lost tight regulation ofkdpFABCexpression. They all carried single amino acid replacements located in a region encompassing the fourth transmembrane helix and the adjacent arginine cluster of KdpD. All mutants exhibited high levels ofkdpFABCexpression regardless of the external K+concentration. However, 3- to 14-fold induction was observed under extreme K+-limiting conditions and in response to an osmotic upshift when sucrose was used as an osmolyte. These KdpD derivatives were characterized by a reduced phosphatase activity in comparison to the autokinase activity in vitro, which explains constitutive expression. Whereas for wild-type KdpD the autokinase activity and also, in turn, the phosphotransfer activity to KdpE were inhibited by increasing concentrations of K+, both activities were unaffected in the KdpD derivatives. These data clearly show that the extension of the fourth transmembrane helix encompassing the arginine cluster is mainly involved in sensing both K+limitation and osmotic upshift, which may not be separated mechanistically.
The
sbcDC
Locus Mediates Repression of Type 5 Capsule Production as Part of the SOS Response in
Staphylococcus aureus
Authors: Chen Zhongyi , Luong Thanh T. , Lee Chia Y. 
Published: August 2007

ABSTRACT

Most strains of
Staphylococcus aureus
produce one type of capsular polysaccharide that belongs to either type 5 or type 8. The production of these capsules has been shown to be regulated by various regulators. Here we report that the
sbcD
and
sbcC
genes are involved in the repression of type 5 capsule production. Chromosomal deletions in the
sbcDC
genes resulted in increased capsule promoter activity, capsule gene transcripts, and capsule production. The survival rates of the
sbcDC
deletion mutant were reduced upon UV irradiation compared to those for the wild-type strain Newman, suggesting that the genes are involved in DNA repair in
S. aureus
. The two genes were organized as an operon and were expressed very early in the exponential growth phase. A subinhibitory concentration of ciprofloxacin or mitomycin C induced
sbcDC
transcription but repressed the capsule promoter activity, suggesting that the
sbcDC
genes and the capsule genes are part of the SOS regulon. By reporter gene fusion and Northern blotting, we found that
sbcDC
regulated capsule by downregulating
arl
and
mgr
. Further genetic studies indicate that
sbcDC
functions upstream of
arl
and
mgr
in capsule regulation. Collectively, our results indicate that
sbcDC
, upon the SOS response, represses type 5 capsule production through an
arl
-
mgr
pathway. To our knowledge, this is the first demonstration that an SbcDC homolog was involved in transcriptional regulation.
Comparison of the BD GeneOhm VanR Assay to Culture for Identification of Vancomycin-Resistant Enterococci in Rectal and Stool Specimens
Authors: Stamper Paul D. , Cai Mian , Lema Clara , Eskey Kim , Carroll Karen C. 
Published: August 2007

ABSTRACT

Active screening for vancomycin-resistant enterococci (VRE) in rectal and stool specimens has been recommended to limit the spread of antimicrobial resistance within certain high-risk populations. Directly from 502 rectal swabs and stool specimens, we evaluated the diagnostic performance of the BD GeneOhm VanR assay (BD GeneOhm, San Diego, CA), a rapid real-time PCR test that detects the presence of
vanA
and/or
vanB
genes. The VanR assay was compared to culture consisting of both bile-esculin-azide agar with 6 μg/ml vancomycin (BEAV agar) (BD Diagnostics, Sparks, MD) and BEAV broth with 8 μg/ml vancomycin (Hardy Diagnostics, Santa Maria, CA). Enterococci were identified to the species level using standard biochemical tests and a Phoenix automated microbiology system (BD Diagnostics, Sparks, MD). The susceptibility of the enterococci to vancomycin and teicoplanin was determined using an Etest (AB Biodisk, Solna, Sweden). VRE were initially isolated from 147 cultures, and the VanR assay detected 142 of the 147 positive cultures for a sensitivity of 96.6%. The specificity was 87.0% (309/355) largely due to false positives seen with the
vanB
portion of the assay. The sensitivity when testing rectal swabs was 98.3%, and the sensitivity for stool samples was 95.4% (
P
= 0.643). The specificity of rectal swabs was comparable to that of the stool specimens (87.5% and 86.5%, respectively). When used only to detect VanA resistance, the VanR assay was 94.4% (136/144) sensitive and 96.4% (345/358) specific, with positive and negative predictive values of 91.3% and 97.7%, respectively. In summary, the BD GeneOhm VanR assay is a good screening test for VRE in our population of predominantly
vanA
-colonized patients. However, patient samples testing only
vanB
positive should be confirmed by another method for the presence of VRE.
Comparisons of self-reported and register data on sickness absence among public employees in Sweden
Authors: Voss M , Stark S , Alfredsson L , Vingård E , Josephson M 
Published: August 2007

Aim:Self-reported assessments of sickness absence are often performed in epidemiological studies. The objective of this study was to compare the number of sick-leave days according to self-reported data over 12 months with data from the employer’s register for the same period. An additional aim was to ascertain whether the self-reported information and the recorded data would show equivalent associations with self-reported general health.Methods:The study was based on a cohort of 4869 municipal employees in Sweden, about 80% women, who answered a questionnaire in 2001–2. The responses provided by the employees included information on number of sick-leave days and self-rated health. Data on sick-leave days, occupation and age were derived from the employers’ computerised registers. The questionnaire information on sick-leave days was compared with the corresponding information retrieved from the employer register by means of calculating sensitivity and specificity, using the employers’ data as the “gold standard”.Results:The annual number of sick-leave days was lower according to the self-reported information than to the register data. For women the agreement between the two sickness absence measures for no sick-leave days, 1–7 days and ≥28 days were 74%, 72% and 67%, respectively. The sensitivity of questionnaire versus register information regarding any self-reported sick-leave day was 91% and the specificity was 74%. Sensitivity and specificity for sickness absence ⩾28 days were 67% and 98%, respectively. The results for men were similar to those for women. Self-reported and recorded sickness absence were both associated with self-rated health. The odds ratios were 7.27 and 8.25, for subjects with ≥28 recorded and self-reported number of sick-leave days respectively, compared to subjects with no sickness absence.Conclusions:Good agreement was found between self-reported and register information on sickness absence. Self-reported data on sickness absence may be useful in common epidemiological applications.
Experimental exposure to wood smoke: effects on airway inflammation and oxidative stress
Authors: Barregard L , Sällsten G , Andersson L , Almstrand A-C , Gustafson P , Andersson M , Olin A-C 
Published: August 2007

Background:Particulate air pollution affects cardiovascular and pulmonary disease and mortality. A main hypothesis about the mechanisms involved is that particles induce inflammation in lower airways, systemic inflammation and oxidative stress.Objectives:To examine whether short-term exposure to wood smoke in healthy subjects affects markers of pulmonary inflammation and oxidative stress.Methods:13 subjects were exposed first to clean air and then to wood smoke in a chamber during 4-hour sessions, 1 week apart. The mass concentrations of fine particles at wood smoke exposure were 240–280 μg/m3, and number concentrations were 95 000–180 000/cm3, about half of the particles being ultrafine (<100 nm). Blood and breath samples were taken before and at various intervals after exposure to wood smoke and clean air and examined for exhaled nitric oxide and Clara cell protein in serum and urine, and malondialdehyde in exhaled breath condensate.Results:Exposure to wood smoke increased alveolar nitric oxide 3 hours post-exposure while malondialdehyde levels in breath condensate were higher both immediately after and 20 hours after exposure. Serum Clara cell protein was increased 20 hours after exposure.Conclusions:Wood smoke at levels that can be found in smoky indoor environments caused an inflammatory response and signs of increased oxidative stress in the respiratory tract, especially in the lower airways.
Cancer risk after cessation of asbestos exposure: a cohort study of Italian asbestos cement workers
Authors: Magnani C , Ferrante D , Barone-Adesi F , Bertolotti M , Todesco A , Mirabelli D , Terracini B 
Published: August 2007

Objectives:We aimed to study mortality for asbestos related diseases and the incidence of mesothelioma in a cohort of Italian asbestos cement workers after cessation of asbestos exposure.Methods:The Eternit factory operated from 1907 to 1986. The cohort included 3434 subjects active in 1950 or hired in 1950–86, ascertained from company records, without selections. Local reference rates were used for both mortality and mesothelioma incidence.Results:Mortality was increased in both sexes for all causes (overall 1809 observed (obs) vs 1312.3 expected (exp); p<0.01), pleural (135 obs vs 3.6 exp; p<0.01) and peritoneal (52 vs 1.9; p<0.01) malignancies and lung cancer (249 vs 103.1; p<0.01). In women, ovarian (9 vs 4.0; p<0.05) and uterine (15 vs 5.8; p<0.01) malignancies were also in excess. No statistically significant increase was found for laryngeal cancer (16 obs vs 12.2 exp). In Poisson regression analyses, the RR of death from pleural neoplasm linearly increased with duration of exposure, while it showed a curvilinear increase with latency and time since cessation of exposure. RR for peritoneal neoplasm continued to increase by latency, duration and time since cessation of exposure. RR for lung cancer showed a reduction after 15 years since cessation of exposure and levelled off after 40 years of latency.Conclusion:This study of a cohort of asbestos exposed workers with very long follow-up confirmed the reduction in risk of death from lung cancer after the end of exposure. It also suggested a reduction in risk for pleural mesothelioma with over 40 years of latency, while risk for peritoneal mesothelioma showed a continuing increase.