bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation, Integrase-Dependent Excision, and Horizontal Transfer of Genomic Islands in Legionella pneumophila
Authors: Lautner Monika , Schunder Eva , Herrmann Vroni , Heuner Klaus 
Published: January 2013

ABSTRACT

Legionella pneumophila
is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages,
Legionella
can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in
L. pneumophila
Corby (named
trb
-
tra
). Analogous versions of
trb
-
tra
are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other
Legionella
strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1,
lpc2818
) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes
lvrRABC
(
lpc2813
to
lpc2816
) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a
Legionella
genomic island (LGI) of
L. pneumophila
Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a
pilT
-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of
L. pneumophila
wild-type and mutant strains revealed that the
int-1
and
lvrRABC
genes (located on Trb-1) as well as
lpc1833
and
pilT
(located on LpcGI-2) do not influence the
in vivo
fitness of
L. pneumophila
in
Acanthamoeba castellanii
.
Streptococcus pneumoniae Folate Biosynthesis Responds to Environmental CO2Levels
Authors: Burghout Peter , Zomer Aldert , van der Gaast-de Jongh Christa E. , Janssen-Megens Eva M. , Françoijs Kees-Jan , Stunnenberg Hendrik G. , Hermans Peter W. M. 
Published: January 2013

ABSTRACTAlthough carbon dioxide (CO2) is known to be essential forStreptococcus pneumoniaegrowth, it is poorly understood how this respiratory tract pathogen adapts to the large changes in environmental CO2levels it encounters during transmission, host colonization, and disease. To identify the molecular mechanisms that facilitate pneumococcal growth under CO2-poor conditions, we generated a randomS. pneumoniaeR6marinertransposon mutant library representing mutations in 1,538 different genes and exposed it to CO2-poor ambient air. With Tn-seq, we found mutations in two genes that were involved inS. pneumoniaeadaptation to changes in CO2availability. The genepca, encoding pneumococcal carbonic anhydrase (PCA), was absolutely essential forS. pneumoniaegrowth under CO2-poor conditions. PCA catalyzes the reversible hydration of endogenous CO2to bicarbonate (HCO3−) and was previously demonstrated to facilitate HCO3−-dependent fatty acid biosynthesis. The genefolCthat encodes the dihydrofolate/folylpolyglutamate synthase was required at the initial phase of bacterial growth under CO2-poor culture conditions. FolC compensated for the growth-phase-dependent decrease inS. pneumoniaeintracellular long-chain (n> 3) polyglutamyl folate levels, which was most pronounced under CO2-poor growth conditions. In conclusion,S. pneumoniaeadaptation to changes in CO2availability involves the retention of endogenous CO2and the preservation of intracellular long-chain polyglutamyl folate pools.
The HtrA Protease of Streptococcus pneumoniae Controls Density-Dependent Stimulation of the Bacteriocin
blp
Locus via Disruption of Pheromone Secretion
Authors: Kochan Travis J. , Dawid Suzanne 
Published: January 2013

ABSTRACT

All fully sequenced strains of
Streptococcus pneumoniae
(pneumococcus) contain a version of the
blp
locus which is responsible for the regulation and secretion of a variable repertoire of pneumococcal bacteriocins called pneumocins and their associated immunity proteins. Pneumocins mediate intra- and interspecies competition
in vitro
and have been shown to provide a competitive advantage
in vivo
. Pneumocin production is stimulated by extracellular accumulation of the peptide pheromone, BlpC. Both BlpC and the functional pneumocins are secreted out of the cell via the Blp transporter, BlpAB. The conserved surface-expressed serine protease, HtrA, has been shown to limit activation of the locus and secretion of functional pneumocins. In this work, we demonstrate that
htrA
mutants stimulate the
blp
locus at lower cell density and to a greater extent than strains expressing wild-type HtrA. This effect is not due to direct proteolytic degradation of secreted pheromone by the protease, but instead is a result of HtrA-mediated disruption of peptide processing and secretion. Because pneumocins are secreted through the same transporter as the pheromone, this finding explains why pheromone supplementation cannot completely restore pneumocin inhibition to strains expressing high levels of HtrA despite restoration of
blp
transcriptional activity. HtrA restricts pneumocin production to high cell density by limiting the rate of accumulation of BlpC in the environment. Importantly, HtrA does not interfere with the ability of a strain to sense environmental pheromones, which is necessary for the induction of protective immunity in the face of pneumocin-secreting competitors.
Identification of the Mutation Responsible for the Temperature-Sensitive Lipopolysaccharide O-Antigen Defect in the Pseudomonas aeruginosa Cystic Fibrosis Isolate 2192
Authors: Davis Michael R. , Muszyński Artur , Lollett Ivonne V. , Pritchett Christopher L. , Carlson Russell W. , Goldberg Joanna B. 
Published: January 2013

ABSTRACT

Pseudomonas aeruginosa
in the lungs of cystic fibrosis (CF) patients is characterized by a series of genotypic and phenotypic changes that reflect the transition from acute to chronic infection. These include the overproduction of the exopolysaccharide alginate and the loss of complete lipopolysaccharide (LPS). LPS is a major component of the Gram-negative outer membrane and is composed of lipid A, core oligosaccharide, and O antigen. In this report, we show that the LPS defect of the
P. aeruginosa
chronic infection isolate 2192 is temperature sensitive. When grown at 25°C, 2192 expresses serotype O1 LPS with a moderate chain length and in reduced amounts relative to those of a wild-type serotype O1 laboratory strain (stO1). In contrast, 2192 expresses no LPS O antigen when grown at 37°C. This is the first time that a temperature-sensitive defect in O-antigen production has been reported. Using complementation analyses with a constructed
wbpM
deletion mutant of stO1, we demonstrate that the temperature-sensitive O-antigen production defect in 2192 is due to a mutation in
wbpM
, which encodes a UDP-4,6-GlcNAc dehydratase involved in O-antigen synthesis. The mutation, a deletion of a single amino acid (V636) from the extreme C terminus of WbpM, renders the protein less stable than its wild-type counterpart. This residue of WbpM, which is critical for stability and function, is located outside of the recognized domains of the protein and may provide insight into the structure-function relationship of this enzyme, which is found in all 20 serotypes of
P. aeruginosa
. We also identify a promoter of
wbpM
, map a transcriptional start site of
wbpM
, and show that mucoidy plays a role in the loss of expression of high-molecular-weight LPS in this CF isolate.
Biochemical Properties of MutT2 Proteins from Mycobacterium tuberculosis and M. smegmatis and Their Contrasting Antimutator Roles in Escherichia coli
Authors: Sang Pau Biak , Varshney Umesh 
Published: January 2013

ABSTRACT

Mycobacterium tuberculosis
, the causative agent of tuberculosis, is at increased risk of accumulating damaged guanine nucleotides such as 8-oxo-dGTP and 8-oxo-GTP because of its residency in the oxidative environment of the host macrophages. By hydrolyzing the oxidized guanine nucleotides before their incorporation into nucleic acids, MutT proteins play a critical role in allowing organisms to avoid their deleterious effects. Mycobacteria possess several MutT proteins. Here, we purified recombinant
M. tuberculosis
MutT2 (
Mtu
MutT2) and
M. smegmatis
MutT2 (
Msm
MutT2) proteins from
M. tuberculosis
(a slow grower) and
M. smegmatis
(fast growing model mycobacteria), respectively, for their biochemical characterization. Distinct from the
Escherichia coli
MutT, which hydrolyzes 8-oxo-dGTP and 8-oxo-GTP, the mycobacterial proteins hydrolyze not only 8-oxo-dGTP and 8-oxo-GTP but also dCTP and 5-methyl-dCTP. Determination of kinetic parameters (

K
m

and
V
max
) revealed that while
Mtu
MutT2 hydrolyzes dCTP nearly four times better than it does 8-oxo-dGTP,
Msm
MutT2 hydrolyzes them nearly equally. Also,
Msm
MutT2 is about 14 times more efficient than
Mtu
MutT2 in its catalytic activity of hydrolyzing 8-oxo-dGTP. Consistent with these observations,
Msm
MutT2 but not
Mtu
MutT2 rescues
E. coli
for MutT deficiency by decreasing both the mutation frequency and A-to-C mutations (a hallmark of MutT deficiency). We discuss these findings in the context of the physiological significance of MutT proteins.
AmrZ Modulates Pseudomonas aeruginosa Biofilm Architecture by Directly Repressing Transcription of thepslOperon
Authors: Jones Christopher J. , Ryder Cynthia R. , Mann Ethan E. , Wozniak Daniel J. 
Published: January 2013

ABSTRACTPseudomonas aeruginosastrains recovered from chronic pulmonary infections in cystic fibrosis patients are frequently mucoid. Such strains express elevated levels of alginate but reduced levels of the aggregative polysaccharide Psl; however, the mechanistic basis for this regulation is not completely understood. ElevatedpslAexpression was observed in anamrZnull mutant and in strains expressing a DNA-binding-deficient AmrZ. AmrZ is a transcription factor that positively regulates twitching motility and alginate synthesis, two phenotypes involved inP. aeruginosabiofilm development. AmrZ bound directly to thepslApromoterin vitro, and molecular analyses indicate that AmrZ repressespslexpression by binding to a site overlapping the promoter. Altered expression ofamrZin nonmucoid strains impacted biofilm structure and architecture, as structured microcolonies were observed with low AmrZ production and flat biofilms withamrZoverexpression. These biofilm phenotypes correlated with Psl levels, since we observed elevated Psl production inamrZmutants and lower Psl production inamrZ-overexpressing strains. These observations support the hypothesis that AmrZ is a multifunctional regulator mediating transition ofP. aeruginosabiofilm infections from colonizing to chronic biofilms through repression of thepsloperon while activating thealgDoperon.
GenR, an IclR-Type Regulator, Activates and Represses the Transcription ofgenGenes Involved in 3-Hydroxybenzoate and Gentisate Catabolism in Corynebacterium glutamicum
Authors: Chao Hongjun , Zhou Ning-Yi 
Published: January 2013

ABSTRACTThe genes required for 3-hydroxybenzoate and gentisate catabolism inCorynebacterium glutamicumare closely clustered in three operons. GenR, an IclR-type regulator, can activate the transcription ofgenKHandgenDFMoperons in response to 3-hydroxybenzoate and gentisate, and it can repress its own expression. Footprinting analyses demonstrated that GenR bound to four sites with different affinities. Two GenR-binding sites (DFMn01 and DFMn02) were found to be located between positions −41 and −84 upstream of the −35 and −10 regions of thegenDFMpromoter, which was involved in positive regulation ofgenDFMtranscription. The GenR binding site R-KHn01 (located between positions −47 and −16) overlapped the −35 region of thegenKHpromoter sequence and is involved in positive regulation of its transcription. The binding site R-KHn02, at which GenR binds to its own promoter, was found within a footprint extending from position −44 to −67. It appeared to be involved in negative regulation of the activity of thegenRpromoter. A consensus motif with a 5-bp imperfect palindromic sequence [ATTCC-N7(5)-GGAAT] was identified among all four GenR binding sites and found to be necessary to GenR regulation through site-directed mutagenesis. The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds.
The use of individual patient-level data (IPD) to quantify the impact of pretreatment predictors of response to treatment in chronic hepatitis B patients
Authors: Ali Shehzad , Mealing Stuart , Hawkins Neil , Lescrauwaet Benedicte , Bjork Stefan , Mantovani Lorenzo , Lampertico Pietro 
Published: January 2013

ObjectivesEvidence synthesis is an integral part decision-making by reimbursement agencies. When direct evidence is not available, network-meta-analysis (NMA) techniques are commonly used. This approach assumes that the trials are sufficiently similar in terms of treatment-effect modifiers. When imbalances in potential treatment-effect modifiers exist, the NMA approach may not produce fair comparisons. The objective of this study was to identify and quantify the interaction between treatment-effect and potential treatment-effect modifiers, including time-of-response measurement and baseline viral load in chronic hepatitis B (CHB) patients.DesignRetrospective patient-level data econometric analysis.Participants1353 individuals from two randomised controlled trials of nucleoside-naïve CHB taking 0.5 mg entecavir (n=679) or 100 mg lamivudine (n=668) daily for 48 weeks.InterventionsHepatitis B virus (HBV) DNA levels for both drugs were measured at baseline and weeks 24, 36 and 48. Generalised estimating equation for repeated binary responses was used to identify treatment-effect modifiers for response defined at ≤400 or ≤300 copies/ml.Primary outcome measuresOR at 48 weeks.ResultsThe OR for the time-of-response measurement and treatment-effect interaction term was 1.039 (p=0.00) and 1.035 (p=0.00) when response was defined at ≤400 or ≤300 copies/ml, respectively. The baseline HBV DNA and treatment-effect interaction OR was 0.94 (p=0.047) and 0.95 (p=0.096), respectively, for the two response definitions suggesting evidence of interaction between baseline disease activity and treatment effect. The interaction between HBeAg status and treatment effect was not statistically significant.ConclusionsThe measurement time point seems to modify the relative treatment effect of entacavir compared to lamivudine, measured on the OR scale. Evidence also suggested that differences in baseline viral load may also alter relative treatment effect. Meta-analyses should account for such modifiers when generating relative efficacy estimates.
Emergency department visits for fall-related fractures among older adults in the USA: a retrospective cross-sectional analysis of the National Electronic Injury Surveillance System All Injury Program, 2001–2008
Authors: Orces Carlos H 
Published: January 2013

ObjectivesTo describe the demographic characteristics and incidence of unintentional fall-related fractures among older adults treated in the US hospital emergency departments (EDs).DesignRetrospective observational study.SettingsHospitals’ ED participants in the National Electronic Injury Surveillance System All Injury Program (NEISS-AIP).ParticipantsThe NEISS-AIP was used to generate national estimates of hospital ED visits for unintentional fall-related fracture among adults aged 65 years or older between 2001 and 2008. Census population estimates were used as the denominator to calculate age-specific and age-adjusted fracture rates per 100 000 persons.Main outcome measuresFall-related fracture rates and ED disposition.ResultsOn the basis of 70 199 cases, an estimated 4.05 million older adults were treated in US hospital EDs for fall-related fracture during the 8-year period. Two-thirds of the injuries occurred at home and 69.5% (95% CI 59.7% to 77.8%) of the affected individuals were white. Fall-related fracture rates increased gradually with age and were on average twofold higher among women. Of those hospitalised, women and fractures of the lower trunk represented 75.2% and 65.1% of the admissions, respectively. The estimated number of fall-related fractures treated in EDs increased from 574 500 in 2001 to 714 800 in 2008, a 24.4% increase. By gender, a non-significant upward trend in age-adjusted fall-related fracture rates was predominantly seen among men at an annual rate of 1.9% (95% CI −0.1% to 4.0%), whereas fracture rates among women remained stable at 0.9% (95% CI −0.7% to 2.5%) per year.ConclusionsThe oldest old, women and lower trunk fractures account for the majority of fall-related fractures among persons aged 65 years or older treated in US hospital EDs. Increasing ED visits and hospitalisations for fall-related fracture among older adults deserve further research.
Heat-related respiratory hospital admissions in Europe in a changing climate: a health impact assessment
Authors: Åström Christofer , Orru Hans , Rocklöv Joacim , Strandberg Gustav , Ebi Kristie L , Forsberg Bertil 
Published: January 2013

ObjectivesRespiratory diseases are ranked second in Europe in terms of mortality, prevalence and costs. Studies have shown that extreme heat has a large impact on mortality and morbidity, with a large relative increase for respiratory diseases. Expected increases in mean temperature and the number of extreme heat events over the coming decades due to climate change raise questions about the possible health impacts. We assess the number of heat-related respiratory hospital admissions in a future with a different climate.DesignA Europe-wide health impact assessment.SettingAn assessment for each of the EU27 countries.MethodsHeat-related hospital admissions under a changing climate are projected using multicity epidemiological exposure–response relationships applied to gridded population data and country-specific baseline respiratory hospital admission rates. Times-series of temperatures are simulated with a regional climate model based on four global climate models, under two greenhouse gas emission scenarios.ResultsBetween a reference period (1981–2010) and a future period (2021–2050), the total number of respiratory hospital admissions attributed to heat is projected to be larger in southern Europe, with three times more heat attributed respiratory hospital admissions in the future period. The smallest change was estimated in Eastern Europe with about a twofold increase. For all of Europe, the number of heat-related respiratory hospital admissions is projected to be 26 000 annually in the future period compared with 11 000 in the reference period.ConclusionsThe results suggest that the projected effects of climate change on temperature and the number of extreme heat events could substantially influence respiratory morbidity across Europe.
Spatial analysis of health effects of large industrial incinerators in England, 1998–2008: a study using matched case–control areas
Authors: Reeve Nicola F , Fanshawe Thomas R , Keegan Thomas J , Stewart Alex G , Diggle Peter J 
Published: January 2013

ObjectivesTo assess whether residential proximity to industrial incinerators in England is associated with increased risk of cancer incidence and mortality.DesignRetrospective study using matched case–control areas.SettingFive circular regions of radius 10 km near industrial incinerators in England (case regions) and five matched control regions, 1998–2008.ParticipantsAll cases of diseases of interest within the circular areas.Primary and secondary outcome measuresCounts of childhood cancer incidence (<15 years); childhood leukaemia incidence (<15 years); leukaemia incidence; liver cancer incidence; lung cancer incidence; non-Hodgkin's lymphoma incidence; all-cause mortality; infant mortality (<1 year) and liver cancer mortality.ResultsThe estimated relative risks for case circles versus control circles for the nine outcomes considered range from 0.94 to 1.14, and show neither elevated risk in case circles compared to control areas nor elevated risk with proximity to incinerators within case circles.ConclusionsThis study applies statistical methods for analysing spatially referenced health outcome data in regions with a hypothesised exposure relative to matched regions with no such exposure. There is no evidence of elevated risk of cancer incidence or mortality in the vicinity of large industrial incinerators in England.
Does implementation of the IMCI strategy have an impact on child mortality? A retrospective analysis of routine data from Egypt
Authors: Rakha Mona Ali , Abdelmoneim Ahmed-Nagaty Mohamed , Farhoud Suzanne , Pièche Sergio , Cousens Simon , Daelmans Bernadette , Bahl Rajiv 
Published: January 2013

BackgroundBetween 1999 and 2007, the Ministry of Health and Population in Egypt scaled up the Integrated Management of Childhood Illness (IMCI) strategy in 84% of public health facilities.ObjectivesThis retrospective analysis, using routinely available data from vital registration, aimed to assess the impact of IMCI implementation between 2000 and 2006 on child mortality. It also presents a systematic and comprehensive approach to scaling-up IMCI interventions and information on quality of child health services, using programme data from supervision and surveys.MethodsWe compared annual levels of under-five mortality in districts before and after they had started implementing IMCI. Mortality data were obtained from the National Bureau for Statistics for 254 districts for the years 2000–2006, 41 districts of which were excluded. For assessment of programme activities, we used information from the central IMCI data base, annual progress reports, follow-up after training visits and four studies on quality of child care in public health facilities.ResultsAcross 213 districts retained in the analysis, the estimated average annual rate of decline in under-five mortality was 3.3% before compared with 6.3% after IMCI implementation (p=0.0001). In 127 districts which started implementing IMCI between 2002 and 2005, the average annual rate of decline of under-five mortality was 2.6% (95% CI 1.1% to 4.1%) before compared with 7.3% (95% CI 5.8% to 8.7%) after IMCI implementation (p<0.0001). IMCI implementation also led to marked improvements in the quality of child health services.InterpretationIMCI implementation was associated with a doubling in the annual rate of under-five mortality reduction (3.3% vs 6.3%). This mortality impact is plausible, since substantial improvements occurred in quality of care provided to sick children in health facilities implementing IMCI.