bluuebunny/crossref_metadata_2025_split huggingface dataset:
DUF3380 Domain from a Salmonella Phage Endolysin Shows Potent
N
-Acetylmuramidase Activity
Authors: Rodríguez-Rubio Lorena , Gerstmans Hans , Thorpe Simon , Mesnage Stéphane , Lavigne Rob , Briers Yves 
Published: June 2016

ABSTRACT

Bacteriophage-encoded endolysins are highly diverse enzymes that cleave the bacterial peptidoglycan layer. Current research focuses on their potential applications in medicine, in food conservation, and as biotechnological tools. Despite the wealth of applications relying on the use of endolysin, little is known about the enzymatic properties of these enzymes, especially in the case of endolysins of bacteriophages infecting Gram-negative species. Automated genome annotations therefore remain to be confirmed. Here, we report the biochemical analysis and cleavage site determination of a novel
Salmonella
bacteriophage endolysin, Gp110, which comprises an uncharacterized
d
omain of
u
nknown
f
unction (DUF3380; pfam11860) in its C terminus and shows a higher specific activity (34,240 U/μM) than that of 14 previously characterized endolysins active against peptidoglycan from Gram-negative bacteria (corresponding to 1.7- to 364-fold higher activity). Gp110 is a modular endolysin with an optimal pH of enzymatic activity of pH 8 and elevated thermal resistance. Reverse-phase high-performance liquid chromatography (RP-HPLC) analysis coupled to mass spectrometry showed that DUF3380 has
N
-acetylmuramidase (lysozyme) activity cleaving the β-(1,4) glycosidic bond between
N
-acetylmuramic acid and
N
-acetylglucosamine residues. Gp110 is active against directly cross-linked peptidoglycans with various peptide stem compositions, making it an attractive enzyme for developing novel antimicrobial agents.

IMPORTANCE
We report the functional and biochemical characterization of the
Salmonella
phage endolysin Gp110. This endolysin has a modular structure with an enzymatically active domain and a cell wall binding domain. The enzymatic activity of this endolysin exceeds that of all other endolysins previously characterized using the same methods. A domain of unknown function (DUF3380) is responsible for this high enzymatic activity. We report that DUF3380 has
N
-acetylmuramidase activity against directly cross-linked peptidoglycans with various peptide stem compositions. This experimentally verified activity allows better classification and understanding of the enzymatic activities of endolysins, which mostly are inferred by sequence similarities. Three-dimensional structure predictions for Gp110 suggest a fold that is completely different from that of known structures of enzymes with the same peptidoglycan cleavage specificity, making this endolysin quite unique. All of these features, combined with increased thermal resistance, make Gp110 an attractive candidate for engineering novel endolysin-based antibacterials.
Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440
Authors: An Ran , Moe Luke A. 
Published: June 2016

ABSTRACT

Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium
Pseudomonas putida
KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (
gcd
) and PQQ biosynthesis genes (
pqq
operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts from the
pqq
operon to more accurately map the operon structure. GDH specific activity and PQQ levels vary according to growth condition, with the highest levels of both occurring when glucose is used as the sole carbon source and under conditions of low soluble phosphate. Under these conditions, however, PQQ levels limit
in vitro
phosphate solubilization. GDH specific activity data correlate well with
gcd
gene expression data, and the levels of expression of the
pqqF
and
pqqB
genes mirror the levels of PQQ synthesized, suggesting that one or both of these genes may serve to modulate PQQ levels according to the growth conditions. The
pqq
gene cluster (
pqqFABCDEG
) encodes at least two independent transcripts, and expression of the
pqqF
gene appears to be under the control of an independent promoter and terminator.

IMPORTANCE
Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a number of different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain through soil, but in many cases it is locked up in forms that are not available for plant uptake. Bacteria such as the model bacterium
Pseudomonas putida
KT2440 can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. Here we have studied how the glucose dehydrogenase enzyme and the PQQ coenzyme are regulated according to differences in bacterial growth conditions. We determined that glucose dehydrogenase activity and PQQ production are optimal under conditions when the bacterium is grown with glucose as the sole carbon source and under conditions of low soluble phosphate.
Metabolism of
myo
-Inositol by Legionella pneumophila Promotes Infection of Amoebae and Macrophages
Authors: Manske Christian , Schell Ursula , Hilbi Hubert 
Published: June 2016

ABSTRACT

Legionella pneumophila
is a natural parasite of environmental amoebae and the causative agent of a severe pneumonia termed Legionnaires' disease. The facultative intracellular pathogen employs a bipartite metabolism, where the amino acid serine serves as the major energy supply, while glycerol and glucose are mainly utilized for anabolic processes. The
L. pneumophila
genome harbors the cluster
lpg1653
to
lpg1649
putatively involved in the metabolism of the abundant carbohydrate
myo
-inositol (here termed inositol). To assess inositol metabolism by
L. pneumophila
, we constructed defined mutant strains lacking
lpg1653
or
lpg1652
, which are predicted to encode the inositol transporter IolT or the inositol-2-dehydrogenase IolG, respectively. The mutant strains were not impaired for growth in complex or defined minimal media, and inositol did not promote extracellular growth. However, upon coinfection of
Acanthamoeba castellanii
, the mutants were outcompeted by the parental strain, indicating that the intracellular inositol metabolism confers a fitness advantage to the pathogen. Indeed, inositol added to
L. pneumophila
-infected amoebae or macrophages promoted intracellular growth of the parental strain, but not of the Δ
iolT
or Δ
iolG
mutant, and growth stimulation by inositol was restored by complementation of the mutant strains. The expression of the P

iol

promoter and bacterial uptake of inositol required the alternative sigma factor RpoS, a key virulence regulator of
L. pneumophila
. Finally, the parental strain and Δ
iolG
mutant bacteria but not the Δ
iolT
mutant strain accumulated [U-
14
C
6
]inositol, indicating that IolT indeed functions as an inositol transporter. Taken together, intracellular
L. pneumophila
metabolizes inositol through the
iol
gene products, thus promoting the growth and virulence of the pathogen.

IMPORTANCE
The environmental bacterium
Legionella pneumophila
is the causative agent of a severe pneumonia termed Legionnaires' disease. The opportunistic pathogen replicates in protozoan and mammalian phagocytes in a unique vacuole. Amino acids are thought to represent the prime source of carbon and energy for
L. pneumophila
. However, genome, transcriptome, and proteome studies indicate that the pathogen not only utilizes amino acids as carbon sources but possesses broader metabolic capacities. In this study, we analyzed the metabolism of inositol by extra- and intracellularly growing
L. pneumophila
. By using genetic, biochemical, and cell biological approaches, we found that
L. pneumophila
accumulates and metabolizes inositol through the
iol
gene products, thus promoting the intracellular growth, virulence, and fitness of the pathogen. Our study significantly contributes to an understanding of the intracellular niche of a human pathogen.
Hypertension in autosomal dominant polycystic kidney disease: a meta-analysis
Authors: Marlais Matko , Cuthell Oliver , Langan Dean , Dudley Jan , Sinha Manish D , Winyard Paul J D 
Published: June 2016

ContextAutosomal dominant polycystic kidney disease (ADPKD) is a common disorder that can cause hypertension during childhood, but the true prevalence of hypertension during childhood is not known.ObjectiveWe undertook a systematic review and meta-analysis to determine the prevalence of hypertension in children with ADPKD.Data sourcesSystematic review of articles published between 1980 and 2015 in MEDLINE and EMBASE.Study selectionStudies selected by two authors independently if reporting data on prevalence of hypertension in children and young persons aged <21 years with a diagnosis of ADPKD. Observational series were included with study populations of >15 children. Articles were excluded if inadequate diagnostic criteria for hypertension were used. Studies with selection bias were included but analysed separately.Data extractionData extracted on prevalence of hypertension, proteinuria and reduced renal function using standardised form. Meta-analysis was performed to calculate weighted mean prevalence.Results903 articles were retrieved from our search; 14 studies met the inclusion criteria: 1 prospective randomised controlled trial; 8 prospective observational studies; and 5 retrospective cross-sectional studies. From 928 children with clinically confirmed ADPKD, 20% (95% CI 15% to 27%) were hypertensive. The estimated prevalence of proteinuria in children with ADPKD is 20% (8 studies; 95% CI 9% to 40%) while reduced renal function occurred in 8% (5 studies; 95% CI 2% to 26%).LimitationsStudies showed a high degree of methodological heterogeneity (I2=73.4%, τ2=0.3408, p<0.0001). Most studies did not use ambulatory blood pressure (BP) monitoring to diagnose hypertension.ConclusionsIn this meta-analysis we estimate 20% of children with ADPKD have hypertension. In the population, many children with ADPKD are not under regular follow-up and remain undiagnosed. We recommend that all children at risk of ADPKD have regular BP measurement.
Applying quality improvement methods to address gaps in medicines reconciliation at transfers of care from an acute UK hospital
Authors: Marvin Vanessa , Kuo Shirley , Poots Alan J , Woodcock Tom , Vaughan Louella , Bell Derek 
Published: June 2016

ObjectivesReliable reconciliation of medicines at admission and discharge from hospital is key to reducing unintentional prescribing discrepancies at transitions of healthcare. We introduced a team approach to the reconciliation process at an acute hospital with the aim of improving the provision of information and documentation of reliable medication lists to enable clear, timely communications on discharge.SettingAn acute 400-bedded teaching hospital in London, UK.ParticipantsThe effects of change were measured in a simple random sample of 10 adult patients a week on the acute admissions unit over 18 months.InterventionsQuality improvement methods were used throughout. Interventions included education and training of staff involved at ward level and in the pharmacy department, introduction of medication documentation templates for electronic prescribing and for communicating information on medicines in discharge summaries co-designed with patient representatives.ResultsStatistical process control analysis showed reliable documentation (complete, verified and intentional changes clarified) of current medication on 49.2% of patients' discharge summaries. This appears to have improved (to 85.2%) according to a poststudy audit the year after the project end. Pharmacist involvement in discharge reconciliation increased significantly, and improvements in the numbers of medicines prescribed in error, or omitted from the discharge prescription, are demonstrated. Variation in weekly measures is seen throughout but particularly at periods of changeover of new doctors and introduction of new systems.ConclusionsNew processes led to a sustained increase in reconciled medications and, thereby, an improvement in the number of patients discharged from hospital with unintentional discrepancies (errors or omissions) on their discharge prescription. The initiatives were pharmacist-led but involved close working and shared understanding about roles and responsibilities between doctors, nurses, therapists, patients and their carers.
Use of hospital services by age and comorbidity after an index heart failure admission in England: an observational study
Authors: Bottle Alex , Goudie Rosalind , Bell Derek , Aylin Paul , Cowie Martin R 
Published: June 2016

ObjectivesTo describe hospital inpatient, emergency department (ED) and outpatient department (OPD) activity for patients in the year following their first emergency admission for heart failure (HF). To assess the proportion receiving specialist assessment within 2 weeks of hospital discharge, as now recommended by guidelines.DesignObservational study of national administrative data.SettingAll acute NHS hospitals in England.Participants82 241 patients with an index emergency admission between April 2009 and March 2011 with a primary diagnosis of HF.Main outcome measuresCardiology OPD appointment within 2 weeks and within a year of discharge from the index admission; emergency department (ED) and inpatient use within a year.Results15.1% died during the admission. Of the 69 848 survivors, 19.7% were readmitted within 30 days and half within a year, the majority for non-HF diagnoses. 6.7% returned to the ED within a week of discharge, of whom the majority (77.6%) were admitted. The two most common OPD specialties during the year were cardiology (24.7% of the total appointments) and anticoagulant services (12.5%). Although half of all patients had a cardiology appointment within a year, the proportion within the recommended 2 weeks of discharge was just 6.8% overall and varied by age, from 2.4% in those aged 90+ to 19.6% in those aged 18–45 (p<0.0001); appointments in other specialties made up only some of the shortfall. More comorbidity at any age was associated with higher rates of cardiology OPD follow-up.ConclusionsPatients with HF are high users of hospital services. Postdischarge cardiology OPD follow-up rates fell well below current National Institute for Health and Care Excellence guidelines, particularly for the elderly and those with less comorbidity.
Healthcare use among preschool children attending GP-led urgent care centres: a descriptive, observational study
Authors: Gnani S , Morton S , Ramzan F , Davison M , Ladbrooke T , Majeed A , Saxena S 
Published: June 2016

ObjectiveUrgent care centres’ (UCCs) hours were developed with the aim of reducing inappropriate emergency department (ED) attendances in England. We aimed to examine the presenting complaint and outcomes of care in 2 general practitioner (GP)-led UCCs with extended opening times.DesignRetrospective observational epidemiological study using routinely collected data.Setting2 GP-led UCCs in London, colocated with a hospital ED.ParticipantsAll children aged under 5 years, attending 2 GP-led UCCs over a 3-year period.OutcomesOutcomes of care for the children including: primary diagnosis; registration status with a GP; destination following review within the UCC; and any medication prescribed. Comparison between GP-led UCC visit rates and routine general practices was also made.Results3% (n=7747/282 947) of all attenders at the GP-led UCCs were children aged under 5 years. The most common reason for attendance was a respiratory illness (27%), followed by infectious illness (17%). 18% (n=1428) were either upper respiratory tract infections or viral infections. The majority (91%) of children attending were registered with a GP, and over two-thirds of attendances were ‘out of hours’. Overall 79% were seen and discharged home. Preschool children were more likely to attend their GP (47.0 per 100) than a GP-led UCC (9.4 per 100; 95% CI 8.9 to 10.0).ConclusionsTwo-thirds of preschool children attending GP-led UCCs do so out of hours, despite the majority being registered with a GP. The case mix is comparable with those presenting to an ED setting, with the majority managed exclusively by the GPs in the UCC before discharge home. Further work is required to understand the benefits of a GP-led urgent system in influencing future use of services especially emergency care.
Changes in Saturday outpatient volume and billings after introducing the Saturday incentive programme to clinics in South Korea: a longitudinal cohort study using claims data from 2012 to 2014
Authors: Ha Hyun Ji , Han Kyu-Tae , Kim Sun Jung , Sohn Tae Yong , Jeon Byungyool , Park Eun-Cheol 
Published: June 2016

ObjectiveIn October 2013, the South Korean government introduced an incentive programme to increase the availability of Saturday treatment at clinics, hoping to increase the role of primary care providers as gatekeepers to medical care. To the best of our knowledge, no one has yet investigated this programme's effect on overall outpatient care. Our study aims to analyse the change in Saturday outpatient volume and billings in clinics that adopted the Saturday incentive programme.SettingOur study used 3 types of data from the period October 2012 to March 2014: National Health Insurance Service (NHIS) claims data, hospital evaluation data and medical institution data.ParticipantsThese data consisted of 66 825 881 outpatient cases from 2837 clinics.InterventionsIntroducing the Saturday incentive programme.Outcome measureWe performed a multilevel analysis that adjusted for clinic-level and outpatient-level variables to examine the difference in the percentage of Saturday outpatient volume and billings after introducing the Saturday incentive programme.ResultsThe percentages of Saturday outpatient volume and billings were higher after introducing the programme (outpatient volume: β=2.065, p<0.001; outpatient billings: β=3.518, p<0.001). In addition, outpatient volume and billings on Friday and Saturday increased after introducing the programme, while those on weekdays, excluding Friday, decreased.ConclusionsOur findings suggest that the Saturday incentive programme has affected clinic outpatient care and is a worthwhile health policy in terms of promoting primary care. Thus, it may improve healthcare accessibility and quality of care, and prevent inappropriate usage such as emergency room visits by providing patients with weekend clinic hours.
Early intervention of patients at risk for acute respiratory failure and prolonged mechanical ventilation with a checklist aimed at the prevention of organ failure: protocol for a pragmatic stepped-wedged cluster trial of PROOFCheck
Authors: Gong M N , Schenk L , Gajic O , Mirhaji P , Sloan J , Dong Y , Festic E , Herasevich V 
Published: June 2016

IntroductionAcute respiratory failure (ARF) often presents and progresses outside of the intensive care unit. However, recognition and treatment of acute critical illness is often delayed with inconsistent adherence to evidence-based care known to decrease the duration of mechanical ventilation (MV) and complications of critical illness. The goal of this trial is to determine whether the implementation of an electronic medical record-based early alert for progressive respiratory failure coupled with a checklist to promote early compliance to best practice in respiratory failure can improve the outcomes of patients at risk for prolonged respiratory failure and death.Methods and analysisA pragmatic stepped-wedged cluster clinical trial involving 6 hospitals is planned. The study will include adult hospitalised patients identified as high risk for MV >48 hours or death because they were mechanically ventilated outside of the operating room or they were identified as high risk for ARF on the Accurate Prediction of PROlonged VEntilation (APPROVE) score. Patients with advanced directives limiting intubation will be excluded. The intervention will consist of (1) automated identification and notification of clinician of high-risk patients by APPROVE or by invasive MV and (2) checklist of evidence-based practices in ARF (Prevention of Organ Failure Checklist—PROOFCheck). APPROVE and PROOFCheck will be developed in the pretrial period. Primary outcome is hospital mortality. Secondary outcomes include length of stay, ventilator and organ failure-free days and 6-month and 12-month mortality. Predefined subgroup analysis of patients with limitation of aggressive care after study entry is planned. Generalised estimating equations will be used to compare patients in the intervention phase with the control phase, adjusting for clustering within hospitals and time.Ethics and disseminationThe study was approved by the institutional review boards. Results will be published in peer-reviewed journals and presented at international meetings.Trial registration numberNCT02488174.
Effect of different financial competing interest statements on readers' perceptions of clinical educational articles: study protocol for a randomised controlled trial
Authors: Schroter Sara , Pakpoor Julia , Morris Julie , Chew Mabel , Godlee Fiona 
Published: June 2016

IntroductionFinancial ties with industry are varied and common among academics, doctors and institutions. Clinical educational articles are intended to guide patient care and convey authors' own interpretation of selected data. Author biases in educational articles tend to be less visible to readers compared to those in research papers. Little is known about which types of competing interest statements affect readers' interpretation of the credibility of these articles. This study aims to investigate how different competing interest statements in educational articles affect clinical readers' perceptions of the articles.Methods and analysis2040 doctors who are members of the British Medical Association (BMA) and receive a copy of theBritish Medical Journal (The BMJ)each week will be randomly selected and invited by an email to participate in the study. They will be randomised to receive 1 of 2 Clinical Reviews, each with 1 of 4 possible competing interest statements. Versions of each review will be identical except for permutations of the competing interest statement. Study participants will be asked to read their article and complete an online questionnaire. The questionnaire will ask participants to rate their confidence in the conclusions drawn in the article, the importance of the article, their level of interest in the article and their likeliness to change their practice from the article. Factorial analyses of variance and analyses of covariance will be carried out to assess the impact of the type of competing interest statement and Clinical Review on level of confidence, importance, interest and likeliness to change practice.Ethics and disseminationThe study protocol, questionnaire and letter of invitation to participants have been reviewed by members ofThe BMJ'sEthics Committee for ethical concerns. The trial results will be disseminated to participants and published in a peer-reviewed journal.Trial registration numberNCT02548312; Pre-results.