bluuebunny/crossref_metadata_2025_split huggingface dataset:
Periplasmic Nicotine Dehydrogenase NdhAB Utilizes Pseudoazurin as Its Physiological Electron Acceptor in Agrobacterium tumefaciens S33
Authors: Yu Wenjun , Wang Rongshui , Huang Haiyan , Xie Huijun , Wang Shuning 
Published: June 2017

ABSTRACT

Agrobacterium tumefaciens
S33 can grow with nicotine as the sole source of carbon, nitrogen, and energy via a novel hybrid of the pyridine pathway and the pyrrolidine pathway. Characterization of the enzymes involved in the hybrid pathway is important for understanding its biochemical mechanism. Here, we report that the molybdenum-containing nicotine dehydrogenase (NdhAB), which catalyzes the initial step of nicotine degradation, is located in the periplasm of strain S33, while the 6-hydroxynicotine oxidase and 6-hydroxypseudooxynicoine oxidase are in the cytoplasm. This is consistent with the fact that NdhA has a Tat signal peptide. Interestingly, an open reading frame (ORF) adjacent to the
ndhAB
gene was verified to encode a copper-containing electron carrier, pseudoazurin (Paz), which has a signal peptide typical of bacterial Paz proteins. Both were transported into the periplasm after being produced in the cytoplasm. We purified NdhAB from the periplasmic fraction of strain S33 and found that with Paz as the physiological electron acceptor, NdhAB catalyzed the hydroxylation of nicotine at a specific rate of 110.52 ± 8.09 μmol · min
−1
· mg of protein
−1
, where the oxygen atom in the hydroxyl group of the product 6-hydroxynicotine was derived from H
2
O. The apparent

K
m

values for nicotine and Paz were 1.64 ± 0.07 μM and 3.61 ± 0.23 μM, respectively. NAD(P)
+
, O
2
, and ferredoxin could not serve as electron acceptors. Disruption of the
paz
gene disabled the strain for nicotine degradation, indicating that Paz is required for nicotine catabolism in the strain. These findings help our understanding of electron transfer during nicotine degradation in bacteria.

IMPORTANCE
Nicotine is a toxic and addictive
N
-heterocyclic aromatic alkaloid produced in tobacco. Its catabolism in organisms and degradation in tobacco wastes have become major concerns for human health and the environment. Bacteria usually decompose nicotine using the classical strategy of hydroxylating the pyridine ring with the help of activated oxygen by nicotine dehydrogenase, which binds one molybdopterin, two [2Fe2S] clusters, and usually one flavin adenine dinucleotide (FAD) as well. However, the physiological electron acceptor for the reaction is still unknown. In this study, we found that the two-component nicotine dehydrogenase from
Agrobacterium tumefaciens
S33, naturally lacking an FAD-binding domain, is located in the periplasmic space and uses a copper-containing electron carrier, pseudoazurin, as its physiological electron acceptor. We report here the role of pseudoazurin in a reaction catalyzed by a molybdopterin-containing hydroxylase occurring in the periplasmic space. These results provide new biochemical knowledge on microbial degradation of
N
-heterocyclic aromatic compounds.
Natural DNA Transformation Is Functional in Lactococcus lactis subsp. cremoris KW2
Authors: David Blandine , Radziejwoski Amandine , Toussaint Frédéric , Fontaine Laetitia , de Frahan Marie Henry , Patout Cédric , van Dillen Sabine , Boyaval Patrick , Horvath Philippe , Fremaux Christophe , Hols Pascal 
Published: June 2017

ABSTRACT

Lactococcus lactis
is one of the most commonly used lactic acid bacteria in the dairy industry. Activation of competence for natural DNA transformation in this species would greatly improve the selection of novel strains with desired genetic traits. Here, we investigated the activation of natural transformation in
L. lactis
subsp.
cremoris
KW2, a strain of plant origin whose genome encodes the master competence regulator ComX and the complete set of proteins usually required for natural transformation. In the absence of knowledge about competence regulation in this species, we constitutively overproduced ComX in a reporter strain of late competence phase activation and showed, by transcriptomic analyses, a ComX-dependent induction of all key competence genes. We further demonstrated that natural DNA transformation is functional in this strain and requires the competence DNA uptake machinery. Since constitutive ComX overproduction is unstable, we alternatively expressed
comX
under the control of an endogenous xylose-inducible promoter. This regulated system was used to successfully inactivate the adaptor protein MecA and subunits of the Clp proteolytic complex, which were previously shown to be involved in ComX degradation in streptococci. In the presence of a small amount of ComX, the deletion of
mecA
,
clpC
, or
clpP
genes markedly increased the activation of the late competence phase and transformability. Altogether, our results report the functionality of natural DNA transformation in
L. lactis
and pave the way for the identification of signaling mechanisms that trigger the competence state in this species.

IMPORTANCE
Lactococcus lactis
is a lactic acid bacterium of major importance, which is used as a starter species for milk fermentation, a host for heterologous protein production, and a delivery platform for therapeutic molecules. Here, we report the functionality of natural transformation in
L. lactis
subsp.
cremoris
KW2 by the overproduction of the master competence regulator ComX. The developed procedure enables a flexible approach to modify the chromosome with single point mutation, sequence insertion, or sequence replacement. These results represent an important step for the genetic engineering of
L. lactis
that will facilitate the design of strains optimized for industrial applications. This will also help to discover natural regulatory mechanisms controlling competence in the genus
Lactococcus
.
Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks
Authors: Walsh Aaron M. , Crispie Fiona , Daari Kareem , O'Sullivan Orla , Martin Jennifer C. , Arthur Cornelius T. , Claesson Marcus J. , Scott Karen P. , Cotter Paul D. 
Published: June 2017

ABSTRACT

The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing
Escherichia coli
in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic
E. coli
and
Klebsiella pneumoniae
strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization.

IMPORTANCE
Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products.
Prevalence, incidence and aetiologies of pulmonary hypertension in Africa: a systematic review and meta-analysis protocol
Authors: Bigna Jean Joel , Noubiap Jean Jacques , Nansseu Jobert Richie , Aminde Leopold Ndemnge 
Published: June 2017

IntroductionThere are no data summarising the epidemiology of pulmonary hypertension (PH) among adults residing in Africa. Establishment of accurate epidemiological data on PH in this region may guide decision-making toward interventions to curb the burden of PH in Africa. The aim of this systematic review is to determine the prevalence, incidence and aetiologies of PH among people residing in Africa.Methods and analysisThis systematic review and meta-analysis will follow the MOOSE guidelines for reporting. Relevant abstracts published until 30 September 2016 will be searched in PubMed/Medline, EMBASE (Excerpta Medica Database), African Journals Online and Africa Index Medicus. Full texts of eligible studies will then be accessed through PubMed, Google Scholar, HINARI and the respective journals’ websites. Relevant unpublished papers and conference proceedings will also be checked. Data will be analysed using STATA version 13 software. The study-specific estimates will be pooled through a random-effects meta-analysis model to obtain an overall summary estimate of the prevalence/incidence and aetiologies of PH across studies. Heterogeneity of studies will be evaluated by the χ2test on Cochrane’s Q statistic. Funnel plot analysis and Egger’s test will be done to detect publication bias. Results will be presented by geographical region (central, eastern, northern, southern and western Africa).Ethics and disseminationThe current study is based on published data; ethical approval is, therefore, not required. This review will guide policy, practice and research by providing information on the magnitude of PH among people residing in Africa. Findings will be presented in evidence tables of individual studies as well as in summary tables. The final report of this systematic review, in the form of a scientific paper, will be published in a peer-reviewed journal. Furthermore, findings will be presented at conferences and submitted to relevant health authorities.Review registration numberPROSPERO CRD42016049351.
GPs' attitudes, beliefs and behaviours regarding exercise for chronic knee pain: a questionnaire survey
Authors: Cottrell Elizabeth , Foster Nadine E , Porcheret Mark , Rathod Trishna , Roddy Edward 
Published: June 2017

ObjectivesThe aim of this study was to investigate general practitioners’ (GPs) attitudes, beliefs and behaviours regarding the use of exercise for patients with chronic knee pain (CKP) attributable to osteoarthritis.SettingPrimary care GPs in the UK.Participants5000 GPs, randomly selected from Binley’s database, were mailed a cross-sectional questionnaire survey.Outcome measuresGPs’ attitudes and beliefs were investigated using attitude statements, and reported behaviours were identified using vignette-based questions. GPs were invited to report barriers experienced when initiating exercise with patients with CKPResults835 (17%) GPs responded. Overall, GPs were positive about general exercise for CKP. 729 (87%) reported using exercise, of which, 538 (74%) reported that they would use both general and local (lower limb) exercises. However, only 92 (11% of all responding) GPs reported initiating exercise in ways aligning with best-evidence recommendations. 815 (98%) GPs reported barriers in using exercise for patients with CKP, most commonly, insufficient time in consultations (n=419; 51%) and insufficient expertise (n=337; 41%).ConclusionsWhile GPs’ attitudes and beliefs regarding exercise for CKP were generally positive, initiation of exercise was often poorly aligned with current recommendations, and barriers and uncertainties were reported. GPs’ use of exercise may be improved by addressing the key barriers of time and expertise, by developing a pragmatic approach that supports GPs to initiate individualised exercise, and/or by other professionals taking on this role.
How do smoking cessation medicines compare with respect to their neuropsychiatric safety? A protocol for a systematic review, network meta-analysis and cost-effectiveness analysis
Authors: Thomas Kyla H , Caldwell Deborah , Dalili Michael N , Gunnell David , Munafò Marcus R , Stevenson Matt , Welton Nicky J 
Published: June 2017

IntroductionCigarette smoking is one of the leading causes of early death in the UK and worldwide. Public health guidance recommends the use of varenicline, bupropion and nicotine replacement therapy (NRT) as smoking cessation aids in the UK. Additionally, the first electronic cigarette has been licensed for use as a smoking cessation medicine. However, there are ongoing concerns about the safety of these medicines. We present a protocol for a systematic review and network meta-analysis (NMA) to determine how these smoking cessation medicines compare to each other with respect to their neuropsychiatric safety in adult smokers. Secondary aims include updating the evidence regarding the effectiveness and cardiovascular safety of these medicines for use in a cost-effectiveness analysis.Methods and analysisWe will include randomised controlled trials and observational studies with control groups comparing monotherapy with varenicline, bupropion, NRT or electronic cigarette and combination therapies to each other, placebo or usual care. The primary composite safety outcome will be serious adverse events, defined as events that resulted in death, were life threatening, required hospitalisation or resulted in significant disability or congenital/birth defect. The preferred effectiveness outcome will be sustained smoking cessation defined as abstinence for a minimum of 6 months as determined by biochemical validation. We will include trials identified by previous reviews and search relevant databases for newly published trials as well as contacting study authors to identify unpublished information. We will conduct fixed-effect and random-effect meta-analyses for each pairwise comparison of treatments and outcome; where these estimates differ, we will consider reasons for heterogeneity, quantified using the between-study variance (τ2). For each outcome, we will construct a NMA in a Bayesian framework which will be compared with the pair-wise results, allowing us to rank treatments. The effectiveness estimates from the NMA will be entered into a probabilistic economic model.Ethics and disseminationEthics approval is not required for this evidence synthesis study as it involves analysis of secondary data from randomised controlled trials and observational studies. The review will make an important contribution to the knowledge base around the effectiveness, safety and cost-effectiveness of smoking cessation medicines. Results will be disseminated to the general public, healthcare practitioners and clinicians, academics, industry and policy makers.PROSPERO registration numberCRD42016041302.
Factors influencing psychological, social and health outcomes after major burn injuries in adults: cohort study protocol
Authors: Druery Martha , Newcombe Peter A , Cameron Cate M , Lipman Jeffrey 
Published: June 2017

IntroductionThe goal of burn care is that ‘the quality of the outcome must be worth the pain of survival’. More research is needed to understand how best to deliver care for patients with burns to achieve this aim. Loss of independence, function as well as loss of income for patients with burns and carers cause a significant burden at both individual and societal levels. Much is being done to advance knowledge in the clinical care field; however, there has been a paucity of research exploring psychosocial outcomes. This paper describes the study background and methods, as implemented in an Australian cohort study of psychosocial outcomes after major burn injuries.Methods and analysisIn this inception cohort study, a target sample of 230 participants, aged 18 years or over, admitted to a single statewide burns centre with a burn injury are identified by hospital staff for inclusion. Baseline survey data are collected either in person or by telephone within 28 days of the injury and participants then followed up with telephone interviews at 3, 6 and 12 months postburn. Injury and burns treatment information is collected from medical records. Social support is measured as a predictor variable using the Multidimensional Scale of Perceived Social Support. Outcome data are collected via standardised measures in the domains of Quality of Life (SF-12, EQ-5D, BSHS-B), depression (PHQ-9), post-traumatic stress disorder (PCL-C, PAS), community integration (CIQ-R) and Quality-Adjusted Life Years (EQ-5D). Additional survey questions measure life satisfaction, return to work and public services utilisation at 12 months postinjury. Data analysis methods will include analysis of variance, Pearson correlation and hierarchical multiple regression analyses.Ethics and disseminationHospital-based and University of Queensland Human Research Ethics Committees have approved the protocol. Results from the study will be disseminated at national and international conferences, in peer-reviewed journals and in a doctoral thesis.Trial registration numberAustralia New Zealand Clinical Trials Registry (ACTRN12616000828426). Retrospectively registered on 23 June 2016; pre-results.
Reducing the number of unnecessary liver function tests requested on the Paediatric Intensive Care Unit
Authors: Sinitsky Lynn , Brierley Joe 
Published: June 2017

Between January and October 2014, Great Ormond Street Hospital Paediatric Intensive Care Unit (PICU) was spending an average £23,392 on blood tests per month. Blood tests should be requested based on previous results and the patient's clinical condition, medication and nutritional status. However, more blood tests were being ordered than clinically indicated: an audit in October 2014 showed liver function tests (LFTs) were requested daily on most patients, even with previous normal results.A driver diagram identified three primary drivers for blood test requesting: decision-making, situational awareness and computer-based ordering. Decision-making for routine blood tests was the responsibility of the bedside nurses on each night shift. The communication between the nurses and doctors was an identified secondary driver. The project's primary aim was to reduce unnecessary LFTs requests on PICU over 6 months by implementing a blood test request form, a table of common investigations to facilitate and document discussion between the nursing and medical teams. The secondary aims were to reduce other unnecessary blood test requests, including full blood counts (FBC), coagulation screens and CRP.This project was conducted in three phases: construction, testing and implementation of the blood test form. PDSA cycles were used within each phase. Two PICU nurse champions were engaged to provide bedside support, education and feedback.In the 8-month period following implementation, there was a significant sustained reduction in LFTs requests. A similar pattern of sustained reduction also occurred for FBC, coagulation screens and CRP requests. This sustained reduction in blood tests requested equated to a saving in excess of £36,000.This project was successful: the reduction in the number of inappropriate blood tests had clear financial benefit for PICU and reduced blood loss for patients. Early engagement and support from key stakeholders avoided conflict, guaranteed data sharing and aided engagement of bedside nurses.
Gender, race and the presentation of acute coronary syndrome and serious cardiopulmonary diagnoses in ED patients with chest pain
Authors: Allabban Ahmed , Hollander Judd E , Pines Jesse M 
Published: June 2017

ObjectiveTo assess the relationship between reported chest pain symptoms and a diagnosis of acute coronary syndrome (ACS) and serious cardiopulmonary diagnoses (SCPD) in black males, white males, black females and white females.MethodsThis was a secondary analysis of a prospective cohort study of 4162 ED patients with chest pain enrolled between 1999 and 2008. We used logistic regression, adjusting for age and cardiovascular comorbidities to test the association between 24 chest pain symptoms and 30-day ACS for the primary outcome and SCPD as the secondary outcome.ResultIn black males, diaphoresis was associated with ACS (OR 1.47; 95% CI 1.02 to 2.13), while in white males, left arm radiation, pressure/tightness and substernal pain were associated with ACS (OR 1.73, 95% CI 1.16 to 2.59; OR 1.65, 95% CI 1.16 to 2.59; OR 1.51, 95% CI 1.07 to 2.11, respectively). In black females, diaphoresis, palpitations and left arm radiation were associated with ACS (OR 1.66, 95% CI 1.17 to 2.35; 1.66, 95% CI 1.13 to 2.45; 1.44, 95% CI 1.02 to 2.03, respectively) while pleuritic pain, and left anterior chest pain lowered ACS risk (OR 0.69, 95% CI 0.5 to 0.96; 0.54, 95% CI 0.35 to 0.84). No symptoms predicted ACS or SCPD in white females. Fewer but similar symptoms predicted SCPD in white males and black females. No symptoms predicted SCPD in black males.ConclusionChest pain symptoms are important predictors of ACS and SCPD in certain combinations of race and gender but less so in others. These differences might explain difficulties using symptoms to identify patients at higher or lower risk of ACS and SCPD in practice.
A homozygous founder mutation inTRAPPC6Bassociates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features
Authors: Marin-Valencia Isaac , Novarino Gaia , Johansen Anide , Rosti Basak , Issa Mahmoud Y , Musaev Damir , Bhat Gifty , Scott Eric , Silhavy Jennifer L , Stanley Valentina , Rosti Rasim O , Gleeson Jeremy W , Imam Farhad B , Zaki Maha S , Gleeson Joseph G 
Published: June 2017

BackgroundTransport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.ObjectiveWe aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.MethodsLinkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.ResultsWe identified six individuals from three unrelated families with a founder homozygous splice mutation inTRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafishtrappc6bmorphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.ConclusionThis study provides clinical and functional evidence of the role ofTRAPPC6Bin brain development and function.