bluuebunny/crossref_metadata_2025_split huggingface dataset:
CpsA, a LytR-CpsA-Psr Family Protein in Mycobacterium marinum, Is Required for Cell Wall Integrity and Virulence
Authors: Wang Qinglan , Zhu Lin , Jones Victoria , Wang Chuan , Hua Yifei , Shi Xujun , Feng Xia , Jackson Mary , Niu Chen , Gao Qian 
Published: May 2015

ABSTRACT

LytR-CpsA-Psr family proteins play an important role in bacterial cell wall integrity. Although the pathogenic relevance of LytR-CpsA-Psr family proteins has been studied in a few bacterial pathogens, their function in mycobacteria remains uncharacterized. In this work, a transposon insertion mutant (
cpsA
::Tn) of
Mycobacterium marinum
was studied. We found that inactivation of CpsA altered bacterial colony morphology, sliding motility, cell surface hydrophobicity, and cell wall permeability. Besides, the
cpsA
mutant exhibited a decreased arabinogalactan content, indicating that CpsA plays a role in cell wall assembly. Moreover, the mutant shows impaired growth within macrophage cell lines and is severely attenuated in zebrafish larvae and adult zebrafish. Taken together, our results indicated that CpsA, a previously uncharacterized protein, is important for mycobacterial cell wall integrity and is required for mycobacterial virulence.
Identification of SlpB, a Cytotoxic Protease from Serratia marcescens
Authors: Shanks Robert M. Q. , Stella Nicholas A. , Hunt Kristin M. , Brothers Kimberly M. , Zhang Liang , Thibodeau Patrick H. 
Published: May 2015

ABSTRACT

The Gram-negative bacterium and opportunistic pathogen
Serratia marcescens
causes ocular infections in healthy individuals. Secreted protease activity was characterized from 44 ocular clinical isolates, and a higher frequency of protease-positive strains was observed among keratitis isolates than among conjunctivitis isolates. A positive correlation between protease activity and cytotoxicity to human corneal epithelial cells
in vitro
was determined. Deletion of
prtS
in clinical keratitis isolate K904 reduced, but did not eliminate, cytotoxicity and secreted protease production. This indicated that PrtS is necessary for full cytotoxicity to ocular cells and implied the existence of another secreted protease(s) and cytotoxic factors. Bioinformatic analysis of the
S. marcescens
Db11 genome revealed three additional open reading frames predicted to code for serralysin-like proteases noted here as
slpB
,
slpC
, and
slpD
. Induced expression of
prtS
and
slpB
, but not
slpC
and
slpD
, in strain PIC3611 rendered the strain cytotoxic to a lung carcinoma cell line; however, only
prtS
induction was sufficient for cytotoxicity to a corneal cell line. Strain K904 with deletion of both
prtS
and
slpB
genes was defective in secreted protease activity and cytotoxicity to human cell lines. PAGE analysis suggests that SlpB is produced at lower levels than PrtS. Purified SlpB demonstrated calcium-dependent and AprI-inhibited protease activity and cytotoxicity to airway and ocular cell lines
in vitro
. Lastly, genetic analysis indicated that the type I secretion system gene,
lipD
, is required for SlpB secretion. These genetic data introduce SlpB as a new cytotoxic protease from
S. marcescens
.
The All-Alpha Domains of Coupling Proteins from the Agrobacterium tumefaciens VirB/VirD4 and Enterococcus faecalis pCF10-Encoded Type IV Secretion Systems Confer Specificity to Binding of Cognate DNA Substrates
Authors: Whitaker Neal , Chen Yuqing , Jakubowski Simon J. , Sarkar Mayukh K. , Li Feng , Christie Peter J. 
Published: May 2015

ABSTRACT

Bacterial type IV coupling proteins (T4CPs) bind and mediate the delivery of DNA substrates through associated type IV secretion systems (T4SSs). T4CPs consist of a transmembrane domain, a conserved nucleotide-binding domain (NBD), and a sequence-variable helical bundle called the all-alpha domain (AAD). In the T4CP structural prototype, plasmid R388-encoded TrwB, the NBD assembles as a homohexamer resembling RecA and DNA ring helicases, and the AAD, which sits at the channel entrance of the homohexamer, is structurally similar to N-terminal domain 1 of recombinase XerD. Here, we defined the contributions of AADs from the
Agrobacterium tumefaciens
VirD4 and
Enterococcus faecalis
PcfC T4CPs to DNA substrate binding. AAD deletions abolished DNA transfer, whereas production of the AAD in otherwise wild-type donor strains diminished the transfer of cognate but not heterologous substrates. Reciprocal swaps of AADs between PcfC and VirD4 abolished the transfer of cognate DNA substrates, although strikingly, the VirD4-AAD
PcfC
chimera (VirD4 with the PcfC AAD) supported the transfer of a mobilizable plasmid. Purified AADs from both T4CPs bound DNA substrates without sequence preference but specifically bound cognate processing proteins required for cleavage at origin-of-transfer sequences. The soluble domains of VirD4 and PcfC lacking their AADs neither exerted negative dominance
in vivo
nor specifically bound cognate processing proteins
in vitro
. Our findings support a model in which the T4CP AADs contribute to DNA substrate selection through binding of associated processing proteins. Furthermore, MOBQ plasmids have evolved a docking mechanism that bypasses the AAD substrate discrimination checkpoint, which might account for their capacity to promiscuously transfer through many different T4SSs.

IMPORTANCE
For conjugative transfer of mobile DNA elements, members of the VirD4/TraG/TrwB receptor superfamily bind cognate DNA substrates through mechanisms that are largely undefined. Here, we supply genetic and biochemical evidence that a helical bundle, designated the all-alpha domain (AAD), of T4SS receptors functions as a substrate specificity determinant. We show that AADs from two substrate receptors,
Agrobacterium tumefaciens
VirD4 and
Enterococcus faecalis
PcfC, bind DNA without sequence or strand preference but specifically bind the cognate relaxases responsible for nicking and piloting the transferred strand through the T4SS. We propose that interactions of receptor AADs with DNA-processing factors constitute a basis for selective coupling of mobile DNA elements with type IV secretion channels.
Characterization of the Dynamic Germination of Individual Clostridium difficile Spores Using Raman Spectroscopy and Differential Interference Contrast Microscopy
Authors: Wang Shiwei , Shen Aimee , Setlow Peter , Li Yong-qing 
Published: May 2015

ABSTRACT

The Gram-positive spore-forming anaerobe
Clostridium difficile
is a leading cause of nosocomial diarrhea. Spores of
C. difficile
initiate infection when triggered to germinate by bile salts in the gastrointestinal tract. We analyzed germination kinetics of individual
C. difficile
spores using Raman spectroscopy and differential interference contrast (DIC) microscopy. Similar to
Bacillus
spores, individual
C. difficile
spores germinating with taurocholate plus glycine began slow leakage of a ∼15% concentration of a chelate of Ca
2+
and dipicolinic acid (CaDPA) at a heterogeneous time
T
1
, rapidly released CaDPA at
T
lag
, completed CaDPA release at
T
release
, and finished peptidoglycan cortex hydrolysis at
T
lysis
.
T
1
and
T
lag
values for individual spores were heterogeneous, but Δ
T
release
periods (
T
release
−
T
lag
) were relatively constant. In contrast to
Bacillus
spores, heat treatment did not stimulate spore germination in the two
C. difficile
strains tested.
C. difficile
spores did not germinate with taurocholate or glycine alone, and different bile salts differentially promoted spore germination, with taurocholate and taurodeoxycholate being best. Transient exposure of spores to taurocholate plus glycine was sufficient to commit individual spores to germinate.
C. difficile
spores did not germinate with CaDPA, in contrast to
B. subtilis
and
C. perfringens
spores. However, the detergent dodecylamine induced
C. difficile
spore germination, and rates were increased by spore coat removal although cortex hydrolysis did not follow
T
release
, in contrast with
B. subtilis
.
C. difficile
spores lacking the cortex-lytic enzyme, SleC, germinated extremely poorly, and cortex hydrolysis was not observed in the few
sleC
spores that partially germinated. Overall, these findings indicate that
C. difficile
and
B. subtilis
spore germination exhibit key differences.

IMPORTANCE
Spores of the Gram-positive anaerobe
Clostridium difficile
are responsible for initiating infection by this important nosocomial pathogen. When exposed to germinants such as bile salts,
C. difficile
spores return to life through germination in the gastrointestinal tract and cause disease, but their germination has been studied only with population-wide measurements. In this work we used Raman spectroscopy and DIC microscopy to monitor the kinetics of germination of individual
C. difficile
spores, the commitment of spores to germination, and the effect of germinant type and concentration, sublethal heat shock, and spore decoating on germination. Our data suggest that the order of germination events in
C. difficile
spores differs from that in
Bacillus
spores and provide new insights into
C. difficile
spore germination.
Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota
Authors: Leyn Semen A. , Rodionova Irina A. , Li Xiaoqing , Rodionov Dmitry A. 
Published: May 2015

ABSTRACT

Autotrophic microorganisms are able to utilize carbon dioxide as their only carbon source, or, alternatively, many of them can grow heterotrophically on organics. Different variants of autotrophic pathways have been identified in various lineages of the phylum
Crenarchaeota
. Aerobic members of the order
Sulfolobales
utilize the hydroxypropionate-hydroxybutyrate cycle (HHC) to fix inorganic carbon, whereas anaerobic
Thermoproteales
use the dicarboxylate-hydroxybutyrate cycle (DHC). Knowledge of transcriptional regulation of autotrophic pathways in
Archaea
is limited. We applied a comparative genomics approach to predict novel autotrophic regulons in the
Crenarchaeota
. We report identification of two novel DNA motifs associated with the autotrophic pathway genes in the
Sulfolobales
(HHC box) and
Thermoproteales
(DHC box). Based on genome context evidence, the HHC box regulon was attributed to a novel transcription factor from the TrmB family named HhcR. Orthologs of HhcR are present in all
Sulfolobales
genomes but were not found in other lineages. A predicted HHC box regulatory motif was confirmed by
in vitro
binding assays with the recombinant HhcR protein from
Metallosphaera yellowstonensis
. For the DHC box regulon, we assigned a different potential regulator, named DhcR, which is restricted to the order
Thermoproteales
. DhcR in
Thermoproteus neutrophilus
(Tneu_0751) was previously identified as a DNA-binding protein with high affinity for the promoter regions of two autotrophic operons. The global HhcR and DhcR regulons reconstructed by comparative genomics were reconciled with available omics data in
Metallosphaera
and
Thermoproteus
spp. The identified regulons constitute two novel mechanisms for transcriptional control of autotrophic pathways in the
Crenarchaeota
.

IMPORTANCE
Little is known about transcriptional regulation of carbon dioxide fixation pathways in
Archaea
. We previously applied the comparative genomics approach for reconstruction of DtxR family regulons in diverse lineages of
Archaea
. Here, we utilize similar computational approaches to identify novel regulatory motifs for genes that are autotrophically induced in microorganisms from two lineages of
Crenarchaeota
and to reconstruct the respective regulons. The predicted novel regulons in archaeal genomes control the majority of autotrophic pathway genes and also other carbon and energy metabolism genes. The HhcR regulon was experimentally validated by DNA-binding assays in
Metallosphaera
spp. Novel regulons described for the first time in this work provide a basis for understanding the mechanisms of transcriptional regulation of autotrophic pathways in
Archaea
.
Acute Care QUAliTy in chronic Kidney disease (ACQUATIK): a prospective cohort study exploring outcomes of patients with chronic kidney disease
Authors: Arnold Julia J , Hayer Manvir , Sharif Adnan , Begaj Irena , Tabriez Mohammed , Bagnall David , Ray Daniel , Hoye Ciaron , Nazir Masood , Dutton Mary , Fifer Lesley , Kirkham Katie , Sims Don , Townend Jonathan N , Gill Paramjit S , Dasgupta Indranil , Cockwell Paul , Ferro Charles J 
Published: May 2015

IntroductionChronic kidney disease (CKD) is common and carries a high risk of morbidity, including hospital admissions and readmissions and mortality. This is largely attributed to an increased risk of cardiovascular disease. Patients with CKD are less likely to receive evidence-based treatments for cardiovascular disease. However, these treatments are based on trials which generally exclude patients with CKD. It is therefore unclear whether this patient group derives the same benefits without an increased risk of adverse effects.Methods and analysisThe Acute Care QUAliTy in chronic Kidney disease (ACQUATIK) study is a prospective, observational, multicentre cohort study. Over 4000 patients will be recruited with an enrolment period of 2 years and a follow-up period of 2–4 years. Patients under follow-up by a renal team will be excluded. Data will be obtained from patient and hospital records during the index admission. Preadmission data will be extracted from general practice records based on the Quality and Outcomes Framework. Diagnosis, comorbidities and procedure data pertaining to the index and subsequent admissions will be extracted from the Hospital Episode Statistics database and long-term mortality data will be tracked using the Office of National Statistics. This information will allow us to examine a complete patient journey through primary and secondary care, providing unequalled levels of information on treatment and outcomes of patients with CKD. The combined data set will be used to compare outcomes and treatments among patients with CKD versus patients without CKD. The primary end point is hospital readmission rates. The relationship between age, sex, ethnicity, socioeconomic status and concurrent comorbidities will be analysed to determine their influence on outcomes and treatments.Ethics and disseminationThe ACQUATIK study has been approved by the NRES Committee West Midlands—South Birmingham—Reference 13/WM/0317. The results from ACQUATIK will be submitted for publication in peer-reviewed journals and presented at primary and secondary care conferences.Trial registration numberISRCTN37237454.
Local food environment interventions to improve healthy food choice in adults: a systematic review and realist synthesis protocol
Authors: Penney Tarra L , Brown Helen Elizabeth , Maguire Eva R , Kuhn Isla , Monsivais Pablo 
Published: May 2015

IntroductionLocal food environments have been linked with dietary intake and obesity in adults. However, overall evidence remains mixed with calls for increased theoretical and conceptual clarity related to how availability of neighbourhood food outlets, and within-outlet food options, influence food purchasing and consumption. The purpose of this work is to develop a programme theory of food availability, supported by empirical evidence from a range of local food environment interventions.Methods and analysisA systematic search of the literature will be followed by duplicate screening and quality assessment (using the Effective Public Health Practice Project tool). Realist synthesis will then be conducted according to the Realist And Meta-narrative Evidence Syntheses: Evolving Standards (RAMESES) publication standards, including transparent appraisal, synthesis and drawing conclusions via consensus.DisseminationThe final synthesis will propose an evidence-based programme theory of food availability, including evidence mapping to demonstrate contextual factors, pathways of influence and potential mechanisms. With the paucity of empirically supported programme theories used in current local food environment interventions to improve food availability, this synthesis may be used to understand how and why interventions work, and thus inform the development of theory-driven, evidence-based interventions to improve healthy food choice and future empirical work.Trial registration numberPROSPERO CRD42014009808.
Direct targeting of risk factors significantly increases the detection of liver cirrhosis in primary care: a cross-sectional diagnostic study utilising transient elastography
Authors: Harman David J , Ryder Stephen D , James Martin W , Jelpke Matthew , Ottey Dominic S , Wilkes Emilie A , Card Timothy R , Aithal Guruprasad P , Guha Indra Neil 
Published: May 2015

ObjectivesTo assess the feasibility of a novel diagnostic algorithm targeting patients with risk factors for chronic liver disease in a community setting.DesignProspective cross-sectional study.SettingTwo primary care practices (adult patient population 10 479) in Nottingham, UK.ParticipantsAdult patients (aged 18 years or over) fulfilling one or more selected risk factors for developing chronic liver disease: (1) hazardous alcohol use, (2) type 2 diabetes or (3) persistently elevated alanine aminotransferase (ALT) liver function enzyme with negative serology.InterventionsA serial biomarker algorithm, using a simple blood-based marker (aspartate aminotransferase:ALT ratio for hazardous alcohol users, BARD score for other risk groups) and subsequently liver stiffness measurement using transient elastography (TE).Main outcome measuresDiagnosis of clinically significant liver disease (defined as liver stiffness ≥8 kPa); definitive diagnosis of liver cirrhosis.ResultsWe identified 920 patients with the defined risk factors of whom 504 patients agreed to undergo investigation. A normal blood biomarker was found in 62 patients (12.3%) who required no further investigation. Subsequently, 378 patients agreed to undergo TE, of whom 98 (26.8% of valid scans) had elevated liver stiffness. Importantly, 71/98 (72.4%) patients with elevated liver stiffness had normal liver enzymes and would be missed by traditional investigation algorithms. We identified 11 new patients with definite cirrhosis, representing a 140% increase in the number of diagnosed cases in this population.ConclusionsA non-invasive liver investigation algorithm based in a community setting is feasible to implement. Targeting risk factors using a non-invasive biomarker approach identified a substantial number of patients with previously undetected cirrhosis.Trial registration numberThe diagnostic algorithm utilised for this study can be found on clinicaltrials.gov (NCT02037867), and is part of a continuing longitudinal cohort study.
How does acupuncture affect insulin sensitivity in women with polycystic ovary syndrome and insulin resistance? Study protocol of a prospective pilot study
Authors: Zheng Yanhua , Stener-Victorin Elisabet , Ng Ernest H Y , Li Juan , Wu Xiaoke , Ma Hongxia 
Published: May 2015

IntroductionHyperinsulinaemia and insulin resistance (IR) are key features of polycystic ovary syndrome (PCOS) and metabolic syndrome. The effect of 5 weeks of acupuncture treatment has been investigated in a completed prospective pilot trial (Clinicaltrials.gov:NCT01457209), and acupuncture with electrical stimulation applied to insulin-resistant rats with dihydrotestosterone-induced PCOS was shown to improve insulin sensitivity. Therefore, we now aim to conduct a prospective pilot study to evaluate whether using the same acupuncture treatment protocol given over a longer period of time (6 months) than in the previous pilot trial will improve insulin sensitivity in women with PCOS and IR. Our hypothesis is that acupuncture with combined manual and low-frequency electrical stimulation of the needles will improve insulin sensitivity in women with PCOS and IR.Methods/analysisThis is a prospective pilot trial. A total of 112 women with PCOS and IR will be recruited and categorised according to their body mass index (BMI) as normal weight (BMI=18.5−23 kg/m2) or as overweight/obese (BMI>23 kg/m2). Acupuncture will be applied three times per week for 6 months at 30 min per treatment. The primary outcome will be the change in insulin sensitivity before and after 6 months of acupuncture treatment, as measured by an oral glucose tolerance test.Ethics/disseminationEthical approval of this study has been granted from the ethics committee of the First Affiliated Hospital of Guangzhou Medical University (No. 2013039). Written and informed consent will be obtained from each patient before any study procedure is performed, according to good clinical practice. The results of this trial will be disseminated in a peer-reviewed journal and presented at international congresses.Trial registration numbersNCT02026323 and ChiCTR-OCH-13003921.
A multisource feedback tool to assess ward round leadership skills of senior paediatric trainees: (2) Testing reliability and practicability
Authors: Goodyear Helen M , Lakshminarayana Indumathy , Wall David , Bindal Taruna 
Published: May 2015

ABSTRACTBackgroundA five-domain multisource feedback (MSF) tool was previously developed in 2009–2010 by the authors to assess senior paediatric trainees’ ward round leadership skills.ObjectivesTo determine whether this MSF tool is practicable and reliable, whether individuals’ feedback varies over time and trainees’ views of the tool.MethodsThe MSF tool was piloted (April–July 2011) and field tested (September 2011–February 2013) with senior paediatric trainees. A focus group held at the end of field testing obtained trainees’ views of the tool.ResultsIn field testing, 96/115 (84%) trainees returned 633 individual assessments from three different ward rounds over 18 months. The MSF tool had high reliability (Cronbach's α 0.84, G coefficient 0.8 for three raters). In all five domains, data were shifted to the right with scores of 3 (good) and 4 (excellent). Consultants gave significantly lower scores (p&lt;0.001), as did trainees for self–assessment (p&lt;0.001). There was no significant change in MSF scores over 18 months but comments showed that trainees’ performance improved. Trainees valued these comments and the MSF tool but had concerns about time taken for feedback and confusion about tool use and the paediatric assessment strategy.ConclusionsA five-domain MSF tool was found to be reliable on pilot and field testing, practicable to use and liked by trainees. Comments on performance were more helpful than scores in giving trainees feedback.
A Pólya Urn Document Language Model for Improved Information Retrieval
Authors: Cummins Ronan , Paik Jiaul H. , Lv Yuanhua 
Published: May 2015

The multinomial language model has been one of the most effective models of retrieval for more than a decade. However, the multinomial distribution does not model one important linguistic phenomenon relating to term dependency—that is, the tendency of a term to repeat itself within a document (i.e., word burstiness). In this article, we model document generation as a random process with reinforcement (a multivariate Pólya process) and develop a Dirichlet compound multinomial language model that captures word burstiness directly.
We show that the new reinforced language model can be computed as efficiently as current retrieval models, and with experiments on an extensive set of TREC collections, we show that it significantly outperforms the state-of-the-art language model for a number of standard effectiveness metrics. Experiments also show that the tuning parameter in the proposed model is more robust than that in the multinomial language model. Furthermore, we develop a constraint for the verbosity hypothesis and show that the proposed model adheres to the constraint. Finally, we show that the new language model essentially introduces a measure closely related to idf, which gives theoretical justification for combining the term and document event spaces in tf-idf type schemes.