bluuebunny/crossref_metadata_2025_split huggingface dataset:
PBP1B Glycosyltransferase and Transpeptidase Activities Play Different Essential Roles during the
De Novo
Regeneration of Rod Morphology in Escherichia coli
Authors: Ranjit Dev K. , Jorgenson Matthew A. , Young Kevin D. 
Published: January 2017

ABSTRACT

Peptidoglycan is a vital component of nearly all cell wall-bearing bacteria and is a valuable target for antibacterial therapy. However, despite decades of work, there remain important gaps in understanding how this macromolecule is synthesized and molded into a three-dimensional structure that imparts specific morphologies to individual cells. Here, we investigated the particularly enigmatic area of how peptidoglycan is synthesized and shaped during the first stages of creating cell shape
de novo
, that is, in the absence of a preexisting template. We found that when lysozyme-induced (LI) spheroplasts of
Escherichia coli
were allowed to resynthesize peptidoglycan, the cells divided first and then elongated to recreate a normal rod-shaped morphology. Penicillin binding protein 1B (PBP1B) was critical for the first stage of this recovery process. PBP1B synthesized peptidoglycan
de novo
, and this synthesis required that PBP1B interact with the outer membrane lipoprotein LpoB. Surprisingly, when LpoB was localized improperly to the inner membrane, recovering spheroplasts synthesized peptidoglycan and divided but then propagated as amorphous spheroidal cells, suggesting that the regeneration of a normal rod shape depends on a particular spatial interaction. Similarly, spheroplasts carrying a PBP1B variant lacking transpeptidase activity or those in which PBP1A was overproduced could synthesize new peptidoglycan and divide but then grew as oddly shaped spheroids. We conclude that
de novo
cell wall synthesis requires the glycosyltransferase activity of PBP1B but that PBP1B transpeptidase activity is needed to assemble cell walls with wild-type morphology.

IMPORTANCE
Bacterial cell wall peptidoglycan is synthesized and modified by penicillin binding proteins (PBPs), which are targeted by about half of all currently prescribed antibiotics, including penicillin and its derivatives. Because antibiotic resistance is rising, it has become increasingly urgent that we fill the gaps in our knowledge about how PBPs create and assemble this protective wall. We report here that PBP1B plays an essential role in synthesizing peptidoglycan in the absence of a preexisting template: its glycosyltransferase activity is responsible for
de novo
synthesis, while its transpeptidase activity is required to construct cell walls of a specific shape. These results highlight the importance of this enzyme and distinguish its biological roles from those of other PBPs and peptidoglycan synthases.
Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer
Authors: Kingston Anthony W. , Ponkratz Christine , Raleigh Elisabeth A. 
Published: January 2017

ABSTRACT

Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five
Escherichia coli
K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents
r
ecombination-
p
romoting
n
uclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert.
In vitro
, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes.

IMPORTANCE
Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four
Escherichia coli
K-12 paralogs contribute to a novel RecA-independent recombination mechanism
in vivo
. For RpnA, we demonstrate
in vitro
action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The cleavage products are capable of providing priming sites for DNA polymerase, which can enable DNA joining by primer-template switching.
Comprehensive Essentiality Analysis of the
Mycobacterium tuberculosis
Genome via Saturating Transposon Mutagenesis
Authors: DeJesus Michael A. , Gerrick Elias R. , Xu Weizhen , Park Sae Woong , Long Jarukit E. , Boutte Cara C. , Rubin Eric J. , Schnappinger Dirk , Ehrt Sabine , Fortune Sarah M. , Sassetti Christopher M. , Ioerger Thomas R. 
Published: January 2017

ABSTRACT

For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed. We sought to overcome this limitation by creating a completely saturated transposon library in
Mycobacterium tuberculosis
. In assessing the composition of this highly saturated library by deep sequencing, we discovered that a previously unknown sequence bias of the
Himar1
element rendered approximately 9% of potential TA dinucleotide insertion sites less permissible for insertion. We used a hidden Markov model of essentiality that accounted for this unanticipated bias, allowing us to confidently evaluate the essentiality of features that contained as few as 2 TA sites, including open reading frames (ORF), experimentally identified noncoding RNAs, methylation sites, and promoters. In addition, several essential regions that did not correspond to known features were identified, suggesting uncharacterized functions that are necessary for growth. This work provides an authoritative catalog of essential regions of the
M. tuberculosis
genome and a statistical framework for applying saturating mutagenesis to other bacteria.

IMPORTANCE
Sequencing of transposon-insertion mutant libraries has become a widely used tool for probing the functions of genes under various conditions. The
Himar1
transposon is generally believed to insert with equal probabilities at all TA dinucleotides, and therefore its absence in a mutant library is taken to indicate biological selection against the corresponding mutant. Through sequencing of a saturated Himar1 library, we found evidence that TA dinucleotides are not equally permissive for insertion. The insertion bias was observed in multiple prokaryotes and influences the statistical interpretation of transposon insertion (TnSeq) data and characterization of essential genomic regions. Using these insights, we analyzed a fully saturated TnSeq library for
M. tuberculosis
, enabling us to generate a comprehensive catalog of
in vitro
essentiality, including ORFs smaller than those found in any previous study, small (noncoding) RNAs (sRNAs), promoters, and other genomic features.
Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes
Authors: Wu Vincent W. , Dana Craig M. , Iavarone Anthony T. , Clark Douglas S. , Glass N. Louise 
Published: January 2017

ABSTRACT

The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases. In mammalian cells, the formation of pyroglutamate is catalyzed by glutaminyl cyclases. Using the model filamentous fungus
Neurospora crassa
, we identified two genes (
qc
-
1
and
qc
-
2
) that encode proteins homologous to mammalian glutaminyl cyclases. We show that
qc
-
1
and
qc
-
2
are essential for catalyzing the formation of an N-terminal pyroglutamate on CBH-1 and GH5-1. CBH-1 and GH5-1 produced in a
Δqc
-
1 Δqc
-
2
mutant, and thus lacking the N-terminal pyroglutamate modification, showed greater sensitivity to thermal denaturation, and for GH5-1, susceptibility to proteolytic cleavage. QC-1 and QC-2 are endoplasmic reticulum (ER)-localized proteins. The pyroglutamate modification is predicted to occur in a number of additional fungal proteins that have diverse functions. The identification of glutaminyl cyclases in fungi may have implications for production of lignocellulolytic enzymes, heterologous expression, and biotechnological applications revolving around protein stability.

IMPORTANCE
Pyroglutamate modification is the post-translational conversion of N-terminal glutamine or glutamate into a cyclized amino acid derivative. This modification is well studied in animal systems but poorly explored in fungal systems. In
Neurospora crassa
, we show that this modification takes place in the ER and is catalyzed by two well-conserved enzymes, ubiquitously conserved throughout the fungal kingdom. We demonstrate that the modification is important for the structural stability and aminopeptidase resistance of CBH-1 and GH5-1, two important cellulase enzymes utilized in industrial plant cell wall deconstruction. Many additional fungal proteins predicted in the genome of
N. crassa
and other filamentous fungi are predicted to carry an N-terminal pyroglutamate modification. Pyroglutamate addition may also be a useful way to stabilize secreted proteins and peptides, which can be easily produced in fungal production systems.
Natural language processing to extract symptoms of severe mental illness from clinical text: the Clinical Record Interactive Search Comprehensive Data Extraction (CRIS-CODE) project
Authors: Jackson Richard G , Patel Rashmi , Jayatilleke Nishamali , Kolliakou Anna , Ball Michael , Gorrell Genevieve , Roberts Angus , Dobson Richard J , Stewart Robert 
Published: January 2017

ObjectivesWe sought to use natural language processing to develop a suite of language models to capture key symptoms of severe mental illness (SMI) from clinical text, to facilitate the secondary use of mental healthcare data in research.DesignDevelopment and validation of information extraction applications for ascertaining symptoms of SMI in routine mental health records using the Clinical Record Interactive Search (CRIS) data resource; description of their distribution in a corpus of discharge summaries.SettingElectronic records from a large mental healthcare provider serving a geographic catchment of 1.2 million residents in four boroughs of south London, UK.ParticipantsThe distribution of derived symptoms was described in 23 128 discharge summaries from 7962 patients who had received an SMI diagnosis, and 13 496 discharge summaries from 7575 patients who had received a non-SMI diagnosis.Outcome measuresFifty SMI symptoms were identified by a team of psychiatrists for extraction based on salience and linguistic consistency in records, broadly categorised under positive, negative, disorganisation, manic and catatonic subgroups. Text models for each symptom were generated using the TextHunter tool and the CRIS database.ResultsWe extracted data for 46 symptoms with a median F1 score of 0.88. Four symptom models performed poorly and were excluded. From the corpus of discharge summaries, it was possible to extract symptomatology in 87% of patients with SMI and 60% of patients with non-SMI diagnosis.ConclusionsThis work demonstrates the possibility of automatically extracting a broad range of SMI symptoms from English text discharge summaries for patients with an SMI diagnosis. Descriptive data also indicated that most symptoms cut across diagnoses, rather than being restricted to particular groups.
Clinical management of unruptured intracranial aneurysm in Germany: a nationwide observational study over a 5-year period (2005–2009)
Authors: Walendy Victor , Stang Andreas 
Published: January 2017

ObjectivesOur aim was to provide nationwide age-standardised rates (ASR) on the usage of endovascular coiling and neurosurgical clipping for unruptured intracranial aneurysm (UIA) treatment in Germany.SettingNationwide observational study using the Diagnosis-Related-Groups (DRG) statistics for the years 2005–2009 (overall 83 million hospitalisations).ParticipantsFrom 2005 to 2009, overall 39 155 hospitalisations with a diagnosis of UIA occurred in Germany.Primary outcome measuresAge-specific and age-standardised hospitalisation rates for UIA with the midyear population of Germany in 2007 as the standard.ResultsOf the 10 221 hospitalisations with UIA during the observation period, 6098 (59.7%) and 4123 (40.3%) included coiling and clipping, respectively. Overall hospitalisation rates for UIA increased by 39.5% (95% CI 24.7% to 56.0%) and 50.4% (95% CI 39.6% to 62.1%) among men and women, respectively. In 2005, the ASR per 100 000 person years for coiling was 0.7 (95% CI 0.62 to 0.78) for men and 1.7 (95% CI 1.58 to 1.82) for women. In 2009, the ASR was 1.0 (95% CI 0.90 to 1.10) and 2.4 (95% CI 2.24 to 2.56), respectively. Similarly, the ASR for clipping in 2005 amounted to 0.6 (95% CI 0.52 to 0.68) for men and 1.1 (95% CI 1.00 to 1.20) for women. These rates increased in 2009 to 0.8 (95% CI 0.72 to 0.88) and 1.7 (95% CI 1.58 to 1.82), respectively. We observed a marked geographical variation of ASR for coiling and less pronounced for clipping. For the federal state of Saarland, the ASR for coiling was 5.64 (95% CI 4.76 to 6.52) compared with 0.68 (95% CI 0.48 to 0.88; per 100 000 person years) in Saxony-Anhalt, whereas, ASR for clipping were highest in Rhineland-Palatinate (2.48, 95% CI 2.17 to 4.75) and lowest in Saxony-Anhalt (0.52, 95% CI 0.34 to 0.70).ConclusionsTo the best of our knowledge, we presented the first representative, nationwide analysis of the clinical management of UIA in Germany. The ASR increased markedly and showed substantial geographical variation among federal states for all treatment modalities during the observation period.
Understanding the importance of therapeutic relationships in the development of self-management behaviours during cancer rehabilitation: a qualitative research protocol
Authors: Wilkinson Wendy M , Rance Jaynie , Fitzsimmons Deborah 
Published: January 2017

IntroductionCancer is a growing health, social and economic problem. 1 in 3 people in the UK will develop cancer in their lifetime. With survival rates rising to over 50%, the long-term needs of cancer survivors are of growing importance. Cancer rehabilitation is tailored to address the physical or psychosocial decline in ability to engage in daily activities. Its use is supported by high-quality international, multicentre research. Incorporating strategies for self-management behaviour development into rehabilitation can prepare individuals for cancer survivorship. However, healthcare professionals will need to adjust their therapeutic interactions accordingly. Research is yet to clarify the impact of the therapeutic relationship on rehabilitation outcomes in cancer. This study aims to explore the impact of therapeutic relationships on self-management behaviours after cancer.Methods and analysisThis qualitative study aims to understand cancer rehabilitation participants’ beliefs regarding the importance of therapeutic relationships in developing self-management behaviours. A sample representative of a local cancer rehabilitation cohort will be asked to complete a semistructured interview to identify their perspectives on the importance of therapeutic relationships in cancer rehabilitation. Data obtained from the interviews will be analysed, coded and entered into a Delphi questionnaire for circulation to a local cancer rehabilitation population to determine if the views expressed by the interviewees are supported by group consensus.Ethics and disseminationThis study was approved by Wales Research Ethics Committee 6 (15/WA/0331) in April 2016. Findings will be disseminated through the first author's doctoral thesis; peer-reviewed journals; local, national and international conference presentations; and public events involving research participants and the general public.
Factors predicting antibiotic prescription and referral to hospital for children with respiratory symptoms: secondary analysis of a randomised controlled study at out-of-hours services in primary care
Authors: Rebnord Ingrid Keilegavlen , Sandvik Hogne , Mjelle Anders Batman , Hunskaar Steinar 
Published: January 2017

ObjectivesAcute respiratory infections and fever among children are highly prevalent in primary care. It is challenging to distinguish between viral and bacterial infections. Norway has a relatively low prescription rate of antibiotics, but it is still regarded as too high as the antimicrobial resistance is increasing. The aim of the study was to identify predictors for prescribing antibiotics or referral to hospital among children.DesignSecondary analysis of a randomised controlled study.Setting4 out-of-hours services and 1 paediatric emergency clinic in Norwegian primary care.Participants401 children aged 0–6 years with respiratory symptoms and/or fever visiting the out-of-hours services.Outcomes2 main outcome variables were registered: antibiotic prescription and referral to hospital.ResultsThe total prescription rate of antibiotics was 23%, phenoxymethylpenicillin was used in 67% of the cases. Findings on ear examination (OR 4.62; 95% CI 2.35 to 9.10), parents' assessment that the child has a bacterial infection (OR 2.45; 95% CI 1.17 to 5.13) and a C reactive protein (CRP) value >20 mg/L (OR 3.57; 95% CI 1.43 to 8.83) were significantly associated with prescription of antibiotics. Vomiting in the past 24 hours was negatively associated with prescription (OR 0.26; 95% CI 0.13 to 0.53). The main predictors significantly associated with referral to hospital were respiratory rate (OR 1.07; 95% CI 1.03 to 1.12), oxygen saturation <95% (OR 3.39; 95% CI 1.02 to 11.23), signs on auscultation (OR 5.57; 95% CI 1.96 to 15.84) and the parents' assessment before the consultation that the child needs hospitalisation (OR 414; 95% CI 26 to 6624).ConclusionsCRP values >20 mg/L, findings on ear examination, use of paracetamol and no vomiting in the past 24 hours were significantly associated with antibiotic prescription. Affected respiration was a predictor for referral to hospital. The parents' assessment was also significantly associated with the outcomes.Trial registration numberNCT02496559; Results.
Chronic symptoms in a representative sample of community-dwelling older people: a cross-sectional study in Switzerland
Authors: Henchoz Yves , Büla Christophe , Guessous Idris , Rodondi Nicolas , Goy René , Demont Maurice , Santos-Eggimann Brigitte 
Published: January 2017

ObjectivesThe burden of multiple diagnoses is well documented in older people, but less is known about chronic symptoms, many of which are even not brought to medical attention. This study aimed to determine the prevalence of chronic symptoms, their relationships with disability in basic activities of daily living (BADL) and quality of life (QoL), and their public health impact.DesignA large cross-sectional population-based study.SettingCommunity in 2 regions of French-speaking Switzerland.ParticipantsCommunity-dwelling older adults aged 68 years and older in 2011 (N=5300).OutcomesDisability in BADL defined as difficulty or help needed with any of dressing, bathing, eating, getting in/out of bed or an arm chair, and using the toilet. Overall QoL dichotomised as favourable (ie, excellent or very good) or unfavourable (ie, good, fair or poor). Disturbance by any of the following 14 chronic symptoms for at least 6 months: joint pain, back pain, chest pain, dyspnoea, persistent cough, swollen legs, memory gaps, difficulty concentrating, difficulty making decisions, dizziness/vertigo, skin problems, stomach/intestine problems, urinary incontinence and impaired sexual life.ResultsOnly 17.1% of participants did not report being disturbed by any of these chronic symptoms. Weighted prevalence ranged from 3.1% (chest pain) to 47.7% (joint pain). Most chronic symptoms were significantly associated with disability in BADL or unfavourable QoL, with substantial gender differences. The number of chronic symptoms was significantly associated with disability in BADL and unfavourable QoL, with gradients suggesting dose–response relationships. Joint pain and back pain had the highest population attributable fractions.ConclusionsChronic symptoms are highly prevalent in older people, and are associated with disability in BADL and unfavourable QoL, particularly when multiple chronic symptoms co-occur. Owing to their high public health impact, musculoskeletal chronic symptoms represent good targets for preventive interventions.