bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic analysis of the large family of poxvirus ankyrin-repeat proteins reveals orthologue groups within and across chordopoxvirus genera
Authors: Sonnberg Stephanie , Fleming Stephen B. , Mercer Andrew A.
Published: July 2011

Ankyrin-repeat (ANK) protein-interaction domains are common in cellular proteins but are relatively rare in viruses. Chordopoxviruses, however, encode a large number of ANK domain-containing ORFs of largely unknown function. Recently, a second protein-interaction domain, an F-box-like motif, was identified in several poxvirus ANK proteins. Cellular F-box proteins recruit substrates to the ubiquitination machinery of the cell, a putative function for ANK/poxviral F-box proteins. Using publicly available genome sequence data we examined all 328 predicted ANK proteins encoded by 27 chordopoxviruses that represented the eight vertebrate poxvirus genera whose members encode ANK proteins. Within these we identified 15 putative ANK protein orthologue groups within orthopoxviruses, five within parapoxviruses, 23 within avipoxviruses and seven across members of the genera Leporipoxvirus, Capripoxvirus, Yatapoxvirus, Suipoxvirus and Cervidpoxvirus. Sequence comparisons showed that members of each of these four clusters of orthologues were not closely related to members of any of the other clusters. Of these ORFs, 67 % encoded a C-terminal poxviral F-box-like motif, whose absence could largely be attributed to fragmentation of ORFs. Our findings suggest that the large family of poxvirus ANK proteins arose by extensive gene duplication and divergence that occurred independently in four major genus-based groups after the groups diverged from each other. It seems likely that the ancestor ANK proteins of poxviruses contained both the N-terminal ANK repeats and a C-terminal F-box-like domain, with the latter domain subsequently being lost in a small subset of these proteins.
An investigation of herpes simplex virus promoter activity compatible with latency establishment reveals VP16-independent activation of immediate-early promoters in sensory neurones
Authors: Proença João T. , Coleman Heather M. , Nicoll Michael P. , Connor Viv , Preston Christopher M. , Arthur Jane , Efstathiou Stacey
Published: July 2011

Herpes simplex virus (HSV) type-1 establishes lifelong latency in sensory neurones and it is widely assumed that latency is the consequence of a failure to initiate virus immediate-early (IE) gene expression. However, using a Cre reporter mouse system in conjunction with Cre-expressing HSV-1 recombinants we have previously shown that activation of the IE ICP0 promoter can precede latency establishment in at least 30 % of latently infected cells. During productive infection of non-neuronal cells, IE promoter activation is largely dependent on the transactivator VP16 a late structural component of the virion. Of significance, VP16 has recently been shown to exhibit altered regulation in neurones; where its de novo synthesis is necessary for IE gene expression during both lytic infection and reactivation from latency. In the current study, we utilized the Cre reporter mouse model system to characterize the full extent of viral promoter activity compatible with cell survival and latency establishment. In contrast to the high frequency activation of representative IE promoters prior to latency establishment, cell marking using a virus recombinant expressing Cre under VP16 promoter control was very inefficient. Furthermore, infection of neuronal cultures with VP16 mutants reveals a strong VP16 requirement for IE promoter activity in non-neuronal cells, but not sensory neurones. We conclude that only IE promoter activation can efficiently precede latency establishment and that this activation is likely to occur through a VP16-independent mechanism.
Cyclosporin A inhibits the replication of diverse coronaviruses
Authors: de Wilde Adriaan H. , Zevenhoven-Dobbe Jessika C. , van der Meer Yvonne , Thiel Volker , Narayanan Krishna , Makino Shinji , Snijder Eric J. , van Hemert Martijn J.
Published: July 2011

Low micromolar, non-cytotoxic concentrations of cyclosporin A (CsA) strongly affected the replication of severe acute respiratory syndrome coronavirus (SARS-CoV), human coronavirus 229E and mouse hepatitis virus in cell culture, as was evident from the strong inhibition of GFP reporter gene expression and a reduction of up to 4 logs in progeny titres. Upon high-multiplicity infection, CsA treatment rendered SARS-CoV RNA and protein synthesis almost undetectable, suggesting an early block in replication. siRNA-mediated knockdown of the expression of the prominent CsA targets cyclophilin A and B did not affect SARS-CoV replication, suggesting either that these specific cyclophilin family members are dispensable or that the reduced expression levels suffice to support replication.
Assessment of palindromes as platforms for DNA amplification in breast cancer
Authors: Guenthoer Jamie , Diede Scott J. , Tanaka Hisashi , Chai Xiaoyu , Hsu Li , Tapscott Stephen J. , Porter Peggy L.
Published: July 2011

DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage–fusion–bridge (BFB) cycle. Therefore, palindromes might be associated with gene amplicons in breast cancer. To address this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-number analyses on a set of breast cancer cell lines and primary tumors to spatially associate palindromes and copy-number gains. We identified GAPF-positive regions distributed nonrandomly throughout cell line and tumor genomes, often in clusters, and associated with copy-number gains. Commonly amplified regions in breast cancer, chromosomes 8q and 11q, had GAPF-positive regions flanking and throughout the copy-number gains. We also identified amplification-associated GAPF-positive regions at similar locations in subsets of breast cancers with similar characteristics (e.g.,ERBB2amplification). These shared positive regions offer the potential to evaluate the utility of palindromes as prognostic markers, particularly in premalignant breast lesions. Our results implicate palindrome formation in the amplification of regions with key roles in breast tumorigenesis, particularly in subsets of breast cancers.
Ectopic Expression ofAtJMTinNicotiana attenuata: Creating a Metabolic Sink Has Tissue-Specific Consequences for the Jasmonate Metabolic Network and Silences Downstream Gene Expression
Authors: Stitz Michael , Gase Klaus , Baldwin Ian T. , Gaquerel Emmanuel
Published: July 2011

To create a metabolic sink in the jasmonic acid (JA) pathway, we generated transgenic Nicotiana attenuata lines ectopically expressing Arabidopsis (Arabidopsis thaliana) jasmonic acid O-methyltransferase (35S-jmt) and additionally silenced in other lines the N. attenuata  methyl jasmonate esterase (35S-jmt/ir-mje) to reduce the deesterification of methyl jasmonate (MeJA). Basal jasmonate levels did not differ between transgenic and wild-type plants; however, after wounding and elicitation with Manduca sexta oral secretions, the bursts of JA, jasmonoyl-isoleucine (JA-Ile), and their metabolites that are normally observed in the lamina, midvein, and petiole of elicited wild-type leaves were largely absent in both transformants but replaced by a burst of endogenous MeJA that accounted for almost half of the total elicited jasmonate pools. In these plants, MeJA became a metabolic sink that affected the jasmonate metabolic network and its spread to systemic leaves, with major effects on 12-oxo-phytodieonic acid, JA, and hydroxy-JA in petioles and on JA-Ile in laminas. Alterations in the size of jasmonate pools were most obvious in systemic tissues, especially petioles. Expression of threonine deaminase and trypsin proteinase inhibitor, two JA-inducible defense genes, was strongly decreased in both transgenic lines without influencing the expression of JA biosynthesis genes that were uncoupled from the wounding and elicitation with M. sexta oral secretions-elicited JA-Ile gradient in elicited leaves. Taken together, this study provides support for a central role of the vasculature in the propagation of jasmonates and new insights into the versatile spatiotemporal characteristics of the jasmonate metabolic network.
Subfunctionalization of Cellulose Synthases in Seed Coat Epidermal Cells Mediates Secondary Radial Wall Synthesis and Mucilage Attachment
Authors: Mendu Venugopal , Griffiths Jonathan S. , Persson Staffan , Stork Jozsef , Downie A. Bruce , Voiniciuc Cătălin , Haughn George W. , DeBolt Seth
Published: July 2011

Arabidopsis (Arabidopsis thaliana) epidermal seed coat cells follow a complex developmental program where, following fertilization, cells of the ovule outer integument differentiate into a unique cell type. Two hallmarks of these cells are the production of a doughnut-shaped apoplastic pocket filled with pectinaceous mucilage and the columella, a thick secondary cell wall. Cellulose is thought to be a key component of both these secondary cell wall processes. Here, we investigated the role of cellulose synthase (CESA) subunits CESA2, CESA5, and CESA9 in the seed coat epidermis. We characterized the roles of these CESA proteins in the seed coat by analyzing cell wall composition and morphology in cesa mutant lines. Mutations in any one of these three genes resulted in lower cellulose content, a loss of cell shape uniformity, and reduced radial wall integrity. In addition, we found that attachment of the mucilage halo to the parent seed following extrusion is maintained by cellulose-based connections requiring CESA5. Hence, we show that cellulose fulfills an adhesion role between the extracellular mucilage matrix and the parent cell in seed coat epidermal cells. We propose that mucilage remains attached to the seed coat through interactions between components in the seed mucilage and cellulose. Our data suggest that CESA2 and CESA9 serve in radial wall reinforcement, as does CESA5, but CESA5 also functions in mucilage biosynthesis. These data suggest unique roles for different CESA subunits in one cell type and illustrate a complex role for cellulose biosynthesis in plant developmental biology.
A comprehensive molecular phylogeny of tardigrades—adding genes and taxa to a poorly resolved phylum‐level phylogeny
Authors: Guil Noemí , Giribet Gonzalo
Published: July 2011

Tardigrades constitute a phylum of miniaturized metazoans with ca. 1030 living species, a fossil record that probably dates back to the Cambrian, and physiological properties that allow them to live in almost any environment known to host life on Earth—they can also survive in space. Despite broad consensus regarding their membership of the superclade Ecdysozoa, the exact position of the phylum remains contested (some analyses suggest onychophorans and arthropods as their closest relatives, while others suggest a relationship to nematodes and nematomorphs) and the internal relationships of the phylum are still poorly understood. In the present study, we present a hypothesis of tardigrade relationships by examining more taxa and more markers than any previously published phylogeny of the group. We generated novel data for three markers (18S rRNA, 28S rRNA, COI) for 42 individuals of 16 carefully identified species, comprising 12 genera and five families from the classes Heterotardigrada and Eutardigrada, and analysed them in conjunction with nearly all data available from GenBank. Our results show certain disagreement with current taxonomy both at higher ranks (families, orders, classes) and at low (generic) taxonomic levels. When studying the sensitivity to outgroup choice, the class Eutardigrada was monophyletic under only one combination of outgroups; all other combinations placed the eutardigrade order Apochela as sister to the class Heterotardigrada. Phylogenetic relationships within the other eutardigrade order, Parachela, were stable to outgroup choice. Eutardigrade superfamilies recently proposed by Sands and collaborators in the order Parachela were tested with the introduction of new sequences from additional genera, and the possible morphological synapomorphies supporting those superfamilies are discussed.

© The Will Henning Society 2011.
BRCA1 contributes to transcription‐coupled repair of DNA damage through polyubiquitination and degradation of Cockayne syndrome B protein
Authors: Wei Leizhen , Lan Li , Yasui Akira , Tanaka Kiyoji , Saijo Masafumi , Matsuzawa Ayako , Kashiwagi Risa , Maseki Emiko , Hu Yiheng , Parvin Jeffrey D. , Ishioka Chikashi , Chiba Natsuko
Published: July 2011

BRCA1 is an important gene involved in susceptibility to breast and ovarian cancer and its product regulates the cellular response to DNA double‐strand breaks. Here, we present evidence that BRCA1 also contributes to the transcription‐coupled repair (TCR) of ultraviolet (UV) light‐induced DNA damage. BRCA1 immediately accumulates at the sites of UV irradiation‐mediated damage in cell nuclei in a manner that is fully dependent on both Cockayne syndrome B (CSB) protein and active transcription. Suppression of BRCA1 expression inhibits the TCR of UV lesions and increases the UV sensitivity of cells proficient in TCR. BRCA1 physically interacts with CSB protein. BRCA1 polyubiquitinates CSB and this polyubiquitination and subsequent degradation of CSB occur following UV irradiation, even in the absence of Cockayne syndrome A (CSA) protein. The depletion of BRCA1 expression increases the UV sensitivity of CSA‐deficient cells. These results indicate that BRCA1 is involved in TCR and that a BRCA1‐dependent polyubiquitination pathway for CSB exists alongside the CSA‐dependent pathway to yield more efficient excision repair of lesions on the transcribed DNA strand. (Cancer Sci 2011; 102: 1840–1847)
Junior doctors prescribing: enhancing their learning in practice
Authors: Rothwell Charlotte , Burford Bryan , Morrison Jill , Morrow Gill , Allen Maggie , Davies Carol , Baldauf Beate , Spencer John , Johnson Neil , Peile Ed , Illing Jan
Published: July 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• A large proportion of medical graduates do not feel prepared for practice.

• Prescribing is one of the biggest steps up from being a student to practising as a doctor.

WHAT THIS STUDY ADDS

• The lack of preparedness of graduates for practice is related to a lack of exposure and preparation for clinical practice. Preparedness may be improved by increasing the number of opportunities to develop the skill‐based, applied aspects of prescribing in a controlled, ‘real’ environment. Simulated activity could provide this experience to undergraduates, or writing prescriptions and drug charts to be checked and signed by a doctor on clinical placements.

AIM This aim of this paper was to explore new doctors' preparedness for prescribing.

METHODS This was a multiple methods study including face‐to‐face and telephone interviews, questionnaires and secondary data from a safe prescribing assessment (n= 284). Three medical schools with differing curricula and cohorts were included: Newcastle (systems‐based, integrated curriculum); Warwick (graduate entry) and Glasgow [problem‐based learning (PBL)], with graduates entering F1 in their local deanery. The primary sample consisted of final year medical students, stratified by academic quartile (n= 65) from each of the three UK medical schools. In addition an anonymous cohort questionnaire was distributed at each site (n= 480), triangulating interviews were conducted with 92 clinicians and questionnaire data were collected from 80 clinicians who had worked with F1s.

RESULTS Data from the primary sample and cohort data highlighted that graduates entering F1 felt under‐prepared for prescribing. However there was improvement over the F1 year through practical experience and support. Triangulating data reinforced the primary sample findings. Participants reported that learning in an applied setting would be helpful and increase confidence in prescribing. No clear differences were found in preparedness to prescribe between graduates of the three medical schools.

CONCLUSION The results form part of a larger study ‘Are medical graduates fully prepared for practice?’. Prescribing was found to be the weakest area of practice in all sources of data. There is a need for more applied learning to develop skill‐based, applied aspects of prescribing which would help to improve preparedness for prescribing.
Family‐related predictors of body weight and weight‐related behaviours among children and adolescents: a systematic umbrella review
Authors: Cislak A. , Safron M. , Pratt M. , Gaspar T. , Luszczynska A.
Published: July 2011

This umbrella review analysed the relationships between family variables and child/adolescent body weight, diet and physical activity. In line with theories of health behaviour change, it was assumed that behaviour‐specific family variables (i.e. beliefs, perceptions and practices referring to food intake or physical activity) would have stronger support than more general family variables (i.e. socio‐economic status or general parental practices). Data obtained from 18 systematic reviews (examining 375 quantitative studies) were analysed. Reviews of experimental trials generally supported the effectiveness of reward/positive reinforcement parental strategies, parental involvement in treatment or prevention programmes, and cognitive–behavioural treatment in reducing child/adolescent body mass and/or obesity. Results across reviews of correlational studies indicated that healthy nutrition of children/adolescents was related to only one parental practice (parental monitoring), but was associated with several behaviour‐specific family variables (e.g. a lack of restrictive control over food choices, high intake of healthy foods and low intake of unhealthy foods by parents and siblings, low pressure to consume foods). With regard to adolescent physical activity, stronger support was also found for behaviour‐specific variables (e.g. physical activity of siblings), and for certain socio‐economic variables (e.g. parental education). Child and adolescent obesity prevention programmes should account for behaviour‐specific family variables.
Asthma control with extrafine‐particle hydrofluoroalkane–beclometasone vs. large‐particle chlorofluorocarbon–beclometasone: a real‐world observational study
Authors: Barnes N. , Price D. , Colice G. , Chisholm A. , Dorinsky P. , Hillyer E. V. , Burden A. , Lee A. J. , Martin R. J. , Roche N. , von Ziegenweidt J. , Israel E.
Published: July 2011

Background The extrafine‐particle formulation of hydrofluoroalkane–beclometasone (EF HFA–BDP; Qvar®) demonstrates improved total and small airway deposition compared with large‐particle chlorofluorocarbon (CFC)–BDP. In some short‐term studies, EF HFA–BDP provides greater effects on lung function than CFC–BDP, and hence is recommended to be prescribed at a lower dose, but whether there are differences in asthma outcomes during long‐term treatment is unknown.

Objective To compare the effectiveness of EF HFA–BDP vs. CFC–BDP over 1 year.

Methods This retrospective matched cohort study examined outcomes in a large primary care database for patients aged 5–60 years with asthma receiving their first inhaled corticosteroid (ICS) prescription (initiation population) or first ICS dose increase (step‐up population) by a pressurized metered‐dose inhaler (pMDI) as EF HFA–BDP or CFC–BDP. Patients were matched on baseline demographic and asthma severity measures in EF HFA–BDP:CFC–BDP ratios of 1 : 3 and 1 : 2 for initiation and step‐up populations, respectively. Step‐up patients were matched also on ICS dose during a baseline year. Co‐primary endpoints were asthma control (composite measure comprising no recorded hospital attendance for asthma, oral corticosteroids, or antibiotics for lower respiratory infection) and exacerbation rate during the outcome year.

Results For the initiation population (EF HFA–BDP n=2882; CFC–BDP n=8646), adjusted odds of achieving asthma control with EF HFA–BDP vs. CFC–BDP was 1.15 (95% CI 1.02–1.28). For the step‐up population (n=258 and 516), adjusted odds of asthma control with EF HFA–BDP was 1.72 (95% CI 1.14–2.56). EF HFA–BDP was prescribed at a median dose half that of CFC–BDP.

Conclusion and Clinical Relevance During 1 year after initiating or stepping up ICS therapy by pMDI, patients who received EF HFA–BDP were more likely to achieve asthma control than those receiving CFC–BDP. These findings suggest that ICS formulation, particle size, and deposition characteristics play important roles in real‐life effectiveness of asthma therapy. This study shows that an EF‐particle formulation of beclometasone can be used at half the dose of the large‐particle formulation with at least as good clinical outcomes.

Cite this as: N. Barnes, D. Price, G. Colice, A. Chisholm, P. Dorinsky, E. V. Hillyer, A. Burden, A. J. Lee, R. J. Martin, N. Roche, J. von Ziegenweidt and E. Israel, Clinical & Experimental Allergy, 2011 (41) 1521–1532.
Why is achieving good ecological outcomes in rivers so difficult?
Authors: HARRIS GRAHAM P. , HEATHWAITE A. LOUISE
Published: July 2011

1. Considerable evidence from around the world shows that achieving good ecological outcomes in rivers from programmes of measures in catchments is difficult. There are a number of reasons for this, which we discuss, but here we focus primarily on the question, ‘Is the knowledge base adequate?’

2. We develop further the thesis that catchments and receiving waters are truly complex systems in which there are fundamental limits to knowledge. Our sampling and data analysis practices come with strong biases and inbuilt ‘framing’ assumptions about the nature and values of ecosystem processes that underestimate complexity and uncertainty.

3. If we reframe our assumptions to think of the problem in terms of the properties of complex systems, then we can rethink our attitudes to uncertainty, causal thickets (multiple stressors) and cross‐scale effects, and we can begin to develop new definitions of what constitutes a ‘good’ ecological outcome. Dealing with inherent variability in data then becomes less of a problem with controlling ‘noise’ and more of a problem of understanding system dynamics. The presence of adaptive dynamics and self‐organisation in complex systems means that uncertainties will always be large and knowledge will be partial and that such systems are fundamentally not computable.

4. We show that small‐scale ‘noise’ in ecosystems is an inherent property of non‐equilibrium systems with predominant advection, reaction–diffusion dynamics. Flow paths in catchments and the dynamics of receiving waters have fractal properties. Fractal dynamics indicate that multiple, cross‐scale interactions are a characteristic of these systems. Small‐scale connectivity is an important (and, from a management point of view, underused) aspect of pattern and process in such systems.

5. In an environment of such complexity, models will be flawed and predictions uncertain. It is therefore necessary to develop new indicators of connectivity and ecological complexity so that indicators of system‐level progress may be found to assist with an improved process of adaptive management that is trend‐orientated as well as outcome‐orientated.
Haemophilia & Exercise Project (HEP): subjective and objective physical performance in adult haemophilia patients – results of a cross‐sectional study
Authors: CZEPA D. , Von MACKENSEN S. , HILBERG T.
Published: July 2011

Summary.  Recurrent musculoskeletal haemorrhages in people with haemophilia (PWH) lead to restrictions in the locomotor system and consequently in physical performance. Patients’ perceptions of their health status have gained an important role in the last few years. The assessment of subjective physical performance in PWH is a new approach. This study aimed to compare the subjective physical performance of PWH with healthy controls and to correlate the results with objective data. Subjective physical performance was assessed via the new questionnaire HEP‐Test‐Q, which consists of 25 items pertaining to four subscales ‘mobility’, ‘strength & coordination’, ‘endurance’ and ‘body perception’. HEP‐Test‐Q subscales were compared with objective data in terms of range of motion, one‐leg‐stand and 12‐minute walk test. Forty‐eight patients (44 ± 11 years) with haemophilia A (43 severe, three moderate) or B (two severe) and 43 controls without haemophilia (42 ± 11 years) were enrolled. PWH showed an impaired subjective physical performance in all HEP‐Test‐Q subscales and in the total score (52 ± 20) compared with controls (77 ± 10; P ≤ 0.001). Correlation analyses for the total score of the HEP‐Test‐Q and objective data revealed values ranging from r = 0.403 (one‐leg‐stand) to r = 0.757 (12‐minute walk test) (P ≤ 0.001). PWH evaluated their physical performance poorer in comparison with healthy people. As self‐assessment did not always correlate highly with objective data, objective examinations of physical performance in PWH should be complemented with subjective perceptions.
Intracranial haemorrhage in the Italian population of haemophilia patients with and without inhibitors
Authors: ZANON E. , IORIO A. , ROCINO A. , ARTONI A. , SANTORO R. , TAGLIAFERRI A. , COPPOLA A. , CASTAMAN G. , MANNUCCI P. M. ,   THE ITALIAN ASSOCIATION OF HEMOPHILIA CENTERS
Published: July 2011

Summary.  Intracranial haemorrhage (ICH) is the most serious bleeding symptom in haemophiliacs, resulting in high rates of mortality and disabling sequelae. The Association of Italian Haemophilia Centres carried out a retrospective survey (1987–2008) of ICH occurring in haemophiliacs with the goals to establish: (i) incidence, location of bleeding, death rate and disabling sequels; (ii) risk factors for ICH; and (iii) treatment used during the acute phase of ICH and for recurrence prevention. A total of 112 ICH episodes had occurred in 88 patients (78 haemophilia A, 10 haemophilia B), 24 of whom experienced recurrences. The cumulative hazard of ICH for the whole cohort over the entire follow‐up period was 26.7 per 1000 patients, and the annualized rate of ICH was 2.50 events per 1000 patients (95% CI 1.90–3.31). The risk of ICH was higher in the youngest children (24.4 per 1000, 95% CI 12.7–47.0 in the first year of age and 14.9, 95% CI 7.1–31.4 in the second year of age) and then progressively rose again after the age of 40. Univariate, bivariate (age‐adjusted) and multivariate analysis investigating the effects of patient characteristics on ICH occurrence showed that haemophilia severity and inhibitor status were strongly associated with ICH [severe vs. mild, HR 3.96 (2.39–6.57); inhibitor vs. non‐inhibitor 2.52 (1.46–4.35)]. HCV infection was also associated with the risk of ICH [HR 1.83 (1.25–2.69)]. Therapeutic suggestions based upon our experience to control ICH recurrence are provided.
Boys with haemophilia have low trabecular bone mineral density and sarcopenia, but normal bone strength at the radius
Authors: SOUCEK O. , KOMRSKA V. , HLAVKA Z. , CINEK O. , ROCEK M. , ZEMKOVA D. , LEBL J. , SUMNIK Z.
Published: July 2011

Summary.  Although a decreased areal bone mineral density (BMD) has been reported in patients with haemophilia, data are lacking that would reflect the three‐dimensional structure of the bone and the muscle‐bone relationship. We aimed to assess volumetric BMD, bone geometry and muscle‐bone phenotype in boys with haemophilia, and to describe the association between clinical characteristics of haemophilia and bone quality and structure. A cross‐sectional study was conducted in 41 boys with haemophilia (mean age 12.4, range 6.6–19.8 years) using peripheral quantitative CT (pQCT) at the nondominant forearm. Results were transformed into Z‐scores using previously published reference data. Significant differences were tested by one‐sample t‐test or sign test. Two‐sample t‐test and anova were used to compare results between subgroups of patients divided according to the severity of the disease, the fracture history and the number of joint and muscle bleedings. Boys with haemophilia had a decreased trabecular volumetric BMD (mean Z‐score −0.5, P < 0.01), while their cortical volumetric BMD was increased (mean Z‐score 0.4, P < 0.05). The volumetric bone mineral content and the bone geometry at the radial diaphysis were normal when adjusted for patients’ shorter body height. Muscle area was decreased (mean Z‐score −1.0, P < 0.001), irrespective of age. No association was observed of bone quality parameters and bone geometry with the disease severity, fracture history or number of bleedings. Bone strength measured at the diaphysis of the radius is not impaired in boys with haemophilia. The finding of the decreased trabecular bone density can be most likely attributed to their sarcopenia.
Adherence to the guideline ‘Triage in emergency departments’: a survey of Dutch emergency departments
Authors: Janssen Maaike AP , van Achterberg Theo , Adriaansen Marian JM , Kampshoff Caroline S , Mintjes‐de Groot Joke
Published: July 2011

Aims and objectives.  The aim of this study was to evaluate the adherence to the 2004 guideline Triage in emergency departments three years after dissemination in Dutch emergency departments.

Background.  In 2004, a Dutch guideline Triage in emergency departments was developed. Triage is the first step performed by nurses when a patient arrives at an emergency department. It includes the prioritisation of patients to ensure that doctors see patients with the highest medical needs first. Although the national guideline was developed and disseminated in 2004, three years on there was no insight into the level of implementation of the guideline in practice.

Design.  A cross‐sectional descriptive design.

Methods.  In February 2007, data were collected from ward managers and triage nurses at all emergency departments in the Netherlands (n = 108), using a questionnaire that was based on the recommendations and performance indicators of the guideline.

Results.  In total, 79% of all 108 Dutch emergency departments responded. The main findings showed that over 31% of the emergency departments did not use a triage system. Emergency departments using the Manchester Triage System had a mean adherence rate of 61% of the guideline’s recommendations and emergency departments using the Emergency System Index adhered to a mean of 65%.

Conclusion.  The guideline Triage in emergency departments was disseminated in 2004, but results from this study indicate that an improvement in adherence to this guideline is required.

Relevance to clinical practice.  Adherence to guidelines is important to standardise practice to ensure that patients receive the appropriate treatment and to improve quality of care.
Clinical learning environment and supervision: experiences of Norwegian nursing students – a questionnaire survey
Authors: Skaalvik Mari Wolff , Normann Hans Ketil , Henriksen Nils
Published: July 2011

Aim and objective.  To measure nursing students’ experiences and satisfaction with their clinical learning environments. The primary interest was to compare the results between students with respect to clinical practice in nursing homes and hospital wards.

Background.  Clinical learning environments are important for the learning processes of nursing students and for preferences for future workplaces. Working with older people is the least preferred area of practice among nursing students in Norway.

Design.  A cross‐sectional design.

Methods.  A validated questionnaire was distributed to all nursing students from five non‐randomly selected university colleges in Norway. A total of 511 nursing students completed a Norwegian version of the questionnaire, Clinical Learning Environment, Supervision and Nurse Teacher (CLES+T) evaluation scale in 2009. Data including descriptive statistics were analysed using the Statistical Program for the Social Sciences. Factor structure was analysed by principal component analysis. Differences across sub‐groups were tested with chi‐square tests and Mann–Whitney U test for categorical variables and t‐tests for continuous variables. Ordinal logistic regression analysis of perceptions of the ward as a good learning environment was performed with supervisory relationships and institutional contexts as independent variables, controlling for age, sex and study year.

Results.  The participating nursing students with clinical placements in nursing homes assessed their clinical learning environment significantly more negatively than those with hospital placements on nearby all sub‐dimensions.

Conclusions.  The evidence found in this study indicates that measures should be taken to strengthen nursing homes as learning environments for nursing students.

Relevance to clinical practice.  To recruit more graduated nurses to work in nursing homes, actions to improve the learning environment are needed.
Lrp–DNA complex stability determines the level of ON cells in type P fimbriae phase variation
Authors: Graveline Richard , Mourez Michaël , Hancock Mark A. , Martin Christine , Boisclair Stéphanie , Harel Josée
Published: July 2011

F1651 and the pyelonephritis‐associated pili (Pap) are two members of the type P family of adhesive factors that play a key role in the establishment of disease caused by extraintestinal Escherichia coli (ExPEC) strains. They are both under the control of an epigenetic and reversible switch that defines the number of fimbriated (ON) and afimbriated (OFF) cells within a clonal population. Our present study demonstrates that the high level of ON cells found during F1651 phase variation is due to altered stability of the DNA complex formed by the leucine‐responsive regulatory protein (Lrp) at its repressor binding sites 1–3; after each cell cycle, complex formation is also modulated by the local regulator FooI (homologue to PapI) which promotes the transit of Lrp towards its activator binding sites 4–6. Furthermore, we identified two nucleotides (T490, G508) surrounding the Lrp binding site 1 that are critical to maintaining a high OFF to ON switch rate during F1651 phase variation, as well as switching Pap fimbriae towards the OFF state.
The novel putative transporter NPT1 plays a critical role in early stages of Plasmodium berghei sexual development
Authors: Boisson Bertrand , Lacroix Céline , Bischoff Emmanuel , Gueirard Pascale , Bargieri Daniel Y. , Franke‐Fayard Blandine , Janse Chris J. , Ménard Robert , Baldacci Patricia
Published: July 2011

Transmission of Plasmodium species from a mammalian host to the mosquito vector requires the uptake, during an infected blood meal, of gametocytes, the precursor cells of the gametes. Relatively little is known about the molecular mechanisms involved in the developmental switch from asexual development to sexual differentiation or the maturation and survival of gametocytes. Here, we show that a gene coding for a novel putative transporter, NPT1, plays a crucial role in the development of Plasmodium berghei gametocytes. Parasites lacking NPT1 are severely compromised in the production of gametocytes and the rare gametocytes produced are unable to differentiate into fertile gametes. This is the earliest block in gametocytogenesis obtained by reverse genetics and the first to demonstrate the role of a protein with a putative transport function in sexual development. These results and the high degree of conservation of NPT1 in Plasmodium species suggest that this protein could be an attractive target for the development of novel drugs to block the spread of malaria.
GLP‐2 receptor expression in excitatory and inhibitory enteric neurons and its role in mouse duodenum contractility
Authors: Cinci L. , Faussone‐Pellegrini M. S. , Rotondo A. , Mulè F. , Vannucchi M. G.
Published: July 2011

Background  Glucagon‐like peptide 2 (GLP‐2), a nutrient‐responsive hormone, exerts various actions in the gastrointestinal tract that are mediated by a G‐protein coupled receptor called GLP‐2R. A little information is available on GLP‐2R expression in enteric neurons and nothing on the interstitial cells of Cajal (ICC).

Methods  We investigated presence and distribution of the GLP‐2R in the mouse duodenum by immunohistochemistry and the potential motor effects of GLP‐2 on the spontaneous and neurally evoked mechanical activity.

Key Results  The GLP‐2R was expressed by the myenteric and submucosal neurons. Labelling was also present in nerve varicosities within the circular muscular layer and at the deep muscular plexus (DMP). No immunoreactive nerve fiber was seen within the longitudinal muscle layer. The GLP‐2R‐positive neurons were either excitatory (SP‐ and choline‐acetyltransferase‐positive) or inhibitory (vasoactive intestinal polypeptide and nNOS‐positive). The ICC, both at the myenteric plexus and at the DMP, never expressed GLP‐2R but, especially those at the DMP, were surrounded by GLP‐2R‐positive nerve varicosities co‐expressing either excitatory or inhibitory neurotransmitters. Quantitative analysis demonstrated a consistent prevalence of GLP‐2R on the excitatory pathways. In agreement, the functional results showed that the administration of GLP‐2 in vitro caused decrease of the spontaneous contractions mediated by nitric oxide release and reduction of the evoked cholinergic contractions.

Conclusions & Inferences  The present findings indicate that the GLP‐2R is expressed by inhibitory and excitatory neurons, the GLP‐2 inhibits the muscle contractility likely decreasing cholinergic neurotransmission and increasing nitric oxide production, and this effect is possibly mediated by the ICC‐DMP recruitment.
Gene discovery in cereals through quantitative trait loci and expression analysis in water‐use efficiency measured by carbon isotope discrimination
Authors: CHEN JING , CHANG SCOTT X. , ANYIA ANTHONY O.
Published: July 2011

Drought continues to be a major constraint on cereal production in many areas, and the frequency of drought is likely to increase in most arid and semi‐arid regions under future climate change scenarios. Considerable research and breeding efforts have been devoted to investigating crop responses to drought at various levels and producing drought‐resistant genotypes. Plant physiology has provided new insights to yield improvement in drought‐prone environments. Crop performance could be improved through increases in water use, water‐use efficiency (WUE) and harvest index. Greater WUE can be achieved by coordination between photosynthesis and transpiration. Carbon isotope discrimination (Δ13C) has been demonstrated to be a simple but reliable measure of WUE, and negative correlation between them has been used to indirectly estimate WUE under selected environments. New tools, such as quantitative trait loci (QTL) mapping and gene expression profiling, are playing vital roles in dissecting drought resistance‐related traits. The combination of gene expression and association mapping could help identify candidate genes underlying the QTL of interest and complement map‐based cloning and marker‐assisted selection. Eventually, improved cultivars can be produced through genetic engineering. Future efficient and effective breeding progress in cereals under targeted drought environments will come from the integrated knowledge of physiology and genomics.
Temperature response of mesophyll conductance in cultivated and wild Oryza species with contrasting mesophyll cell wall thickness
Authors: SCAFARO ANDREW P. , VON CAEMMERER SUSANNE , EVANS JOHN R. , ATWELL BRIAN J.
Published: July 2011

A critical component of photosynthetic capacity is the conductance of CO2 from intercellular airspaces to the sites of CO2 fixation in the stroma of chloroplasts, termed mesophyll conductance (gm). Leaf anatomy has been identified as an important determinant of gm. There are few studies of the temperature response of gm and none has examined the implications of leaf anatomy. Hence, we compared a cultivar of Oryza sativa with two wild Oryza relatives endemic to the hot northern savannah of Australia, namely Oryza meridionalis and Oryza australiensis. All three species had similar leaf anatomical properties, except that the wild relatives had significantly thicker mesophyll cell walls than O. sativa. Thicker mesophyll cell walls in the wild rice species are likely to have contributed to the reduction in gm, which was associated with a greater drawdown of CO2 into chloroplasts (Ci–Cc) compared with O. sativa. Mesophyll conductance increased at higher temperatures, whereas the rate of CO2 assimilation was relatively stable between 20 and 40 °C. Consequently, Ci–Cc decreased for all three species as temperature increased.
Concepts of plant health – reviewing and challenging the foundations of plant protection
Authors: Döring T. F. , Pautasso M. , Finckh M. R. , Wolfe M. S.
Published: July 2011

Plant health is a frequently used but ill‐defined term. However, there is an extensive literature on general health definitions and health criteria in human medicine. Taking up ideas from these philosophical debates, concepts of plant health are reviewed and a framework developed to locate these concepts according to their position in several philosophical controversies. In particular, (i) the role of values in defining plant health in a naturalist versus a normativist approach; (ii) negative and positive definitions of plant health; (iii) reductionist versus holistic perspectives; (iv) the focus on functionality versus resilience, i.e. the ability of the plant to perform under stress with or without human interference; (v) materialist versus vitalist approaches; and (vi) biocentric versus anthropocentric views, are surveyed. The ways in which these perspectives relate to mainstream and alternative approaches to plant protection are explored and we suggest how the contradicting views might be reconciled. It is argued that none of these perspectives is without inherent contradictions, but that by combining contrasting approaches it is possible to provide a comprehensive though fuzzy concept. Rather than giving a new definition of plant health, a conceptual framework is developed that suggests what questions may be answered in debates on plant health issues and how such debates could be organized.
Estimation of the accuracy of two diagnostic methods for the detection of Plum pox virus in nursery blocks by latent class models
Authors: Vidal E. , Moreno A. , Bertolini E. , Cambra M.
Published: July 2011

The control of Plum pox virus (PPV), the most important viral disease that affects stone fruit trees, requires the use of reliable detection methods. The effectiveness of spot real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) for the detection of PPV in samples collected from nursery blocks was compared with a validated PPV detection technique, the double antibody sandwich indirect enzyme‐linked immunosorbent assay (DASI‐ELISA) using the PPV‐specific monoclonal antibody 5B‐IVIA/AMR. In total, 5047 nursery plants were analysed by both techniques. The agreement between the techniques was almost perfect (Cohen’s kappa index of 0·88 ± 0·01). The diagnostic parameters (sensitivity, specificity and likelihood ratios) of both techniques were simultaneously evaluated in 2473 nursery plants by latent class models using maximum likelihood functions and a Bayesian approach. The sensitivity and specificity of both techniques did not vary according to the latent model applied. Spot real‐time RT‐PCR was more sensitive while DASI‐ELISA was more specific for PPV detection. In addition, the findings demonstrate that latent class models are a flexible and potent statistical method to estimate the accuracy of diagnostic tests for plant pathology.
Vented sediments and tsunami deposits in the Puget Lowland, Washington – differentiating sedimentary processes
Authors: MARTIN MARIA ELIZABETH , BOURGEOIS JOANNE
Published: July 2011

The sandy deposits produced by tsunamis and liquefaction share many sedimentary features, and distinctions between the two are important in seismically active coastal zones. Both types of deposits are present in the wetlands bordering Puget Sound, where one or more earthquakes about 1100 years ago caused both tsunami flooding and sediment venting. This co‐occurrence allows an examination of the resulting deposits and a comparison with tsunami and liquefaction features of modern events. Vented sediments occur at four of five wetland field localities and tsunami deposits at two. In comparison with tsunami deposits, vented sediments in this study and from other studies tend to be thicker (although they can be thin). Vented sediments also have more variable thickness at both outcrop and map scale, are associated with injected dykes and contain clasts derived from underlying deposits. Further, vented sediments tend to contain a greater variety of sedimentary structures, and these structures vary laterally over metres. Tsunami deposits compared with vented sediments are commonly thinner, fine and thin landward more consistently, have more uniform thickness on outcrop and map scales, and have the potential of containing coarser clasts, up to boulders. For both tsunami deposits and vented sediments, the availability and grain size of source material condition the characteristics of the deposit. In the cases presented in this paper, both foraminifera and diatom assemblages within tsunami deposits and vented sediments consisted of brackish and marine species, and no distinction between processes could be made based on microfossils. In summary, this study indicates a need for more careful analysis and mapping of coastal sediments associated with earthquakes to avoid misidentification of processes and misevaluation of hazards.
BnaC.Tic40, a plastid inner membrane translocon originating from Brassica oleracea, is essential for tapetal function and microspore development in Brassica napus
Authors: Dun Xiaoling , Zhou Zhengfu , Xia Shengqian , Wen Jing , Yi Bin , Shen Jinxiong , Ma Chaozhi , Tu Jinxing , Fu Tingdong
Published: July 2011

Here, we describe the characteristics of a Brassica napus male sterile mutant 7365A with loss of the BnMs3 gene, which exhibits abnormal enlargement of the tapetal cells during meiosis. Later in development, the absence of the BnMs3 gene in the mutant results in a loss of the secretory function of the tapetum, as suggested by abortive callose dissolution and retarded tapetal degradation. The BnaC.Tic40 gene (equivalent to BnMs3) was isolated by a map‐based cloning approach and was confirmed by genetic complementation. Sequence analyses suggested that BnaC.Tic40 originated from BolC.Tic40 on the Brassica oleracea linkage group C9, whereas its allele Bnms3 was derived from BraA.Tic40 on the Brassica rapa linkage group A10. The BnaC.Tic40 gene is highly expressed in the tapetum and encodes a putative plastid inner envelope membrane translocon, Tic40, which is localized into the chloroplast. Transmission electron microscopy (TEM) and lipid staining analyses suggested that BnaC.Tic40 is a key factor in controlling lipid accumulation in the tapetal plastids. These data indicate that BnaC.Tic40 participates in specific protein translocation across the inner envelope membrane in the tapetal plastid, which is required for tapetal development and function.