bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syringyl Lignin Is Unaltered by Severe Sinapyl Alcohol Dehydrogenase Suppression in Tobacco
Authors: Barakate Abdellah , Stephens Jennifer , Goldie Alison , Hunter William N. , Marshall David , Hancock Robert D. , Lapierre Catherine , Morreel Kris , Boerjan Wout , Halpin Claire 
Published: December 2011

Abstract
The manipulation of lignin could, in principle, facilitate efficient biofuel production from plant biomass. Despite intensive study of the lignin pathway, uncertainty exists about the enzyme catalyzing the last step in syringyl (S) monolignol biosynthesis, the reduction of sinapaldehyde to sinapyl alcohol. Traditional schemes of the pathway suggested that both guaiacyl (G) and S monolignols are produced by a single substrate-versatile enzyme, cinnamyl alcohol dehydrogenase (CAD). This was challenged by the discovery of a novel sinapyl alcohol dehydrogenase (SAD) that preferentially uses sinapaldehyde as a substrate and that was claimed to regulate S lignin biosynthesis in angiosperms. Consequently, most pathway schemes now show SAD (or SAD and CAD) at the sinapaldehyde reduction step, although functional evidence is lacking. We cloned SAD from tobacco (Nicotiana tabacum) and suppressed it in transgenic plants using RNA interference–inducing vectors. Characterization of lignin in the woody stems shows no change to content, composition, or structure, and S lignin is normal. By contrast, plants additionally suppressed in CAD have changes to lignin structure and S:G ratio and have increased sinapaldehyde in lignin, similar to plants suppressed in CAD alone. These data demonstrate that CAD, not SAD, is the enzyme responsible for S lignin biosynthesis in woody angiosperm xylem.
Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage
Authors: Jeong Dong-Hoon , Park Sunhee , Zhai Jixian , Gurazada Sai Guna Ranjan , De Paoli Emanuele , Meyers Blake C. , Green Pamela J. 
Published: December 2011

AbstractSmall RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ~400 annotated miRNAs with current criteria and the finding that among these, ~150 had small interfering RNA–like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.
POPCORNFunctions in the Auxin Pathway to Regulate Embryonic Body Plan and Meristem Organization inArabidopsis
Authors: Xiang Daoquan , Yang Hui , Venglat Prakash , Cao Yongguo , Wen Rui , Ren Maozhi , Stone Sandra , Wang Edwin , Wang Hong , Xiao Wei , Weijers Dolf , Berleth Thomas , Laux Thomas , Selvaraj Gopalan , Datla Raju 
Published: December 2011

AbstractThe shoot and root apical meristems (SAM and RAM) formed during embryogenesis are crucial for postembryonic plant development. We report the identification of POPCORN (PCN), a gene required for embryo development and meristem organization in Arabidopsis thaliana. Map-based cloning revealed that PCN encodes a WD-40 protein expressed both during embryo development and postembryonically in the SAM and RAM. The two pcn alleles identified in this study are temperature sensitive, showing defective embryo development when grown at 22°C that is rescued when grown at 29°C. In pcn mutants, meristem-specific expression of WUSCHEL (WUS), CLAVATA3, and WUSCHEL-RELATED HOMEOBOX5 is not maintained; SHOOTMERISTEMLESS, BODENLOS (BDL) and MONOPTEROS (MP) are misexpressed. Several findings link PCN to auxin signaling and meristem function: ectopic expression of DR5rev:green fluorescent protein (GFP), pBDL:BDL-GFP, and pMP:MP-β-glucuronidase in the meristem; altered polarity and expression of pPIN1:PIN1-GFP in the apical domain of the developing embryo; and resistance to auxin in the pcn mutants. The bdl mutation rescued embryo lethality of pcn, suggesting that improper auxin response is involved in pcn defects. Furthermore, WUS, PINFORMED1, PINOID, and TOPLESS are dosage sensitive in pcn, suggesting functional interaction. Together, our results suggest that PCN functions in the auxin pathway, integrating auxin signaling in the organization and maintenance of the SAM and RAM.
ArabidopsisATM and ATR Kinases Prevent Propagation of Genome Damage Caused by Telomere Dysfunction
Authors: Amiard Simon , Depeiges Annie , Allain Elisabeth , White Charles I. , Gallego Maria Eugenia 
Published: December 2011

AbstractThe ends of linear eukaryotic chromosomes are hidden in nucleoprotein structures called telomeres, and loss of the telomere structure causes inappropriate repair, leading to severe karyotypic and genomic instability. Although it has been shown that DNA damaging agents activate a DNA damage response (DDR), little is known about the signaling of dysfunctional plant telomeres. We show that absence of telomerase in Arabidopsis thaliana elicits an ATAXIA-TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR)-dependent DDR at telomeres, principally through ATM. By contrast, telomere dysfunction induces an ATR-dependent response in telomeric Conserved telomere maintenance component1 (Ctc1)-Suppressor of cdc thirteen (Stn1)-Telomeric pathways in association with Stn1 (CST)–complex mutants. These results uncover a new role for the CST complex in repressing the ATR-dependent DDR pathway in plant cells and show that plant cells use two different DNA damage surveillance pathways to signal telomere dysfunction. The absence of either ATM or ATR in ctc1 and stn1 mutants significantly enhances developmental and genome instability while reducing stem cell death. These data thus give a clear illustration of the action of ATM/ATR-dependent programmed cell death in maintaining genomic integrity through elimination of genetically unstable cells.
12‐hydroxy‐eicosatetraenoic acid (12‐HETE): a biomarker of Churg‐Strauss syndrome
Authors: Szczeklik W. , Sanak M. , Mastalerz L. , Sokołowska B. M. , Gielicz A. , Soja J. , Kumik J. , Musiał J. , Szczeklik A. 
Published: December 2011

SummaryBackgroundChurg‐Strauss syndrome (CSS) shares similarities with asthma and hypereosinophilic syndrome (HES). Eicosanoids – important inflammatory and signaling molecules – are present in exhaled breath condensate (EBC) and broncho‐alveolar lavage fluid (BALF).ObjectivesTo assess eicosanoid profile both in EBC and BALF of CSS subjects searching for a pattern characteristic of this syndrome.MethodsEBCs from 23 CSS patients, 30 asthmatics, 12 HES patients and 54 healthy controls (HC) were assessed quantitatively for 19 eicosanoids by a high‐performance liquid chromatography ‐ tandem mass spectrometry (HPLC‐MS/MS). In addition, in 21 of 23 CSS subjects and in nine asthmatics, eicosanoids were determined in BALF.ResultsEBC from CSS patients showed markedly elevated levels of 12‐HETE as compared with other studied groups. BALF was characterized by a significant elevation of 12‐HETE and its metabolite 12‐tetranor HETE in CSS as compared with asthma. Clinical activity of CSS correlated with 12‐HETE and its metabolites levels in BALF, but not in EBC.Conclusion and Clinical RelevanceCSS is clearly distinguished from bronchial asthma, and HES by a marked increase in 12‐HETE concentration in both EBC and BALF. This points to a possible new pathogenic mechanism in CSS and may help in future in establishing the diagnosis of CSS.
Changes in the surface of four calcium silicate‐containing endodontic materials and an epoxy resin‐based sealer after a solubility test
Authors: Borges R. P. , Sousa‐Neto M. D. , Versiani M. A. , Rached‐Júnior F. A. , De‐Deus G. , Miranda C. E. S. , Pécora J. D. 
Published: December 2011

Borges RP, Sousa‐Neto MD, Versiani MA, Rached‐Júnior FA, De‐Deus G, Miranda CES, Pécora JD. Changes in the surface of four calcium silicate‐containing endodontic materials and an epoxy resin‐based sealer after a solubility test. International Endodontic Journal, 45, 419–428, 2012.AbstractAim  To compare the changes in the surface structure and elemental distribution, as well as the percentage of ion release, of four calcium silicate‐containing endodontic materials with a well‐established epoxy resin‐based sealer, submitted to a solubility test.Methodology  Solubility of AH Plus, iRoot SP, MTA Fillapex, Sealapex and MTA‐Angelus (MTA‐A) was tested according to ANSI/ADA Specification 57. The deionized water used in the solubility test was submitted to atomic absorption spectrophotometry to determine and quantify Ca2+, Na+, K+, Zn2+, Ni2+ and Pb2+ ions release. In addition, the outer and inner surfaces of nonsubmitted and submitted samples of each material to the solubility test were analysed by means of scanning electron microscopy and energy‐dispersive spectroscopy (SEM/EDX). Statistical analysis was performed by using one‐way anova and Tukey’s post hoc tests (α = 0.05).Results  Solubility results, in percentage, sorted in an increasing order were −1.24 ± 0.19 (MTA‐A), 0.28 ± 0.08 (AH Plus), 5.65 ± 0.80 (Sealapex), 14.89 ± 0.73 (MTA Fillapex) and 20.64 ± 1.42 (iRoot SP). AH Plus and MTA‐A were statistically similar (P > 0.05), but different from the other materials (P < 0.05). High levels of Ca2+ ion release were observed in all groups except AH Plus sealer. MTA‐A also had the highest release of Na2+ and K+ ions. Zn+2 ion release was observed only with AH Plus and Sealapex sealers. After the solubility test, all surfaces had morphological changes. The loss of matrix was evident and the filler particles were more distinguishable. EDX analysis displayed high levels of calcium and carbon at the surface of Sealapex, MTA Fillapex and iRoot SP.Conclusions  AH Plus and MTA‐A were in accordance with ANSI/ADA’s requirements regarding solubility whilst iRoot SP, MTA Fillapex and Sealapex did not fulfil ANSI/ADA’s protocols. High levels of Ca2+ ion release were observed in all materials except AH Plus. SEM/EDX analysis revealed that all samples had morphological changes in both outer and inner surfaces after the solubility test. High levels of calcium and carbon were also observed at the surface of all materials except AH Plus and MTA‐A.
Modelling spread of British wind‐dispersed plants under future wind speeds in a changing climate
Authors: Bullock James M. , White Steven M. , Prudhomme Christel , Tansey Christine , Perea Ramón , Hooftman Danny A. P. 
Published: December 2011

Summary1. Climate change impacts on habitat suitability and demography are often studied, but direct effects on plant dispersal are rarely considered. To address this we analysed climate model projections of future wind speeds and modelled their possible impacts on dispersal and spread of wind‐dispersed plants.2. Projections for 17 Global Climate Models and three emission scenarios suggested great uncertainty about wind speeds in southern England by the period 2070–99. Projections ranged from −90% to +100% change in the mean wind speed, although the average projection was for large falls in both summer and winter wind speeds.3. Using a novel method for converting projected changes in mean wind speed to new seasonal wind speed distributions, we parameterized a mechanistic model of seed dispersal by wind using baseline and changes in mean wind speed from −80% to +80%.4. The mechanistic seed dispersal model was combined with demographic data in an analytical model of plant spread. This was carried out for three British native and three non‐native species, which represented a range of life‐forms.5. Dispersal kernels and population spread rates were affected disproportionately by changes in wind speed, demonstrating nonlinear propagation of uncertainty in wind speed projections through to modelled plant spread rates.6. Sensitivity analyses showed differences among the plant species in which demographic transitions were most important in determining spread rates. By contrast, sensitivity of spread rates to dispersal parameters showed great consistency among species, with seed release height being more important than seed terminal velocity.7. Synthesis. Plant populations will need to shift their geographic ranges to keep pace with climate change‐driven habitat loss. This study shows that climate change may affect that ability by decreasing the dispersal distances of wind‐dispersed plants and thus their potential spread rates. However, the modelling approach presented here illustrates that uncertainty in climate models leads to an even greater uncertainty about how dispersal and spread will change in future climates. Caution should therefore be exercised in making predictions as to how fast plant species may spread in response to climate change.
Quality improvement in medical education: current state and future directions
Authors: Wong Brian M , Levinson Wendy , Shojania Kaveh G 
Published: December 2011

Medical Education 2012: 46: 107–119Context  During the last decade, there has been a drive to improve the quality of patient care and prevent the occurrence of avoidable errors. This review describes current efforts to teach or engage trainees in patient safety and quality improvement (QI), summarises progress to date, as well as successes and challenges, and lists our recommendations for the next steps that will shape the future of patient safety and QI in medical education.Current status  Trainees encounter patient safety and QI through three main groups of activity. First are formal curricula that teach concepts or methods intended to facilitate trainees’ participation in QI activities. These curricula increase learner knowledge and may improve clinical processes, but demonstrate limited capacity to modify learner behaviours. Second are educational activities that impart specific skills related to safety or quality which are considered to represent core doctor competencies (e.g. effective patient handover). These are frequently taught effectively, but without emphasis on the general safety or quality principles that inform the relevant skills. Third are real‐life QI initiatives that involve trainees as active or passive participants. These innovative approaches expose trainees to safety and quality by integrating QI activities into trainees’ day‐to‐day work. However, this integration can be challenging and can sometimes result in tension with broader educational goals.Future directions  To prepare the next generation of doctors to make meaningful contributions to the quality mission, we propose the following call to action. Firstly, a major effort to build faculty capacity, especially among teachers of QI, should be instigated. Secondly, accreditation standards and assessment methods, both during training and at end‐of‐training certification examinations, should explicitly target these competencies. Finally, and perhaps most importantly, we must refocus our attention at all levels of training and instil fundamental, collaborative, open‐minded behaviours so that future clinicians are primed to promote a culture of safer, higher‐quality care.
Making sense of work‐based assessment: ask the right questions, in the right way, about the right things, of the right people
Authors: Crossley Jim , Jolly Brian 
Published: December 2011

Medical Education 2012: 46: 28–37Context  Historically, assessments have often measured the measurable rather than the important. Over the last 30 years, however, we have witnessed a gradual shift of focus in medical education. We now attempt to teach and assess what matters most. In addition, the component parts of a competence must be marshalled together and integrated to deal with real workplace problems. Workplace‐based assessment (WBA) is complex, and has relied on a number of recently developed methods and instruments, of which some involve checklists and others use judgements made on rating scales. Given that judgements are subjective, how can we optimise their validity and reliability?Methods  This paper gleans psychometric data from a range of evaluations in order to highlight features of judgement‐based assessments that are associated with better validity and reliability. It offers some issues for discussion and research around WBA. It refers to literature in a selective way. It does not purport to represent a systematic review, but it does attempt to offer some serious analyses of why some observations occur in studies of WBA and what we need to do about them.Results and Discussion  Four general principles emerge: the response scale should be aligned to the reality map of the judges; judgements rather than objective observations should be sought; the assessment should focus on competencies that are central to the activity observed, and the assessors who are best‐placed to judge performance should be asked to participate.
Prokinetic effect of a standardized yarrow (Achillea millefolium) extract and its constituent choline: studies in the mouse and human stomach
Authors: Borrelli F. , Romano B. , Fasolino I. , Tagliatatela‐Scafati O. , Aprea G. , Capasso R. , Capasso F. , Coppola Bottazzi E. , Izzo A. A. 
Published: December 2011

AbstractBackground  Functional dyspepsia (FD) is a highly prevalent gastrointestinal disorder characterized by alterations in gastric motility. Yarrow (Achillea millefolium L., Fam Asteraceae) preparations are traditional remedies used to treat dyspeptic complaints. Herein, we investigated the effect of a standardized dry water extract obtained from A. millefolium flowering tops (AME) on gastric motility.Methods  The effect of AME on motility was evaluated on the resting tone of the isolated gastric antrum and on gastric emptying in vivo (phenol red meal method) both in control mice and in the model of cancer chemotherapy (cisplatin)‐induced gastric abnormalities.Key Results  The AME contracted mouse and human gastric strips and this action was unaffected by hexamethonium and tetrodotoxin, but strongly reduced by atropine. Among various chemical ingredients in yarrow, choline, but not the flavonoids rutin and apigenin, mimicked the action of AME. Furthermore, AME deprived of choline did not exert a contractile effect. In vivo, AME stimulated gastric emptying both in control and in cisplatin‐treated mice, being more active in pathological states.Conclusions & Inferences  It is concluded that (i) AME exerts a direct spasmogenic effect on gastric antrum; (ii) choline is the chemical ingredient responsible of such effect; (iii) the prokinetic effect of AME observed in vivo could provide the pharmacological basis underlying its traditional use in the treatment of dyspepsia.
A 2‐oxoglutarate‐dependent dioxygenase from Ruta graveolens L. exhibits p‐coumaroyl CoA 2′‐hydroxylase activity (C2′H): a missing step in the synthesis of umbelliferone in plants
Authors: Vialart Guilhem , Hehn Alain , Olry Alexandre , Ito Kyoko , Krieger Celia , Larbat Romain , Paris Cedric , Shimizu Bun‐ichi , Sugimoto Yukihiro , Mizutani Masaharu , Bourgaud Frederic 
Published: December 2011

SummaryCoumarins are important compounds that contribute to the adaptation of plants to biotic or abiotic stresses. Among coumarins, umbelliferone occupies a pivotal position in the plant phenylpropanoid network. Previous studies indicated that umbelliferone is derived from the ortho‐hydroxylation of p‐coumaric acid by an unknown biochemical step to yield 2,4‐dihydroxycinnamic acid, which then undergoes spontaneous lactonization. Based on a recent report of a gene encoding a 2‐oxoglutarate‐dependent dioxygenase from Arabidopsis thaliana that exhibited feruloyl CoA 6′‐hydroxylase activity (Bourgaud et al., 2006), we combined a bioinformatic approach and a cDNA library screen to identify an orthologous ORF (Genbank accession number JF799117) from Ruta graveolens L. This ORF shares 59% amino acid identity with feruloyl CoA 6′‐hydroxylase, was functionally expressed in Escherichia coli, and converted feruloyl CoA into scopoletin and p‐coumaroyl CoA into umbelliferone with equal activity. Its bi‐functionality was further confirmed in planta: transient expression of JF799117 in Nicotiana benthamiana yielded plants with leaves containing high levels of umbelliferone and scopoletin when compared to control plants, which contained barely detectable traces of these compounds. The expression of JF799117 was also tightly correlated to the amount of umbelliferone that was found in UV‐elicited R. graveolens leaves. Therefore, JF799117 encodes a p‐coumaroyl CoA 2′‐hydroxylase in R. graveolens, which represents a previously uncharacterized step in the synthesis of umbelliferone in plants. Psoralen, which is an important furanocoumarin in R. graveolens, was found to be a competitive inhibitor of the enzyme, and it may exert this effect through negative feedback on the enzyme at an upstream position in the pathway.
Demethylation of the FCER1G promoter leads to FcεRI overexpression on monocytes of patients with atopic dermatitis
Authors: Liang Y. , Wang P. , Zhao M. , Liang G. , Yin H. , Zhang G. , Wen H. , Lu Q. 
Published: December 2011

To cite this article: Liang Y, Wang P, Zhao M, Liang G, Yin H, Zhang G, Wen H, Lu Q. Demethylation of the FCER1G promoter leads to FcεRI overexpression on monocytes of patients with atopic dermatitis. Allergy 2012; 67: 424–430.Abstract
Background:  Overexpression of the high‐affinity receptor for immunoglobulin E on atopic monocytes and dendritic cells is known to contribute to the pathogenesis of atopic dermatitis (AD). However, it remains unclear what is the underlying mechanism of FcεRI deregulation. It has been speculated that epigenetic deregulation may play a role.
Methods:  Global DNA methylation levels of monocytes from 10 AD patients and 10 healthy controls were measured using a global DNA methylation kit. Bisulfite sequencing was performed to determine the methylation status of the FCER1G promoter region. FcεRIγ mRNA and FcεRI protein levels were detected by real‐time RT‐PCR, Western blotting, and flow cytometry, respectively. Patch methylation and the demethylating agent, 5‐azacytidine, were used to determine the functional significance of methylation changes on FcεRI expression.
Results:  Monocytes from AD patients show a global hypomethylation, as well as a locus‐specific hypomethylation at FCER1G promoter, as compared to healthy controls. Furthermore, this hypomethylation of FCER1G is inversely correlated with its expression. Patch methylation in combination with luciferase reporter assay confirmed the direct relationship between methylation and expression. Moreover, treating healthy monocytes with 5‐azacytidine caused a reduction in methylation levels and an induction in FcεRIγ transcription and surface expression of FcεRI.
Conclusion:  Demethylation of specific regulatory elements within the FCER1G locus contributes to FcεRI overexpression on monocytes from patients with AD.