bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars
Authors: Lin Hong , Rao Jun , Shi Jianxin , Hu Chaoyang , Cheng Fang , Wilson Zoe A. , Zhang Dabing , Quan Sheng 
Published: June 2014

AbstractSoybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics” studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large‐scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography‐mass spectrometry and ultra‐performance liquid chromatography‐tandem mass spectrometry. One hundred sixty‐nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite–metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.
Ensuring a proactive, evidence‐based, patient safety approach to patient assessment
Authors: Considine Julie , Currey Judy 
Published: June 2014

Aims and objectivesTo argue that if all nurses were to adopt the primary survey approach (assessment of airway, breathing, circulation and disability) as the first element of patient assessment, they would be more focused on active detection of clinical deterioration rather than passive collection of patient data.BackgroundNurses are the professional group that carry the highest level of responsibility for patient assessment, accurate data collection and interpretation. The timely recognition of, and response to deteriorating patients, is dependent on the measurement and interpretation of pertinent physiological data by nurses.DesignDiscursive paper.MethodsTraditionally taught and commonly used approaches to patient assessment such as ‘vital signs’ and ‘body systems’ are not evidence‐based nor framed in patient safety. The primary survey approach as the first element in patient assessment has three major advantages: (1) data are collected according to clinical importance; (2) data are collected using the same framework as most organisation's rapid response system activation criteria; and (3) the primary survey acts as a patient safety checklist, thereby decreasing the risk of failure to recognise, and therefore respond to, deteriorating patients.ConclusionThe vital signs and body systems approaches to patient assessment have significant limitations in identifying clinical deterioration. The primary survey approach provides nurses with a consistent, evidence‐based and sequenced approach to patient assessment in every clinical setting.Relevance to clinical practiceAll nurses should use a primary survey approach as the first element of patient assessment in every patient encounter as a patient safety strategy.
Addressing adolescent substance use in a paediatric health‐care setting
Authors: Phillips Natalie Lynette , Milne Bronwyn , Silsbury Catherine , Zappia Popi , Zehetner Anthony , Klineberg Emily , Towns Susan , Steinbeck Katharine 
Published: June 2014

AimThe aim of this study is to review the operation of a specialist adolescent drug and alcohol consultation liaison service in a tertiary paediatric hospital.MethodA retrospective review of patient records was conducted to identify patient characteristics and assess service utilisation.ResultsTwo hundred adolescents were referred over 4 years. Most presented during mid‐adolescence (14–16 years). Alcohol, cannabis and nicotine were the most frequently reported substances, and almost half of referrals involved polysubstance use. Mental health diagnoses and behavioural problems were commonly reported. Almost two‐thirds (63.5%) attended an appointment for drug and alcohol assessment and intervention (n = 92) or were referred to appropriate services (n = 35). Adolescents more likely to engage and attend an appointment with the specialist adolescent addiction medicine service included those with amphetamine use, polysubstance use, chronic illness, any mental health diagnosis and mood disorder. Indigenous Australians and those with a history of aggression were more difficult to engage.ConclusionsAdolescents present to paediatric health settings with drug‐ and alcohol‐related issues, including associated harms. These comprise, but are not limited to, physical and sexual assault, family conflict, mood and behavioural concerns (including psychosis), and forensic issues. Early intervention aims to reduce long‐term risks such as dependence in adulthood. Specialist adolescent drug and alcohol services may assist in identifying and engaging these high‐risk and often complex young people in developmentally appropriate treatment.
Nursing perceptions of high‐flow nasal cannulae treatment for very preterm infants
Authors: Roberts Calum T , Manley Brett J , Dawson Jennifer A , Davis Peter G 
Published: June 2014

AimThis study aims to assess nursing perceptions of high‐flow nasal cannulae (HFNC) in comparison with nasal continuous positive airway pressure (NCPAP) as post‐extubation respiratory support for very preterm infants.MethodsA standardised questionnaire form was distributed in person to nursing staff in The Royal Women's Hospital neonatal unit, where HFNC had been recently introduced in the context of a clinical trial. Nursing staff were eligible to participate if they routinely cared for infants receiving respiratory support.ResultsThe survey was completed by 99/144 eligible nurses. The majority of the 99 nurses surveyed felt that HFNC was less likely than NCPAP to prevent re‐intubation of infants 24–26 weeks' gestation but equally likely to prevent re‐intubation of infants 28–30 weeks' gestation. Nurses preferred NCPAP for post‐extubation support of 24‐ and 26‐week infants, and HFNC for 28‐ and 30‐week infants, despite being less experienced with HFNC. Perceptions of HFNC compared with NCPAP included increased ease‐of‐use, improved infant comfort and reduced nasal trauma.ConclusionsNeonatal nurses preferred NCPAP for post‐extubation support of infants <28 weeks' gestation and HFNC for infants of 28 or 30 weeks' gestation. Nurses accurately predicted varying efficacy of HFNC across different gestational ages, consistent with the findings of a contemporaneous randomised trial. In the context of clinical non‐inferiority, as shown in the randomised trial, nursing preference for HFNC over NCPAP in preterm infants ≥28 weeks' gestation supports the use of HFNC as post‐extubation support in this population.
Melatonin reduces cardiac remodeling and improves survival in rats with isoproterenol‐induced heart failure
Authors: Simko Fedor , Bednarova Kristina Repova , Krajcirovicova Kristina , Hrenak Jaroslav , Celec Peter , Kamodyova Natalia , Gajdosechova Lucia , Zorad Stefan , Adamcova Michaela 
Published: June 2014

AbstractMelatonin was previously shown to reduce blood pressure and left ventricular (LV) remodeling in several models of experimental heart damage. This study investigated whether melatonin preventsLVremodeling and improves survival in isoproterenol‐induced heart failure. In the first experiment, four groups of 3‐month‐old male Wistar rats (12 per group) were treated for 2 wk as follows: controls, rats treated with melatonin (10 mg/kg/day) (M), rats treated with isoproterenol (5 mg/kg/day intraperitoneally the second week) (Iso), and rats treated with melatonin (2 wk) and isoproterenol (the second week) in corresponding doses (IsoM). In the second experiment, 30 rats were treated with isoproterenol and 30 rats with isoproterenol plus melatonin for a period of 28 days and their mortality was investigated. Isoproterenol‐induced heart failure with hypertrophy of the left and right ventricles (LV,RV), lowered systolic blood pressure (SBP) and elevated pulmonary congestion. Fibrotic rebuilding was accompanied by alterations of tubulin level in theLVand oxidative stress development. Melatonin failed to reduce the weight of theLVorRV; however, it curtailed the weight of the lungs and attenuated the decline inSBP. Moreover, melatonin decreased the level of oxidative stress and of insoluble and total collagen and partly prevented the beta‐tubulin alteration in theLV. Most importantly, melatonin reduced mortality and prolonged the average survival time. In conclusion, melatonin exerts cardioprotective effects and improves outcome in a model of isoproterenol‐induced heart damage. The antiremodeling effect of melatonin may be of potential benefit in patients with heart failure.
Vegetation patterns and their underlying processes: where are we now?
Authors: Helm Aveliina , Kalamees Rein , Zobel Martin 
Published: June 2014

AbstractThis Special Feature of the Journal of Vegetation Science contains ten contributions from the 56th Symposium of the International Association for Vegetation Science (IAVS), which was held in Tartu, Estonia, 26–30 Jun 2013, and focused on processes underlying vegetation patterns. These contributions give an overview of recent advances in vegetation science, with topics ranging from the introduction of new methods and ideas to comprehensive analysis of vegetation patterns on a global scale. The focus of these Special Feature contributions indicates that vegetation science is becoming more global, more complex and more interdisciplinary. It is likely that progress in methods and accumulation of data have led vegetation science into a ‘new era of discovery’.
Fine‐scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica)
Authors: Wenzel Marius A. , Piertney Stuart B. 
Published: June 2014

AbstractEpigenetic modification of cytosine methylation states can be elicited by environmental stresses and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their host, but there is little understanding in how parasites may influence host methylation states. Here, we estimate epigenetic diversity and differentiation among 21 populations of red grouse (Lagopus lagopus scotica) in north‐east Scotland and test for association of gastrointestinal parasite load (caecal nematode Trichostrongylus tenuis) with hepatic genome‐wide and locus‐specific methylation states. Following methylation‐sensitive AFLP (MSAP), 129 bands, representing 73 methylation‐susceptible and 56 nonmethylated epiloci, were scored across 234 individuals. The populations differed significantly in genome‐wide methylation levels and were also significantly epigenetically (FSC = 0.0227; P < 0.001) and genetically (FSC = 0.0058; P < 0.001) differentiated. Parasite load was not associated with either genome‐wide methylation levels or epigenetic differentiation. Instead, we found eight disproportionately differentiated epilocus‐specific methylation states (FST outliers) using bayescan software and significant positive and negative association of 35 methylation states with parasite load from bespoke generalized estimating equations (GEE), simple logistic regression (sam) and Bayesian environmental analysis (bayenv2). Following Sanger sequencing, genome mapping and geneontology (go) annotation, some of these epiloci were linked to genes involved in regulation of cell cycle, signalling, metabolism, immune system and notably rRNA methylation, histone acetylation and small RNAs. These findings demonstrate an epigenetic signature of parasite load in populations of a wild bird and suggest intriguing physiological effects of parasite‐associated cytosine methylation.
A unique gene cluster for the utilization of the mucosal and human milk‐associated glycans galacto‐N‐biose and lacto‐N‐biose in Lactobacillus casei
Authors: Bidart Gonzalo N. , Rodríguez‐Díaz Jesús , Monedero Vicente , Yebra María J. 
Published: June 2014

SummaryThe probiotic Lactobacillus casei catabolizes galacto‐N‐biose (GNB) and lacto‐N‐biose (LNB) by using a transport system and metabolic routes different from those of Bifidobacterium. L. casei contains a gene cluster, gnbREFGBCDA, involved in the metabolism of GNB, LNB and also N‐acetylgalactosamine. Inactivation of gnbC (EIIC) or ptsI (Enzyme I) of the phosphoenolpyruvate : sugar phosphotransferase system (PTS) prevented the growth on those three carbohydrates, indicating that they are transported and phosphorylated by the same PTSGnb. Enzyme activities and growth analysis with knockout mutants showed that GnbG (phospho‐β‐galactosidase) hydrolyses both disaccharides. However, GnbF (N‐acetylgalactosamine‐6P deacetylase) and GnbE (galactosamine‐6P isomerase/deaminase) are involved in GNB but not in LNB fermentation. The utilization of LNB depends on nagA (N‐acetylglucosamine‐6P deacetylase), showing that the N‐acetylhexosamine moieties of GNB and LNB follow different catabolic routes. A lacAB mutant (galactose‐6P isomerase) was impaired in GNB and LNB utilization, indicating that their galactose moiety is channelled through the tagatose‐6P pathway. Transcriptional analysis showed that the gnb operon is regulated by substrate‐specific induction mediated by the transcriptional repressor GnbR, which binds to a 26 bp DNA region containing inverted repeats exhibiting a 2T/2A conserved core. The data represent the first characterization of novel metabolic pathways for human milk oligosaccharides and glycoconjugate structures in Firmicutes.
Functional and biological diversity of foliar spectra in tree canopies throughout the Andes to Amazon region
Authors: Asner Gregory P. , Martin Roberta E. , Carranza‐Jiménez Loreli , Sinca Felipe , Tupayachi Raul , Anderson Christopher B. , Martinez Paola 
Published: June 2014

Summary

Spectral properties of foliage express fundamental chemical interactions of canopies with solar radiation. However, the degree to which leaf spectra track chemical traits across environmental gradients in tropical forests is unknown.

We analyzed leaf reflectance and transmittance spectra in 2567 tropical canopy trees comprising 1449 species in 17 forests along a 3400‐m elevation and soil fertility gradient from the Amazonian lowlands to the Andean treeline. We developed quantitative links between 21 leaf traits and 400–2500‐nm spectra, and developed classifications of tree taxa based on spectral traits.

Our results reveal enormous inter‐specific variation in spectral and chemical traits among canopy trees of the western Amazon. Chemical traits mediating primary production were tightly linked to elevational changes in foliar spectral signatures. By contrast, defense compounds and rock‐derived nutrients tracked foliar spectral variation with changing soil fertility in the lowlands. Despite the effects of abiotic filtering on mean foliar spectral properties of tree communities, the spectra were dominated by phylogeny within any given community, and spectroscopy accurately classified 85–93% of Amazonian tree species.

Our findings quantify how tropical tree canopies interact with sunlight, and indicate how to measure the functional and biological diversity of forests with spectroscopy.
Relatedness defies biogeography: the tale of two island endemics (Acacia heterophylla and A. koa)
Authors: Le Roux Johannes J. , Strasberg Dominique , Rouget Mathieu , Morden Clifford W. , Koordom Megan , Richardson David M. 
Published: June 2014

Summary

Despite the normally strong link between geographic proximity and relatedness of recently diverged taxa, truly puzzling biogeographic anomalies to this expectation exist in nature.

Using a dated phylogeny, population genetic structure and estimates of ecological niche overlap, we tested the hypothesis that two geographically very disjunct, but morphologically very similar, island endemics (Acacia heterophylla from Réunion Island and A. koa from the Hawaiian archipelago) are the result of dispersal between these two island groups, rather than independent colonization events from Australia followed by convergent evolution.

Our genetic results indicated that A. heterophylla renders A. koa paraphyletic and that the former colonized the Mascarene archipelago directly from the Hawaiian Islands ≤ 1.4 million yr ago. This colonization sequence was corroborated by similar ecological niches between the two island taxa, but not between A. melanoxylon from Australia (a sister, and presumed ancestral, taxon to A. koa and A. heterophylla) and Hawaiian A. koa.

It is widely accepted that the long‐distance dispersal of plants occurs more frequently than previously thought. Here, however, we document one of the most exceptional examples of such dispersal. Despite c. 18 000 km separating A. heterophylla and A. koa, these two island endemics from two different oceans probably represent a single taxon as a result of recent extreme long‐distance dispersal.
Association ofFLOWERING LOCUST/TERMINAL FLOWER1‐like geneFTL2expression with growth rhythm in Scots pine (Pinus sylvestris)
Authors: Avia Komlan , Kärkkäinen Katri , Lagercrantz Ulf , Savolainen Outi 
Published: June 2014

SummaryUnderstanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait.We compared the regulation of their bud set biology by examining the expression ofPsFTL2, aPinus sylvestrishomolog toPaFTL2, aFLOWERING LOCUST/TERMINAL FLOWER1(FT/TFL1)‐like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression ofPsFTL2in a set of Scots pine populations from different latitudes.The expression ofPsFTL2increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations.Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association ofFTL2with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.
The S‐layer proteins of Tannerella forsythia are secreted via a type IX secretion system that is decoupled from protein O‐glycosylation
Authors: Tomek M.B. , Neumann L. , Nimeth I. , Koerdt A. , Andesner P. , Messner P. , Mach L. , Potempa J.S. , Schäffer C. 
Published: June 2014

SummaryConserved C‐terminal domains (CTD) have been shown to act as a signal for the translocation of certain proteins across the outer membrane of Bacteroidetes via a type IX secretion system (T9SS). The genome sequence of the periodontal pathogen Tannerella forsythia predicts the presence of the components for a T9SS in conjunction with a suite of CTD proteins. T. forsythia is covered with a two‐dimensional crystalline surface (S‐) layer composed of the glycosylated CTD proteins TfsA and TfsB. To investigate, if T9SS is functional in T. forsythia, T9SS‐deficient mutants were generated by targeting either TF0955 (putative C‐terminal signal peptidase) or TF2327 (PorK ortholog), and the mutants were analyzed with respect to secretion, assembly and glycosylation of the S‐layer proteins as well as proteolytic processing of the CTD and biofilm formation. In either mutant, TfsA and TfsB were incapable of translocation, as evidenced by the absence of the S‐layer in transmission electron microscopy of ultrathin‐sectioned bacterial cells. Despite being entrapped within the periplasm, mass spectrometry analysis revealed that the S‐layer proteins were modified with the complete, mature glycan found on the secreted proteins, indicating that protein translocation and glycosylation are two independent processes. Further, the T9SS mutants showed a denser biofilm with fewer voids compared with the wild‐type. This study demonstrates the functionality of T9SS and the requirement of CTD for the outer membrane passage of extracellular proteins in T. forsythia, exemplified by the two S‐layer proteins. In addition, T9SS protein translocation is decoupled from O‐glycan attachment in T. forsythia.
Anion channel SLAH3 functions in nitrate‐dependent alleviation of ammonium toxicity in Arabidopsis
Authors: ZHENG XIAOJIANG , HE KAI , KLEIST THOMAS , CHEN FANG , LUAN SHENG 
Published: June 2014

AbstractSlow anion channels (SLAC/SLAH) are efflux channels previously shown to be critical for stomatal regulation. However, detailed analysis using the β‐glucuronidase reporter gene showed that members of the SLAC/SLAH gene family are predominantly expressed in roots, in addition to stomatal guard cells, implicating distinct function(s) of SLAC/SLAH in the roots. Comprehensive mutant analyses of all slac/slah mutants indicated that slah3 plants showed a greater growth defect than wild‐type plants when ammonium was supplied as the sole nitrogen source. Ammonium toxicity was mimicked by acidic pH in nitrogen‐free external medium, suggesting that medium acidification by ammonium‐fed plants may underlie ammonium toxicity. Interestingly, such toxicity was more severe in slah3 mutants and, particularly in wild‐type plants, was alleviated by supplementing the media with micromolar levels of nitrate. These data thus provide evidence that SLAH3, a nitrate efflux channel, plays a role in nitrate‐dependent alleviation of ammonium toxicity in plants.
Characterisation of circadian rhythms of various duckweeds
Authors: Muranaka T. , Okada M. , Yomo J. , Kubota S. , Oyama T. 
Published: June 2014

AbstractThe plant circadian clock controls various physiological phenomena that are important for adaptation to natural day–night cycles. Many components of the circadian clock have been identified in Arabidopsis thaliana, the model plant for molecular genetic studies. Recent studies revealed evolutionary conservation of clock components in green plants. Homologues of clock‐related genes have been isolated from Lemna gibba and Lemna aequinoctialis, and it has been demonstrated that these homologues function in the clock system in a manner similar to their functioning in Arabidopsis. While clock components are widely conserved, circadian phenomena display diversity even within the Lemna genus. In order to survey the full extent of diversity in circadian rhythms among duckweed plants, we characterised the circadian rhythms of duckweed by employing a semi‐transient bioluminescent reporter system. Using a particle bombardment method, circadian bioluminescent reporters were introduced into nine strains representing five duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna gibba, L. aequinoctialis and Wolffia columbiana. We then monitored luciferase (luc+) reporter activities driven by AtCCA1, ZmUBQ1 or CaMV35S promoters under entrainment and free‐running conditions. Under entrainment, AtCCA1::luc+ showed similar diurnal rhythms in all strains. This suggests that the mechanism of biological timing under day–night cycles is conserved throughout the evolution of duckweeds. Under free‐running conditions, we observed circadian rhythms of AtCCA1::luc+, ZmUBQ1::luc+ and CaMV35S::luc+. These circadian rhythms showed diversity in period length and sustainability, suggesting that circadian clock mechanisms are somewhat diversified among duckweeds.