bluuebunny/crossref_metadata_2025 huggingface dataset:
Disruption of macrophage pro‐inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients
Authors: Smith Andrew M. , Sewell Gavin W. , Levine Adam P. , Chew Thean S. , Dunne Jenny , O'Shea Nuala R. , Smith Philip J. , Harrison Penelope J. , Macdonald Carol M. , Bloom Stuart L. , Segal Anthony W.
Published: June 2014

Crohn's disease (CD) is a complex and highly heterogeneous chronic inflammatory disorder, primarily affecting the gastrointestinal tract. Genetic and functional studies have highlighted a key role for innate immunity in its pathogenesis. Profound systemic defects in innate immunity and acute inflammation are understood to result in markedly delayed clearance of bacteria from the tissues, leading to local chronic granulomatous inflammation and compensatory adaptive immunological changes. Macrophages, key orchestrators of acute inflammation, are likely to play an important role in the initial impaired innate immune response. Monocyte‐derived macrophages from CD patients stimulated with Escherichia coli were shown to release attenuated levels of tumour necrosis factor and interferon‐γ with normal secretion of interleukin‐8 (IL‐8), IL‐10 and IL‐6. In controls, the secretion of these cytokines was strongly positively correlated, which was not seen with CD macrophages. The transcriptomes of CD and control macrophages were examined in an attempt to understand the molecular basis of this defect. There were no differentially expressed genes identified between the two groups, consistent with genetic heterogeneity; however, a number of molecules were found to be under‐expressed in subgroups of CD patients. The most common of these was optineurin (OPTN) which was under‐expressed in approximately 10% of the CD patients. Reduced OPTN expression coincided with lower intracellular protein levels and diminished cytokine secretion after bacterial stimulation both in the patients and with small interfering RNA knockdown in THP‐1 cells. Identifying and studying subgroups of patients with shared defective gene expression could aid our understanding of the mechanisms underlying highly heterogeneous diseases such as CD.
Interleukin‐4 up‐regulation of epidermal interleukin‐19 expression in keratinocytes involves the binding of signal transducer and activator of transcription 6 (Stat6) to the imperfect Stat6 sites
Authors: Bao Lei , Alexander Jaime B. , Shi Vivian Y. , Mohan Girish C. , Chan Lawrence S.
Published: June 2014

Interleukin‐19 (IL‐19) plays an important role in asthma by stimulating T helper type 2 (Th2) cytokine production. Interestingly, IL‐4, a key Th2 cytokine, in turn up‐regulates IL‐19 expression in bronchial epithelial cells, so forming a positive feedback loop. In atopic dermatitis (AD), another Th2 disease closely related to asthma, IL‐19 is up‐regulated in the skin. We propose to use IL‐4 transgenic (Tg) mice and human keratinocyte culture to delineate the molecular mechanisms involved in the up‐regulation of IL‐19 in AD. IL‐19 is similarly up‐regulated in the skin of IL‐4 Tg mice as in human AD. Next we show that IL‐4 up‐regulates IL‐19 expression in keratinocytes. Interestingly, the up‐regulation was suppressed by a pan‐Janus kinase (Jak) inhibitor, suggesting that the Jak–signal transducer and activator of transcription (Jak‐STAT) pathway may be involved. Dominant negative studies further indicate that STAT6, but not other STATs, mediates the up‐regulation. Serial 5′ deletion of the IL‐19 promoter and mutagenesis studies demonstrate that IL‐4 up‐regulation of IL‐19 in keratinocytes involves two imperfect STAT6 response elements. Finally, chromatin immunoprecipitation assay studies indicate that IL‐4 increases the binding of STAT6 to its response elements in the IL‐19 promoter. Taken together, we delineate the detailed molecular pathway for IL‐4 up‐regulation of IL‐19 in keratinocytes, which may play an important role in AD pathogenesis.
‘As above, so below’ examining the interplay between emotion and the immune system
Authors: Brod Samuel , Rattazzi Lorenza , Piras Giuseppa , D'Acquisto Fulvio
Published: June 2014

While the concept of a palpable relationship between our mental and physical well‐being is certainly not new, it is only in the light of modern scientific research that we have begun to realize how deeply connected our emotional and immune states may be. We begin this review with a series of studies demonstrating how four fundamental emotional responses: anger, anxiety, mirth and relaxation are able modulate cytokine production and cellular responses to a variety of immune stimuli. These modulations are shown to be either detrimental or beneficial to a patient's health dependent on the context and duration of the emotion. We also discuss the reverse, highlighting research demonstrating how the loss of key immune cells such as T lymphocytes in clinical and animal studies can negatively impact both emotional well‐being and cognition. Additionally, to give a more complete picture of the manifold pathways that link emotion and the immune system, we give a brief overview of the influence the digestive system has upon mental and immunological health. Finally, throughout this review we attempt to highlight the therapeutic potential of this burgeoning field of research in both the diagnosis and treatment of immune and disorders. As well as identifying some of the key obstacles the field must address in order to put this potential into practice.
‘Default’ generated neonatal regulatory T cells are hypomethylated at conserved non‐coding sequence 2 and promote long‐term cardiac allograft survival
Authors: Cheng Chao , Wang Sihua , Ye Ping , Huang Xiaofan , Liu Zheng , Wu Jie , Sun Yuan , Xie Aini , Wang Guohua , Xia Jiahong
Published: June 2014

Regulatory T (Treg) cells play an important role in the maintenance of immune self‐tolerance and homeostasis. We previously reported that neonatal CD4+ T cells have an intrinsic ‘default’ mechanism to become Treg (neoTreg) cells in response to T‐cell receptor (TCR) stimulation. However, the underlying mechanisms are unclear and the effects of neoTreg cells on regulating immune responses remain unknown. Due to their involvement in Foxp3 regulation, we examined the role of DNA methyltransferase 1 (DNMT1) and DNMT3b during the induction of neoTreg cells in the Foxp3gfp mice. The function of neoTreg cells was assessed in an acute allograft rejection model established in RAG2−/− mice with allograft cardiac transplantation and transferred with syngeneic CD4+ effector T cells. Following ex vivo TCR stimulation, the DNMT activity was increased threefold in adult CD4+ T cells, but not significantly increased in neonatal cells. However, adoptively transferred neoTreg cells significantly prolonged cardiac allograft survival (mean survival time 47 days, P < 0·001) and maintained Foxp3 expression similar to natural Treg cells. The neoTreg cells were hypomethylated at the conserved non‐coding DNA sequence 2 locus of Foxp3 compared with adult Treg cells. The DNMT antagonist 5‐aza‐2′‐deoxycytidine (5‐Aza) induced increased Foxp3 expression in mature CD4+ T cells. 5‐Aza‐inducible Treg cells combined with continuous 5‐Aza treatment prolonged graft survival. These results indicate that the ‘default’ pathway of neoTreg cell differentiation is associated with reduced DNMT1 and DNMT3b response to TCR stimulus. The neoTreg cells may be a strategy to alleviate acute allograft rejection.
Mitochondrial DNA diversity of Anatolian indigenous domestic goats
Authors: Akis I. , Oztabak K. , Mengi A. , Un C.
Published: June 2014

Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats (Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds.
Effect and cardiovascular safety of adding rosiglitazone to insulin therapy in type 2 diabetes: A meta‐analysis
Authors: Lu Yu , Ma Delin , Xu Weijie , Shao Shiying , Yu Xuefeng
Published: June 2014

Aims/Introduction

Recently, the use of rosiglitazone has been limited or withdrawn from the market as a result of cardiovascular risk. However, theoretically adding rosiglitazone to insulin could help insulin to decrease the glucose level. The present meta‐analysis was designed to investigate the effect and safety of adding rosiglitazone to insulin therapy in type 2 diabetes.

Materials and Methods

We searched published and unpublished databases through to March 2012. Randomized controlled trials (RCTs) comparing rosiglitazone in combination with insulin (RSG + INS) vs insulin alone (INS) in type 2 diabetes with outcomes including glycated hemoglobin levels, insulin dose, lipid parameters, blood pressure, edema and cardiovascular adverse events were selected.

Results

Nine RCTs with durations of 24–26 weeks involving 1,916 patients were included. The RSG + INS group showed significantly decreased glycated hemoglobin levels by 0.89% (P < 0.00001) with an 8.48‐U reduction in daily insulin dose (P <0.00001). However, the risks of hypoglycemia and edema were more frequent in the RSG+INS group (P < 0.0001; P = 0.03, respectively). Total cholesterol level was significantly increased in the RSG+INS group (P < 0.00001), but none of the high‐density lipoprotein cholesterol, low‐density lipoprotein cholesterol, very low‐density lipoprotein cholesterol or triglyceride levels were significantly different between groups. There were no significant differences between groups with regard to the risks of myocardial infarction, heart failure, cardiovascular death or all‐cause death.

Conclusions

Rosiglitazone could help type 2 diabetes patients with poorly controlled glucose with insulin therapy to decrease glucose levels and reduce their daily insulin dose, but at the cost of increased total cholesterol level, hypoglycemia and edema risk. Compared with insulin therapy, adding rosiglitazone to insulin did not increase the risks of myocardial infarction, heart failure, cardiovascular death or all‐cause death.
Effect of a state‐based incentive programme on the use of electronic health records
Authors: Vest Joshua R. , Kern Lisa M. , Abramson Erika , Ancker Jessica S. , Kaushal Rainu ,   HITEC Investigators
Published: June 2014

Rationale, aims and objectives

In 2004, New York passed the Health Care Efficiency and Affordability Law for New Yorkers (HEAL NY) Capital Grants Program, which was the largest state‐based investment in health information technology adoption in the United States. We sought to evaluate the effects of this programme on electronic health records (EHR) usage.

Methods

We undertook a case‐control study of health care providers who had signed up with a regional extension centre, some of whom had also received HEAL funding through programmes intended to support EHR adoption. The outcome of interest was achievement of Medicare or Medicaid Meaningful Use and the primary exposure was any link to HEAL NY funding. The association between Meaningful Use status and independent variables was measured using logistic regression models.

Results

Meaningful Users were more likely to have had a history of HEAL NY funding (OR = 1.83; 95% CI = 1.59, 2.09). Also, achievement of Meaningful Use was associated with having an EHR before 2011 (OR = 1.64; 95% CI = 146, 1.83). Among those with EHRs prior to 2011, the odds of achieving Meaningful Use were statistically higher if coupled with HEAL NY funding (OR = 3.12; 95% CI = 2.50, 3.90).

Conclusion

Achieving Meaningful Use was associated with a history of HEAL NY funding. However, it was the combination of HEAL NY funding and historic usage of EHRs that was associated with the largest increase in the odds that the provider was a Meaningful User. These findings indicate that state‐based incentive programmes can support the effective usage of health
information technologies.
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

Soybean [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.
Activity‐Dependent Notch Signalling in the Hypothalamic‐Neurohypophysial System of Adult Mouse Brains
Authors: Mannari T. , Miyata S.
Published: June 2014

Notch signalling has a key role in cell fate specification in developing brains; however, recent studies have shown that Notch signalling also participates in the regulation of synaptic plasticity in adult brains. In the present study, we examined the expression of Notch3 and Delta‐like ligand 4 (DLL4) in the hypothalamic‐neurohypophysial system (HNS) of the adult mouse. The expression of DLL4 was higher in the supraoptic nucleus (SON) and paraventricular nucleus (PVN) compared to adjacent hypothalamic regions. Double‐labelling immunohistochemistry using vesicular GABA transporter and glutamate transporter revealed that DLL4 was localised at a subpopulation of excitatory and inhibitory axonal boutons against somatodendrites of arginine vasopressin (AVP)‐ and oxytocin (OXT)‐containing magnocellular neurones. In the neurohypophysis (NH), the expression of DLL4 was seen at OXT‐ but not AVP‐containing axonal terminals. The expression of Notch3 was seen at somatodendrites of AVP‐ and OXT‐containing magnocellular neurones in the SON and PVN and at pituicytes in the NH. Chronic physiological stimulation by salt loading, which remarkably enhances the release of AVP and OXT, decreased the number of DLL4‐immunoreactive axonal boutons in the SON and PVN. Moreover, chronic and acute osmotic stimulation promoted proteolytic cleavage of Notch3 to yield the intracellular fragments of Notch3 in the HNS. Thus, the present study demonstrates activity‐dependent reduction of DLL4 expression and proteolytic cleavage of Notch3 in the HNS, suggesting that Notch signalling possibly participates in synaptic interaction in the hypothalamic nuclei and neuroglial interaction in the NH.
Ensuring a proactive, evidence‐based, patient safety approach to patient assessment
Authors: Considine Julie , Currey Judy
Published: June 2014

Aims and objectives

To 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.

Background

Nurses 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.

Design

Discursive paper.

Methods

Traditionally 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.

Conclusion

The 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 practice

All 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

Aim

The aim of this study is to review the operation of a specialist adolescent drug and alcohol consultation liaison service in a tertiary paediatric hospital.

Method

A retrospective review of patient records was conducted to identify patient characteristics and assess service utilisation.

Results

Two 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.

Conclusions

Adolescents 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

Aim

This 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.

Methods

A 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.

Results

The 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.

Conclusions

Neonatal 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

Melatonin 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

This 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

Epigenetic 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

The 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

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

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

Understanding 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

Conserved 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.
The stability of xylem water under tension: a long, slow spin proves illuminating
Authors: ZHANG YONG‐JIANG , HOLBROOK N. MICHELE
Published: June 2014

This article comments on:Water relations of Robinia pseudoacacia L.: Do vessels cavitate and refill diurnally or are R‐shaped curves invalid in Robinia?
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

Slow 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

The 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.
Evaluation of phylogenetic relationships in Lemnaceae using nuclear ribosomal data
Authors: Tippery N. P. , Les D. H. , Crawford D. J.
Published: June 2014

Nuclear DNA sequence data are essential for obtaining a complete understanding of plant species relationships, yet these data have been conspicuously absent from phylogenetic analyses of Lemnaceae (duckweeds). Using a modified Sanger sequencing protocol, we obtained DNA sequences of duckweed nuclear ribosomal regions, including 18S and 26S rDNA genes, the external transcribed spacer (ETS) and the frequently used internal transcribed spacer (ITS). After obtaining sequence data for all Lemnaceae species, we ascertained that prior difficulty in sequencing the ITS regions likely resulted from extremely rigid secondary structures, precipitated by a high proportion of G/C nucleotides. In phylogenetic analyses, nuclear ribosomal data largely supported relationships that had been inferred using chloroplast DNA sequence data.
Forced Collapse of the Blastocoel Cavity Improves Developmental Potential in Cryopreserved Bovine Blastocysts by Slow‐Rate Freezing and Vitrification
Authors: Min S‐H , Kim J‐W , Lee Y‐H , Park S‐Y , Jeong P‐S , Yeon J‐Y , Park H , Chang K‐T , Koo D‐B
Published: June 2014

Contents

This study was conducted to evaluate the effectiveness of forced collapse of the blastocoel before slow‐rate freezing and vitrification of bovine blastocysts. Cryopreservation of bovine blastocysts has been proposed as a tool to improve the feasibility of cattle production using the embryo transfer technique. However, the low efficiency of frozen–thawed embryos survival and further development is a crucial problem. In this study, bovine in vitro and in vivo blastocysts were slow‐rate frozen and vitrified after forced blastocoele collapse (FBC) of the blastocyst cavity by puncturing the blastocoele with a pulled Pasteur pipet. Differences in the developmental potential of frozen–thawed blastocysts derived from FBC and non‐FBC groups were found in both slow‐rate freezing and vitrification. Furthermore, we found that the total cell number of blastocysts in FBC groups was increased and the index of apoptosis in FBC groups was decreased. Consistent with these results, real‐time RT‐PCR analysis data showed that expression of the anti‐apoptotic Bcl‐XL gene was significantly increased by FBC groups, whereas expression of the pro‐apoptotic Bax gene was significantly decreased by FBC groups. Our results also showed that pregnancy outcomes in both slow‐rate frozen and vitrified bovine in vivo blastocysts could be improved by reducing the fluid content after FBC of the blastocyst cavity. Therefore, we suggest that FBC of the blastocyst cavity with a pulled Pasteur pipet is an effective pre‐treatment technique for both slow‐rate freezing and vitrification of bovine blastocysts.
Roles of small RNAs in soybean defense against Phytophthora sojae infection
Authors: Wong James , Gao Lei , Yang Yang , Zhai Jixian , Arikit Siwaret , Yu Yu , Duan Shuyi , Chan Vicky , Xiong Qin , Yan Jun , Li Shengben , Liu Renyi , Wang Yuanchao , Tang Guiliang , Meyers Blake C. , Chen Xuemei , Ma Wenbo
Published: June 2014

The genus Phytophthora consists of many notorious pathogens of crops and forestry trees. At present, battling Phytophthora diseases is challenging due to a lack of understanding of their pathogenesis. We investigated the role of small RNAs in regulating soybean defense in response to infection by Phytophthora sojae, the second most destructive pathogen of soybean. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are universal regulators that repress target gene expression in eukaryotes. We identified known and novel small RNAs that differentially accumulated during P. sojae infection in soybean roots. Among them, miR393 and miR166 were induced by heat‐inactivated P. sojae hyphae, indicating that they may be involved in soybean basal defense. Indeed, knocking down the level of mature miR393 led to enhanced susceptibility of soybean to P. sojae; furthermore, the expression of isoflavonoid biosynthetic genes was drastically reduced in miR393 knockdown roots. These data suggest that miR393 promotes soybean defense against P. sojae. In addition to miRNAs, P. sojae infection also resulted in increased accumulation of phased siRNAs (phasiRNAs) that are predominantly generated from canonical resistance genes encoding nucleotide binding‐leucine rich repeat proteins and genes encoding pentatricopeptide repeat‐containing proteins. This work identifies specific miRNAs and phasiRNAs that regulate defense‐associated genes in soybean during Phytophthora infection.
The powdery mildew resistance gene Pm8 derived from rye is suppressed by its wheat ortholog Pm3
Authors: Hurni Severine , Brunner Susanne , Stirnweis Daniel , Herren Gerhard , Peditto David , McIntosh Robert A. , Keller Beat
Published: June 2014

The powdery mildew resistance gene Pm8 derived from rye is located on a 1BL.1RS chromosome translocation in wheat. However, some wheat lines with this translocation do not show resistance to isolates of the wheat powdery mildew pathogen avirulent to Pm8 due to an unknown genetically dominant suppression mechanism. Here we show that lines with suppressed Pm8 activity contain an intact and expressed Pm8 gene. Therefore, the absence of Pm8 function in certain 1BL.1RS‐containing wheat lines is not the result of gene loss or mutation but is based on suppression. The wheat gene Pm3, an ortholog of rye Pm8, suppressed Pm8‐mediated powdery mildew resistance in lines containing Pm8 in a transient single‐cell expression assay. This result was further confirmed in transgenic lines with combined Pm8 and Pm3 transgenes. Expression analysis revealed that suppression is not the result of gene silencing, either in wheat 1BL.1RS translocation lines carrying Pm8 or in transgenic genotypes with both Pm8 and Pm3 alleles. In addition, a similar abundance of the PM8 and PM3 proteins in single or double homozygous transgenic lines suggested that a post‐translational mechanism is involved in suppression of Pm8. Co‐expression of Pm8 and Pm3 genes in Nicotiana benthamiana leaves followed by co‐immunoprecipitation analysis showed that the two proteins interact. Therefore, the formation of a heteromeric protein complex might result in inefficient or absent signal transmission for the defense reaction. These data provide a molecular explanation for the suppression of resistance genes in certain genetic backgrounds and suggest ways to circumvent it in future plant breeding.
Red blood cell storage increases hypoxia‐induced nitric oxide bioavailability and methemoglobin formation in vitro and in vivo
Authors: Almac Emre , Bezemer Rick , Hilarius‐Stokman Petra M. , Goedhart Peter , de Korte Dirk , Verhoeven Arthur J. , Ince Can
Published: June 2014

Background

In this study we investigated whether storage of red blood cells (RBCs) leads to alterations in nitrite reductase activity, hence in altered hypoxia‐induced nitric oxide (NO) bioavailability and methemoglobin formation.

Study Design and Methods

Hypoxia‐induced NO bioavailability and methemoglobin formation were measured in vitro after nitrite administration to fresh (<1 week of storage) and aged (5‐6 weeks of storage) human RBC units and in blood samples of hemodiluted rats subjected to hypoxic ventilation after transfusion with fresh or aged human RBCs.

Results

In vitro, NO and methemoglobin levels 10 minutes after nitrite administration were lower in the fresh RBC samples compared to the aged RBC samples (p = 0.026 and p = 0.022, respectively). In vivo, NO bioavailability was also significantly lower in the rats receiving fresh RBCs compared to the group receiving aged RBCs (p = 0.003). In line with NO bioavailability, methemoglobin levels were higher, albeit not significantly, in the group receiving aged RBCs compared to in the group receiving fresh RBCs (p = 0.154). The difference in methemoglobin formation after nitrite administration between fresh and aged RBCs was only present under deoxygenated conditions and not under oxygenated conditions. There were no differences in methemoglobin reductase activity between fresh and aged RBCs.

Conclusions

Storage of RBCs leads to an increased rate of hypoxia‐induced nitrite reduction to NO and this is associated with increased methemoglobin formation. The increased methemoglobin formation and consequent decrease in oxygen delivery capacity might contribute to the storage‐related impairment of aged RBCs to oxygenate the microcirculation.