bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules
Authors: Tan Chuan Hao , Koh Kai Shyang , Xie Chao , Tay Martin , Zhou Yan , Williams Rohan , Ng Wun Jern , Rice Scott A , Kjelleberg Staffan 
Published: January 2014

Abstract
Quorum sensing (QS) signalling has been extensively studied in single species populations. However, the ecological role of QS in complex, multi-species communities, particularly in the context of community assembly, has neither been experimentally explored nor theoretically addressed. Here, we performed a long-term bioreactor ecology study to address the links between QS, organization and composition of complex microbial communities. The conversion of floccular biomass to highly structured granules was found to be non-random, but strongly and positively correlated with N-acyl-homoserine-lactone (AHL)-mediated QS. Specific AHLs were elevated up to 100-fold and were strongly associated with the initiation of granulation. Similarly, the levels of particular AHLs decreased markedly during the granular disintegration phase. Metadata analysis indicated that granulation was accompanied by changes in extracellular polymeric substance (EPS) production and AHL add-back studies also resulted in increased EPS synthesis. In contrast to the commonly reported nanomolar to micromolar signal concentrations in pure culture laboratory systems, QS signalling in the granulation ecosystem occurred at picomolar to nanomolar concentrations of AHLs. Given that low concentrations of AHLs quantified in this study were sufficient to activate AHL bioreporters in situ in complex granular communities, AHL mediated QS may be a common feature in many natural and engineered ecosystems, where it coordinates community behaviour.
Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)
Authors: Vetriani Costantino , Voordeckers James W , Crespo-Medina Melitza , O’Brien Charles E , Giovannelli Donato , Lutz Richard A 
Published: January 2014

AbstractDespite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.
Microorganisms persist at record depths in the subseafloor of the Canterbury Basin
Authors: Ciobanu Maria-Cristina , Burgaud Gaëtan , Dufresne Alexis , Breuker Anja , Rédou Vanessa , Ben Maamar Sarah , Gaboyer Frédéric , Vandenabeele-Trambouze Odile , Lipp Julius Sebastian , Schippers Axel , Vandenkoornhuyse Philippe , Barbier Georges , Jebbar Mohamed , Godfroy Anne , Alain Karine 
Published: January 2014

Abstract
The subsurface realm is colonized by microbial communities to depths of &gt;1000 meters below the seafloor (m.b.sf.), but little is known about overall diversity and microbial distribution patterns at the most profound depths. Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. Representatives of some microbial taxa were also cultivated using methods mimicking in situ conditions. These results suggest that diverse microorganisms persist down to 1922 m.b.sf. in the seafloor of the Canterbury Basin and extend the previously known depth limits of microbial evidence (i) from 159 to 1740 m.b.sf. for Eukarya and (ii) from 518 to 1922 m.b.sf. for Bacteria.
Circulating miRNA profiles provide a biomarker for severity of stroke outcomes associated with age and sex in a rat model
Authors: Selvamani Amutha , Williams Madison H. , Miranda Rajesh C. , Sohrabji Farida 
Published: January 2014

Small non-coding RNA [miRNA (microRNA)] found in the circulation have been used successfully as biomarkers and mechanistic targets for chronic and acute disease. The present study investigated the impact of age and sex on miRNA expression following ischaemic stroke in an animal model. Adult (6 month) and middle-aged (11–12 months) female and male rats were subject to MCAo (middle cerebral artery occlusion) using ET-1 (endothelin-1). Circulating miRNAs were analysed in blood samples at 2 and 5 days post-stroke, and brain miRNAs were analysed at 5 days post-stroke. Although stroke-associated infarction was observed in all groups, infarct volume and sensory-motor deficits were significantly reduced in adult females compared with middle-aged females, adult males or middle-aged males. At 2 days post-stroke, 21 circulating miRNAs were differentially regulated and PCA (principal component analysis) confirmed that most of the variance was due to age. At 5 days post-stroke, 78 circulating miRNAs exhibited significantly different regulation, and most of the variance was associated with sex. A small cohort (five) of miRNAs, miR-15a, miR-19b, miR-32 miR-136 and miR-199a-3p, were found to be highly expressed exclusively in adult females compared with middle-aged females, adult males and middle-aged males. Predicted gene targets for these five miRNAs analysed for KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways revealed that the top ten KEGG pathways were related to growth factor signalling, cell structure and PI3K (phosphoinositide 3-kinase)/Akt and mTOR (mammalian target of rapamycin) signalling. Overall, the pattern of circulating miRNA expression suggests an early influence of age in stroke pathology, with a later emergence of sex as a factor for stroke severity.
Characterization of aerobically fit individuals with cardiovascular disease
Authors: Lesser Iris A. , Farias‐Godoy Alejandra , Isserow Saul , Myers Jonathan , Lear Scott A. 
Published: January 2014

AbstractWith an ageing population there is an increased prevalence of individuals living with cardiovascular disease (CVD). Characteristics of older aerobically fit individuals with previously diagnosed CVD have not been studied. Therefore, our knowledge is limited as to how, or if, aerobically fit individuals with CVD attempt to adapt their physical activity and the intensity of their training programmes. The objective of this paper is to characterise the physical activity habits and behaviours of older aerobically fit individuals with CVD. We identified 28 aerobically fit patients with CVD from those who completed a minimum of 15 and 12 min of the Bruce treadmill protocol for men and women, respectively. Consenting participants responded to questionnaires regarding physical activity levels, competitive event participation and self‐monitoring since diagnosis of heart disease. Average age and treadmill time of participants were 56 and 49 years and 15.6 and 13.0 min for males and females, respectively. Data were obtained regarding recent medical history (medical diagnoses, surgeries/procedures). Despite the majority of individuals participating in the same or more activity since their diagnosis, 25% indicated that their condition limited their activity and 39% reported having symptoms during activity. Nearly all participants (93%) indicated that they monitored their heart rate during exercise. However, only 14% of participants stated that their physician advised them on how to exercise safely. It is necessary for physicians and cardiac rehabilitation programmes to be involved in safe and effective exercise programming to allow individuals to return to sport after CVD.
Effect of Simulation Training on Compliance with Difficult Airway Management Algorithms, Technical Ability, and Skills Retention for Emergency Cricothyrotomy
Authors: Hubert Vincent , Duwat Antoine , Deransy Romain , Mahjoub Yazine , Dupont Hervé 
Published: January 2014

Abstract

Background:
The effectiveness of simulation is rarely evaluated. The aim of this study was to assess the impact of a short training course on the ability of anesthesiology residents to comply with current difficult airway management guidelines.

Methods:
Twenty-seven third-year anesthesiology residents were assessed on a simulator in a “can’t intubate, can’t ventilate” scenario before the training (the pretest) and then randomly 3, 6, or 12 months after training (the posttest). The scenario was built so that the resident was prompted to perform a cricothyrotomy. Compliance with airway management guidelines and the cricothyrotomy’s duration and technical quality were assessed as a checklist score [0 to 10] and a global rating scale [7 to 35].

Results:
After training, all 27 residents (100%) complied with the airway management guidelines, compared with 17 (63%) in the pretest (P < 0.005). In the pretest and the 3-, 6-, and 12-month posttests, the median [range] duration of cricothyrotomy was respectively 117 s [70 to 184], 69 s [43 to 97], 52 s [43 to 76], and 62 s [43 to 74] (P < 0.0001 vs. in the pretest), the median [range] checklist score was 3 [0 to 7], 10 [8 to 10], 9 [6 to 10], and 9 [4 to 10] (P < 0.0001 vs. in the pretest) and the median [range] global rating scale was 12 [7 to 22], 30 [20 to 35], 33 [23 to 35], and 31 [18 to 33] (P < 0.0001 vs. in the pretest). There were no significant differences between performance levels achieved in the 3-, 6-, and 12-month posttests.

Conclusion:
The training session significantly improved the residents’ compliance with guidelines and their performance of cricothyrotomy.
Behavioural and physiological responses of limpet prey to a seastar predator and their transmission to basal trophic levels
Authors: Manzur Tatiana , Vidal Francisco , Pantoja José F. , Fernández Miriam , Navarrete Sergio A. 
Published: January 2014

Summary

Besides the well‐documented behavioural changes induced by predators on prey, predator‐induced stress can also include a suite of biochemical, neurological and metabolic changes that may represent important energetic costs and have long‐lasting effects on individuals and on the demography of prey populations. The rapid transmission of prey behavioural changes to lower trophic levels, usually associated with alteration of feeding rates, can substantially change and even reverse direction over the long term as prey cope with the energetic costs associated with predation‐induced stress. It is therefore critical to evaluate different aspects and assess the costs of non‐consumptive predator effects on prey.

We investigated the behavioural and physiological responses of an herbivorous limpet, Fissurella limbata, to the presence of chemical cues and direct non‐lethal contact by the common seastar predator, Heliaster helianthus. We also evaluated whether the limpets feeding behaviour was modified by the predator and whether this translated into positive or negative effects on biomass of the green alga, Ulva sp.

Our experimental results show the presence of Heliaster led to increased movement activity, increased distances travelled, changes in time budget over different environmental conditions and increased feeding rate in the keyhole limpets. Moreover, additional experiments showed that, beyond the increased metabolic rate associated with limpet increased activity, predator chemical cues heighten metabolic rate as part of the induced stress response.

Changes in individual movement and displacement distances observed through the 9‐day experiment can be interpreted as part of the escape response exhibited by limpets to reduce the risk of being captured by the predator. Increased limpet feeding rate on algae can be visualized as a way individuals compensate for the elevated energetic costs of movement and heightened metabolic rates produced by the predator‐induced stress, which can lead to negative effects on abundance of the lower trophic level.

We suggest that in order to understand the total non‐consumptive effect of predators in natural communities, it is necessary to evaluate not only short‐term behavioural responses, but also the costs associated with the multiple interdependent pathways triggered by predator‐induced stress, and determine how individuals cope with these costs in the long term.
Characterizing microbial communities and processes in a modern stromatolite (SharkBay) using lipid biomarkers and two‐dimensional distributions of porewater solutes
Authors: Pagès Anais , Grice Kliti , Vacher Michael , Welsh David T. , Teasdale Peter R. , Bennett William W. , Greenwood Paul 
Published: January 2014

SummaryModern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two‐dimensional distributions of porewater solutes during day and night time. Two‐dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers includedn‐alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate‐reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two‐dimensional solute distributions showed considerable small‐scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.
Metagenomic characterization of ‘Candidatus Defluviicoccus tetraformis strain TFO71’, a tetrad‐forming organism, predominant in an anaerobic–aerobic membrane bioreactor with deteriorated biological phosphorus removal
Authors: Nobu Masaru K. , Tamaki Hideyuki , Kubota Kengo , Liu Wen‐Tso 
Published: January 2014

SummaryIn an acetate‐fed anaerobic–aerobic membrane bioreactor with deteriorated enhanced biological phosphorus removal (EBPR), Defluviicoccus‐related tetrad‐forming organisms (DTFO) were observed to predominate in the microbial community. Using metagenomics, a partial genome of the predominant DTFO, ‘Candidatus Defluviicoccus tetraformis strain TFO71’, was successfully constructed and characterized. Examining the genome confirmed the presence of genes related to the synthesis and degradation of glycogen and polyhydroxyalkanoate (PHA), which function as energy and carbon storage compounds. TFO71 and ‘Candidatus Accumulibacter phosphatis’ (CAP) UW‐1 and CAP UW‐2, representative polyphosphate‐accumulating organisms (PAO), have PHA metabolism‐related genes with high homology, but TFO71 has unique genes for PHA synthesis, gene regulation and granule management. We further discovered genes encoding DTFO polyphosphate (polyP) synthesis, suggesting that TFO71 may synthesize polyP under untested conditions. However, TFO71 may not activate these genes under EBPR conditions because the retrieved genome does not contain all inorganic phosphate transporters that are characteristic of PAOs (CAP UW‐1, CAP UW‐2, Microlunatus phosphovorus NM‐1 and Tetrasphaera species). As a first step in characterizing EBPR‐associated DTFO metabolism, this study identifies important differences between DTFO and PAO that may contribute to EBPR community competition and deterioration.
The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors
Authors: Abellón‐Ruiz Javier , Bernal‐Bernal Diego , Abellán María , Fontes Marta , Padmanabhan S. , Murillo Francisco J. , Elías‐Arnanz Montserrat 
Published: January 2014

SummaryExtracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ∼45 putative ECF‐σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well‐studied ECF‐σ, CarQ, binds to its anti‐σ, CarR, and is inactive in the dark but drives its own expression from promoter PQRS on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD‐binding site upstream of PQRS. Here, we show that DdvS, a previously uncharacterized ECF‐σ, activates its own expression in a CarD/CarG‐dependent manner but is inhibited when specifically bound to the N‐terminal zinc‐binding anti‐σ domain of its cognate anti‐σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF‐σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD‐binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG‐linked ECF‐σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.
Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity
Authors: Yamamoto Naomichi , Bibby Kyle 
Published: January 2014

SummaryNext‐generation DNA sequencing has enabled a rapid expansion in the size of molecular fungal ecology studies employing the nuclear internal transcribed spacer (ITS) region. Many sequence‐processing pipelines and protocols require sequence clustering to generate operational taxonomic units (OTUs) based on sequence similarity as a step to reduce total data quantity and complexity prior to taxonomic assignment. However, the consequences of ITS sequence clustering in regard to sample taxonomic coverage have not been carefully examined. Here we demonstrate that typically used clustering thresholds for fungal ITS sequences result in statistically significant losses in taxonomic coverage. Analyses using environmentally derived fungal sequences indicated an average of 3.1% of species went undetected (P < 0.05) if the sequences were denoised and clustered at a 97% threshold prior to taxonomic assignment. Additionally, an in silico analysis using a reference fungal ITS database suggested that approximately 25% of species went undetected if the sequences were clustered prior to taxonomic assignment. Finally, analysis of sequences derived from pure‐cultured fungal isolates of known identity indicated sequence denoising and clustering were not critical in improving identification accuracy.
Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep‐sea anoxic brine lake as potential polysaccharide degrader
Authors: Werner Johannes , Ferrer Manuel , Michel Gurvan , Mann Alexander J. , Huang Sixing , Juarez Silvia , Ciordia Sergio , Albar Juan P. , Alcaide María , La Cono Violetta , Yakimov Michail M. , Antunes André , Taborda Marco , da Costa Milton S. , Hai Tran , Glöckner Frank Oliver , Golyshina Olga V. , Golyshin Peter N. , Teeling Hanno ,   The MAMBA Consortium
Published: January 2014

SummaryEuryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX‐2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4BT from the Shaban deep‐sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant‐derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low‐oxygen conditions. Likewise, proteomics indicated quinone‐mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light‐dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep‐sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase‐rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.
Converging on euroscepticism: Online polity contestation duringEuropeanParliament elections
Authors: de Wilde Pieter , Michailidou Asimina , Trenz Hans‐Jörg 
Published: January 2014

AbstractDoes the increasing politicisation ofEurope signify a step towards the legitimation of theUnion? This could be the case if the increased public intensity of debate and polarisation of opinion brought about by politicisation do not fragment the audience and if arguments presented in public are sufficiently clear about the desired nature of the polity. To answer this question, the focus of this article is on dynamic contestation in the public sphere using original data of news platforms and political blogs in 12EU MemberStates and transnational websites during theEuropeanParliament election campaign of 2009. The results are, first, that diffuse eurosceptic evaluations dominate public debates despite large variation in the intensity of debate acrossMemberStates. Second, a majority of evaluations made, particularly those by citizens leaving comments online, are negative in all countries included in this study. A gap between elites and citizens persists, but it appears less pronounced than often proclaimed in the literature. And third, democracy is a primary concern inEUpolity contestation, especially for those evaluating theEUnegatively. Although little evidence is found of a fragmentation of audiences, the prominence of diffuse euroscepticism poses a major challenge to legitimation of theUnion.