Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora)

The Nassophorea and Prostomatea are two of the key classes in understanding the morphological diversification and higher classification of the phylum Ciliophora. However, their phylogenetic relationships with other ciliate groups within the subphylum Intramacronucleata remain elusive. In this study, we investigated the small and large subunit (SSU and LSU) rRNA gene-based phylogeny of these groups with sequences of additional taxa including several key species. The results show that: (1) the class Nassophorea remains polyphyletic, with the microthoracids clustering with the Phyllopharyngea, whereas the nassulids represent a basal group of the CONthreeP superclade in the SSU tree; (2) the Prostomatea is not depicted as a monophyletic group in phylogenetic trees, and the monophyly of this class is marginally rejected by statistical tree topology tests; (3) the nassulid genus Parafurgasonia is more closely related to the family Colpodidiidae than to Furgasonia; (4) Paranassula, which was previously thought to be a nassulid, is phylogenetically related to the oligohymenophorean peniculids in both the SSU and LSU trees; (5) the microthoracid genus Discotricha does not group with the other microthoracids in either SSU or LSU trees; (6) the family Plagiocampidae is closely related to the prostome parasite Cryptocaryon irritans and to the family Urotrichidae in the order Prorodontida; and (7) the family Placidae, represented by Placus salinus, is sister to the family Holophryidae in the order Prorodontida. Based on the present data, we consider the genus Discotricha to be an unclassified taxon within the CONthreeP. We also propose resurrecting the order Paranassulida and classifying it within the subclass Peniculia, class Oligohymenophorea. Primary and secondary structure signatures for higher taxa within Phyllopharyngea and Nassophorea are supplied. (C) 2013 Elsevier Inc. All rights reserved.The Nassophorea and Prostomatea are two of the key classes in understanding the morphological diversification and higher classification of the phylum Ciliophora. However, their phylogenetic relationships with other ciliate groups within the subphylum Intramacronucleata remain elusive. In this study, we investigated the small and large subunit (SSU and LSU) rRNA gene-based phylogeny of these groups with sequences of additional taxa including several key species. The results show that: (1) the class Nassophorea remains polyphyletic, with the microthoracids clustering with the Phyllopharyngea, whereas the nassulids represent a basal group of the CONthreeP superclade in the SSU tree; (2) the Prostomatea is not depicted as a monophyletic group in phylogenetic trees, and the monophyly of this class is marginally rejected by statistical tree topology tests; (3) the nassulid genus Parafurgasonia is more closely related to the family Colpodidiidae than to Furgasonia; (4) Paranassula, which was previously thought to be a nassulid, is phylogenetically related to the oligohymenophorean peniculids in both the SSU and LSU trees; (5) the microthoracid genus Discotricha does not group with the other microthoracids in either SSU or LSU trees; (6) the family Plagiocampidae is closely related to the prostome parasite Cryptocaryon irritans and to the family Urotrichidae in the order Prorodontida; and (7) the family Placidae, represented by Placus salinus, is sister to the family Holophryidae in the order Prorodontida. Based on the present data, we consider the genus Discotricha to be an unclassified taxon within the CONthreeP. We also propose resurrecting the order Paranassulida and classifying it within the subclass Peniculia, class Oligohymenophorea. Primary and secondary structure signatures for higher taxa within Phyllopharyngea and Nassophorea are supplied. (C) 2013 Elsevier Inc. All rights reserved

Effects of sand burial and overstory tree age on seedling establishment in coastal Pinus thunbergii forests in the northern Shandong Peninsula, China

Coastal Pinus thunbergii (Japanese black pine) forests in the northern Shandong Peninsula of China recently experienced widespread natural regeneration failure. This study identifies critical factors that affect natural regeneration of P. thunbergii. Seeds from trees of various ages (13-32 years) were used to investigate the effects of age and burial depth in sand on germination and seedling establishment. Results show that seed density in 2-5 cm soil decreased with increased distance from the shoreline. Sand burial decreased seed germination but did not affect the relative growth rate of seedlings at depths from 0.5 to 3 cm. Germination, leaf mass ratio, and relative growth rates were higher with seedlings originating from older trees, all of which enhanced seedling resistance to sand burial. Tree age and seed burial were found to be determining factors for natural regeneration of the coastal P. thunbergii forest. Silvicultural treatments that promote quality of seed sources and mitigation of sand burial can be used in the future to improve the regeneration of these coastal forests

First Assessment of NOx Sources at a Regional Background Site in North China Using Isotopic Analysis Linked with Modeling

important role in the formation of atmospheric particles. Thus, NOx emission reduction is critical for improving air quality, especially in severely air-polluted regions (e.g., North China). In this study, the source of NOx was investigated by the isotopic composition (delta N-15) of particulate nitrate (p-NO3-) at Beihuangcheng Island (BH), a regional background site in North China. It was found that the delta N-15-NO3- (n = 120) values varied between -1.7 parts per thousand and +24.0 parts per thousand and the delta O-18-NO3- values ranged from 49.4 parts per thousand to 103.9 parts per thousand. On the basis of the Bayesian mixing model, 27.78 +/- 8.89%, 36.53 +/- 6.66%, 22.01 +/- 6.92%, and 13.68 +/- 3.16% of annual NOx could be attributed to biomass burning, coal combustion, mobile sources, and biogenic soil emissions, respectively. Seasonally, the four sources were similar in spring and fall. Biogenic soil emissions were augmented in summer in association with the hot and rainy weather. Coal combustion increased significantly in winter with other sources showing an obvious decline. This study confirmed that isotope-modeling by delta N-15-NO3- is a promising tool for partitioning NOx sources and provides guidance to policymakers with regard to options for NOx reduction in North China

Gig1, a novel antiviral effector involved in fish interferon response

Vertebrate interferon (IFN) response defenses against viral infection through the induction of hundreds of IFN-stimulated genes (ISGs). Most ISGs are conserved across vertebrates; however, little is known about the species-specific ISGs. In this study, we reported that grass carp reovirus (GCRV)-induced gene 1 (Gig1), previously screened as a virus-induced gene from UV-inactivated GCRV-infected crucian carp (Carassius auratus) blastulae embryonic (CAB) cells, was a typical fish ISG, which was significantly induced by intracellular poly(I:C) through retinoic acid-inducible gene I (RIG-I)-like receptors-triggered IFN signaling pathway. Transient or stable overexpression of Gig1 prevented GCRV replication efficiently in cultured fish cells. Strikingly, Gig1 homologs were found exclusively in fish species forming a novel gene family. These results illustrate that there exists a Gig1 gene family unique to fish species and the founding gene mediates a novel fish IFN antiviral pathway. (C) 2013 Elsevier Inc. All rights reserved.Vertebrate interferon (IFN) response defenses against viral infection through the induction of hundreds of IFN-stimulated genes (ISGs). Most ISGs are conserved across vertebrates; however, little is known about the species-specific ISGs. In this study, we reported that grass carp reovirus (GCRV)-induced gene 1 (Gig1), previously screened as a virus-induced gene from UV-inactivated GCRV-infected crucian carp (Carassius auratus) blastulae embryonic (CAB) cells, was a typical fish ISG, which was significantly induced by intracellular poly(I:C) through retinoic acid-inducible gene I (RIG-I)-like receptors-triggered IFN signaling pathway. Transient or stable overexpression of Gig1 prevented GCRV replication efficiently in cultured fish cells. Strikingly, Gig1 homologs were found exclusively in fish species forming a novel gene family. These results illustrate that there exists a Gig1 gene family unique to fish species and the founding gene mediates a novel fish IFN antiviral pathway. (C) 2013 Elsevier Inc. All rights reserved

In-Plane Deformation Mechanics for Highly Stretchable Electronics

Scissoring in thick bars suppresses buckling behavior in serpentine traces that have thicknesses greater than their widths, as detailed in a systematic set of analytical and experimental studies. Scissoring in thick copper traces enables elastic stretchability as large as approximate to 350%, corresponding to a sixfold improvement over previously reported values for thin geometries (approximate to 60%).</p

Flow characteristic of highly underexpanded jets from various nozzle geometries

Flow characteristics of highly underexpanded jets at the same nozzle pressure ratio of 5.60 but issuing from four different nozzles, i.e., the circular, elliptic, square, and rectangular nozzles, are studied using large eddy simulations. The results show that the square jet penetrates fastest, although the turbulence transition is similar for different jets. The penetration rates of different jets show the similar linear dependency on the square root of time, but the penetration constant Gamma for the noncircular jets deviates more than 5% from the theoretical value of 3.0. The circular and square jets both correspond to a three-dimensional helical instability mode, while the elliptic and rectangular jets haveatwo-dimensional flapping instability in their minor axis planes. All the jets undergo a Mach reflection forming the Mach disk, but the Mach disk in the elliptic and rectangular jets is not easily visible. The intercepting shocks in the square jet originate at the four corners of the nozzle exit at first, while the formation of the intercepting shocks is only observed in the major axis planes for the elliptic and rectangular jets. In addition, great differences are observed on the mixing characteristics between different jets. In particular, the elliptic jet penetrates slowest, has the shortest length of jet potential core, and takes the largest mixing area. (C) 2017 Elsevier Ltd. All rights reserved.</p

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Coupling mesoscale transport to catalytic surface reactions in a hybrid model

In heterogeneous catalysis, reactivity and selectivity are not only influenced by chemical processes occurring on catalytic surfaces but also by physical transport phenomena in the bulk fluid and fluid near the reactive surfaces. Because these processes take place at a large range of time and length scales, it is a challenge to model catalytic reactors, especially when dealing with complex surface reactions that cannot be reduced to simple mean-field boundary conditions. As a particle-based mesoscale method, Stochastic Rotation Dynamics (SRD) is well suited for studying problems that include both microscale effects on surfaces and transport phenomena in fluids. In this work, we demonstrate how to simulate heterogeneous catalytic reactors by coupling an SRD fluid with a catalytic surface on which complex surface reactions are explicitly modeled. We provide a theoretical background for modeling different stages of heterogeneous surface reactions. After validating the simulation method for surface reactions with mean-field assumptions, we apply the method to non-mean-field reactions in which surface species interact with each other through a Monte Carlo scheme, leading to island formation on the catalytic surface. We show the potential of the method by simulating a more complex three-step reaction mechanism with reactant dissociation. Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Complex Fluid ProcessingEngineering Thermodynamic