Phylogenetic relationships among the major lineages of the birds-of-paradise (Paradisaeidae) using mitochondrial DNA gene sequences.

PubMed

Nunn, G B; Cracraft, J

1996-06-01

Complete mitochondrial cytochrome b gene sequences were determined from 12 species of the Australo-Papuan birds-of-paradise (Paradisaeidae) representing 9 genera. Phylogenetic analysis of these and 5 previously published sequences reveals a radiation of the main paradisaeinine lineages that took place over a relatively short evolutionary time scale. The core paradisaeinines are resolved as the monophyletic sister-group to the crow-like manucodines. The genus Parotia is basal to other paradisaeinines and is not closely related to the morphologically similar genera Ptiloris and Lophorina. Three major clades within the paradisaeinine ingroup include: (1) Cicinnurus and Diphyllodes, (2) Ptiloris and Lophorina, and (3) the genus Paradisaea. The monotypic genus Seleucidis is apparently closely related to clades (1) and (2). Cytochrome b sequences did not provide evidence for the monophyly of the sicklebill genera Epimachus and Drepanornis. The paradisaeid tree is characterized by short internodal distances. Thus, some clades cannot be strongly resolved by cytochrome b sequences alone.

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

PubMed

Suchan, Tomasz; Espíndola, Anahí; Rutschmann, Sereina; Emerson, Brent C; Gori, Kevin; Dessimoz, Christophe; Arrigo, Nils; Ronikier, Michał; Alvarez, Nadir

2017-09-01

Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years. Here we examine the potential and limitations of one of such techniques-Restriction-site Associated DNA (RAD) sequencing, a method that produces thousands of (mostly) anonymous nuclear markers, in disentangling the phylogeny of the fly genus Chiastocheta (Diptera: Anthomyiidae). In Europe, this genus encompasses seven species of seed predators, which have been widely studied in the context of their ecological and evolutionary interactions with the plant Trollius europaeus (Ranunculaceae). So far, phylogenetic analyses using mitochondrial markers failed to resolve monophyly of most of the species from this recently diversified genus, suggesting that their taxonomy may need a revision. However, relying on a single, non-recombining marker and ignoring potential incongruences between mitochondrial and nuclear loci may provide an incomplete account of the lineage history. In this study, we applied both classical Sanger sequencing of three mtDNA regions and RAD-sequencing, for reconstructing the phylogeny of the genus. Contrasting with results based on mitochondrial markers, RAD-sequencing analyses retrieved the monophyly of all seven species, in agreement with the morphological species assignment. We found robust nuclear-based species assignment of individual samples, and low levels of estimated contemporary gene flow among them. However, despite recovering species' monophyly, interspecific relationships varied depending on the set of RAD loci considered, producing contradictory topologies. Moreover, coalescence-based phylogenetic analyses revealed low supports for most of the interspecific relationships. Our results indicate that despite the higher performance of RAD-sequencing in terms of species trees resolution compared to cytoplasmic markers, reconstructing inter-specific relationships among recently-diverged lineages may lie beyond the possibilities offered by large sets of RAD-sequencing markers in cases of strong gene tree incongruence. Copyright © 2017 Elsevier Inc. All rights reserved.

Cretaceous origin of the unique prey-capture apparatus in mega-diverse genus: stem lineage of Steninae rove beetles discovered in Burmese amber

PubMed Central

Żyła, Dagmara; Yamamoto, Shûhei; Wolf-Schwenninger, Karin; Solodovnikov, Alexey

2017-01-01

Stenus is the largest genus of rove beetles and the second largest among animals. Its evolutionary success was associated with the adhesive labial prey-capture apparatus, a unique apomorphy of that genus. Definite Stenus with prey-capture apparatus are known from the Cenozoic fossils, while the age and early evolution of Steninae was hardly ever hypothesized. Our study of several Cretaceous Burmese amber inclusions revealed a stem lineage of Steninae that possibly possesses the Stenus-like prey-capture apparatus. Phylogenetic analysis of extinct and extant taxa of Steninae and putatively allied subfamilies of Staphylinidae with parsimony and Bayesian approaches resolved the Burmese amber lineage as a member of Steninae. It justified the description of a new extinct stenine genus Festenus with two new species, F. robustus and F. gracilis. The Late Cretaceous age of Festenus suggests an early origin of prey-capture apparatus in Steninae that, perhaps, drove the evolution towards the crown Stenus. Our analysis confirmed the well-established sister relationships between Steninae and Euaesthetinae and resolved Scydmaeninae as their next closest relative, the latter having no stable position in recent phylogenetic studies of rove beetles. Close affiliation of Megalopsidiinae, a subfamily often considered as a sister group to Euaesthetinae + Steninae clade, is rejected. PMID:28397786

Evolutionary relationships and divergence times among the native rats of Australia.

PubMed

Robins, Judith H; McLenachan, Patricia A; Phillips, Matthew J; McComish, Bennet J; Matisoo-Smith, Elizabeth; Ross, Howard A

2010-12-02

The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.

The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes.

PubMed

Urantowka, Adam Dawid; Kroczak, Aleksandra; Mackiewicz, Paweł

2017-07-14

Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration. Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific

PubMed Central

Price, Mark T.; Fullerton, Heather; Moyer, Craig L.

2015-01-01

Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera. PMID:26441901

Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line.

PubMed

Nikiforova, Svetlana V; Cavalieri, Duccio; Velasco, Riccardo; Goremykin, Vadim

2013-08-01

Both the origin of domesticated apple and the overall phylogeny of the genus Malus are still not completely resolved. Having this as a target, we built a 134,553-position-long alignment including two previously published chloroplast DNAs (cpDNAs) and 45 de novo sequenced, fully colinear chloroplast genomes from cultivated apple varieties and wild apple species. The data produced are free from compositional heterogeneity and from substitutional saturation, which can adversely affect phylogeny reconstruction. Phylogenetic analyses based on this alignment recovered a branch, having the maximum bootstrap support, subtending a large group of the cultivated apple sorts together with all analyzed European wild apple (Malus sylvestris) accessions. One apple cultivar was embedded in a monophylum comprising wild M. sieversii accessions and other Asian apple species. The data demonstrate that M. sylvestris has contributed chloroplast genome to a substantial fraction of domesticated apple varieties, supporting the conclusion that different wild species should have contributed the organelle and nuclear genomes to the domesticated apple.

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).

PubMed

Foster, Charles S P; Henwood, Murray J; Ho, Simon Y W

2018-05-25

Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics. Copyright © 2018 Elsevier Inc. All rights reserved.

Operators and higher genus mirror curves

NASA Astrophysics Data System (ADS)

Codesido, Santiago; Gu, Jie; Mariño, Marcos

2017-02-01

We perform further tests of the correspondence between spectral theory and topological strings, focusing on mirror curves of genus greater than one with nontrivial mass parameters. In particular, we analyze the geometry relevant to the SU(3) relativistic Toda lattice, and the resolved C{^3}/Z_6 orbifold. Furthermore, we give evidence that the correspondence holds for arbitrary values of the mass parameters, where the quantization problem leads to resonant states. We also explore the relation between this correspondence and cluster integrable systems.

Flexible colour patterns obscure identification and mimicry in Indo-Pacific Chromodoris nudibranchs (Gastropoda: Chromodorididae).

PubMed

Layton, Kara K S; Gosliner, Terrence M; Wilson, Nerida G

2018-07-01

Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris. This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus. Copyright © 2018 Elsevier Inc. All rights reserved.

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

PubMed Central

Choi, Young-Joon; Klosterman, Steven J.; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2017-01-01

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. PMID:25772799

Comparative analysis of chloroplast genomes of the genus Citrus and its close relatives.

PubMed

Liu, Xiaogang; Wu, Hongkun; Luo, Yan; Xi, Wanpeng; Zhou, Zhiqin

2017-01-01

The genus Citrus and its close relatives are economically and nutritionally important fruit trees. However, the huge controversy over the phylogeny of key wild species, as well as the genetic relationship between the cultivated species and their putative wild progenitors, remains unresolved. Comparative analyses of chloroplast (cp) genomes have been useful in resolving various phylogenetic issues. Thus far, the cp genomes of only two Citrus species have been sequenced. In this study, we sequenced six complete cp genomes, four belonging to the genus Citrus, and two belonging to the genera Fortunella and Poncirus, respectively. These newly sequenced genomes together with the two publicly available were used for comparative analyses of the genus Citrus and its close relatives. All eight cp genomes share similar basic structure, gene order and gene content. Phylogenetic analyses supported the monophyly of the three genera in the order Sapindales within the major clade Malvidae.

Phylogenetic relationships in the genus Leontopodium (Asteraceae: Gnaphalieae) based on AFLP data

PubMed Central

SAFER, STEFAN; TREMETSBERGER, KARIN; GUO, YAN-PING; KOHL, GUDRUN; SAMUEL, MARY R.; STUESSY, TOD F.; STUPPNER, HERMANN

2012-01-01

The genus Leontopodium comprises 30–41 species. The centre of diversity is the Sino-Himalayan region in south-western China, where about 15 species occur. The two species native to Europe, L. alpinum (known as the common ‘Edelweiss’) and L. nivale, are part of the cultural heritage of the people living there. Despite its importance, very little is known about the systematics of the genus. Because recent molecular studies have shown that species within this genus are closely related and difficult to distinguish with rDNA and cpDNA data, we used AFLPs to obtain a more detailed understanding of the phylogeny of the genus. Our main aims were as follows: (1) to clarify species relationships within the genus; and (2) to reveal information about the biogeography of the genus. We used AFLPs with six primer combinations to investigate 216 individuals in 38 populations of 16 different species. With AFLPs, we were able to recognize 10 different groups, all of which had strong bootstrap support. These results were also congruent with the morphology-based taxonomy of the genus. Most private and rare fragments were found in the Yunnan region (south-western China) relative to Europe and Mongolia/central China, suggesting a long-lasting in situ history of populations in the centre of diversity of the genus. Our results illustrate the utility of AFLPs to resolve phylogenetic relationships between these closely related species. PMID:23258943

Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

PubMed Central

Smith, Geoff M.; Hutson, Jarod M.; Kindler, Lutz; Garcia-Moreno, Alejandro; Villaluenga, Aritza; Turner, Elaine

2017-01-01

Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies. PMID:28316883

Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.

PubMed

Welker, Frido; Smith, Geoff M; Hutson, Jarod M; Kindler, Lutz; Garcia-Moreno, Alejandro; Villaluenga, Aritza; Turner, Elaine; Gaudzinski-Windheuser, Sabine

2017-01-01

Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus . No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros ( Dicerorhinus sumatrensis ). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus . ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus , subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera ( Equus , Tapirus ), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus . The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros , opposed to forming a clade with the black and white rhinoceros species. The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus . This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

Climate and soil type together explain the distribution of microendemic species in a biodiversity hotspot.

PubMed

Nattier, Romain; Grandcolas, Philippe; Pellens, Roseli; Jourdan, Hervé; Couloux, Arnaud; Poulain, Simon; Robillard, Tony

2013-01-01

The grasshopper genus Caledonula, endemic to New Caledonia, was studied to understand the evolution of species distributions in relation to climate and soil types. Based on a comprehensive sampling of 80 locations throughout the island, the genus was represented by five species, four of which are new to science, of which three are described here. All the species have limited distributions in New Caledonia. Bioclimatic niche modelling shows that all the species were found in association with a wet climate and reduced seasonality, explaining their restriction to the southern half of the island. The results suggest that the genus was ancestrally constrained by seasonality. A molecular phylogeny was reconstructed using two mitochondrial and two nuclear markers. The partially resolved tree showed monophyly of the species found on metalliferous soils, and molecular dating indicated a rather recent origin for the genus. Adaptation to metalliferous soils is suggested by both morphological changes and radiation on these soils. The genus Caledonula is therefore a good model to understand the origin of microendemism in the context of recent and mixed influences of climate and soil type.

Notes on the taxonomic position of several species of the genus Diphascon (Tardigrada, Hypsibiidae).

PubMed

Tumanov, Denis V

2018-03-20

For this paper I analysed the descriptions of all species, attributed to the genus Diphascon Plate, 1889, to ascertain if they fit the diagnosis of this genus, provided by Bertolani et al. 2014. Thirty four species (the majority of the species diversity classified within the genus) fully match its emended diagnosis, while three: Diphascon opisthoglyptum Maucci, 1987, Diphascon procerum Pilato, Sabella Lisi, 2014 and Diphascon ziliense Lisi, Sabella Pilato, 2014, demonstrate a combination of characters, typical to the genus Pilatobius Bertolani et al., 2014. I propose the transfer these three species to the genus Pilatobius, thus their new taxonomic positions are as follows: Pilatobius opisthoglyptus (Maucci, 1987) comb. nov., Pilatobius procerus (Pilato, Sabella Lisi, 2014) comb. nov. and Pilatobius ziliense (Lisi, Sabella Pilato, 2014) comb. nov. Descriptions of three other Diphascon species (Diphascon mariae (Mihelčič, 1951), Diphascon rivulare (Mihelčič, 1967) and Diphascon punctatum (Iharos, 1962)) contain too little detail to conclude on their taxonomic position. The species Pilatobius halapiense (Iharos, 1964) was erroneously transferred from the genus Diphascon, and here I suggest it is transferred back to Diphascon. The new taxonomic position of this species is: Diphascon halapiense (Iharos, 1964) comb. nov. Emended list of species, attributed to the genus Diphascon is given.

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach.

PubMed

Choi, Young-Joon; Klosterman, Steven J; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2015-05-01

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

Absurdaster, a new genus of basal atelostomate from the Early Cretaceous of Europe and its phylogenetic position☆

PubMed Central

Kroh, Andreas; Lukeneder, Alexander; Gallemí, Jaume

2014-01-01

Field work in the Lower Cretaceous of the Dolomites (Italy) has resulted in the recovery of a new genus of ‘disasteroid’ echinoid, which successively was also discovered in slightly older strata in Northern Hungary. This new genus, Absurdaster, is characterized by its highly modified, disjunct apical disc in which all genital plate except genital plate 2 are reduced or fused. The gonopores (which may be multiple) have shifted and pierce interambulacral plates. Anteriorly ambulacrum III is distinctly sunken and forms a distinct frontal notch, while the posterior end is pointed and features a small sharply defined posterior face bearing the periproct. Two new species are established: Absurdaster puezensis sp. nov. from the Upper Hauterivian to Lower Barremian Puez Formation of Northern Italy is characterized by its rudimentary ambulacral pores in the paired ambulacra, high hexagonal ambulacral plates aborally and multiple gonopores in the most adapical plates of interambulacral columns 1b and 4a. Absurdaster hungaricus sp. nov. from the Lower Hauterivian Bersek Marl Formation of Northern Hungary, in contrast, shows circumflexed ambulacral pores, low ambulacral plates, a single gonopore each in the most adapical plates of interambulacral columns 1b and 4a and a flaring posterior end, with sharp margin and invaginated periproct. In addition to those two species Collyrites meriani Ooster, 1865 from the uppermost Berriasian to basal Barremian of Switzerland is attributed to the new genus. Despite the poor knowledge on this form it seems to be distinguished from the new species by its smaller ambulacral plates and higher interambulacral/ambulacral plate ratio. Phylogenetic analyses based on previous work by Barras (2007) and Saucède et al. (2007) indicate that the new genus is a highly derived stem-group member of the Atelostomata close to the split of holasteroids and spatangoids. A combined analysis based on a subset of the characters employed in these two studies for the first time results in a fully resolved tree for ‘disasteroids’. Absurdaster, shows two notable morphological peculiarities: 1) it is one of the first echinoids to develop fascioles and exhibits a yet unknown type of fasciole circling the periproct, termed circumanal fasciole here; 2) it is extraordinary among echinoderms as its extraxial skeleton is reduced to a single plate, the madreporite (genital plate 2), and because its genital pores pierce axial elements rather than extraxial ones. PMID:27087720

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

PubMed Central

Harlin-Cognato, April D; Honeycutt, Rodney L

2006-01-01

Background Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution. Results Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution. Conclusion The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses. PMID:17078887

Redescription of poorly known species of Ceratothoa Dana, 1852 (Crustacea, Isopoda, Cymothoidae), based on original type material

PubMed Central

Hadfield, Kerry A.; Bruce, Niel L.; Smit, Nico J.

2016-01-01

Abstract Due to the difficulty in accurately identifying cymothoids, these parasitic isopods are often incorrectly named or confused with other species. Within the genus Ceratothoa, a number of recent studies have aimed at clarifying some of the problematic species; however, several of the less studied species still require revision. This paper redescribes, from type material, several poorly known Ceratothoa species including Ceratothoa angulata, Ceratothoa capri, Ceratothoa carinata, Ceratothoa collaris, Ceratothoa gilberti, Ceratothoa gobii, Ceratothoa guttata, Ceratothoa italica, Ceratothoa oestroides, and Ceratothoa verrucosa, further resolving taxonomic uncertainties within the genus. PMID:27408544

The spiny dogfish (Squalus cubensis/megalops group): the envenoming of a fisherman, with taxonomic and toxinological comments on the Squalus genus.

PubMed

Haddad, Vidal; Gadig, Otto Bismarck Fazzano

2005-12-01

The authors report a spiny dogfish (Squalus cubensis/megalops group) sting of a professional fisherman. He was injured on the left hand by the spine anterior to the fish's dorsal fin and manifested local edema, erythema, and excruciating pain for 6 h. Sharks of the genus Squalus megalops/cubensis and Squalus acanthias are found throughout the world; they have two spines in front of their dorsal fins and channels with a whitish mass containing large vacuolated cells which secrete venom. The Squalus genus has a complex taxonomy; the species involved in this injury belongs to the megalops/cubensis group. A detailed taxonomic and toxinological study on the Squalus genus is important and would complement other work on these fish, especially as stings in humans are very rare and not fully understood.

Endogenous pro-resolving and anti-inflammatory lipid mediators: a new pharmacologic genus

PubMed Central

Serhan, C N; Chiang, N

2008-01-01

Complete resolution of an acute inflammatory response and its return to homeostasis are essential for healthy tissues. Here, we overview ongoing efforts to characterize cellular and molecular mechanisms that govern the resolution of self-limited inflammation. Systematic temporal analyses of evolving inflammatory exudates using mediator lipidomics-informatics, proteomics, and cellular trafficking with murine resolving exudates demonstrate novel endogenous pathways of local-acting mediators that share both anti-inflammatory and pro-resolving properties. In murine systems, resolving-exudate leukocytes switch their phenotype to actively generate new families of mediators from major omega-3 fatty acids EPA and DHA termed resolvins and protectins. Recent advances on their biosynthesis and actions are reviewed with a focus on the E-series resolvins (RvE1, RvE2), D series resolvins (RvD1, RvD2) and the protectins including neuroprotectin D1/protectin D1 (NPD1/PD1) as well as their aspirin-triggered epimeric forms. Members of each new family demonstrate potent stereo-specific actions, joining the lipoxins as endogenous local signals that govern resolution and endogenous anti-inflammation mechanisms. In addition to their origins and roles in resolution biology in the immune system, recent findings indicate that these new mediator families also display potent protective actions in lung, kidney, and eye as well as enhance microbial clearance. Thus, these endogenous agonists of resolution pathways constitute a novel genus of chemical mediators that possess pro-resolving, anti-inflammatory, and antifibrotic as well as host-directed antimicrobial actions. These may be useful in the design of new therapeutics and treatments for diseases with the underlying trait of uncontrolled inflammation and redox organ stress. PMID:17965751

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology.

PubMed

Simmons, M P; Clevinger, C C; Savolainen, V; Archer, R H; Mathews, S; Doyle, J J

2001-02-01

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

PubMed

Reck-Kortmann, Maikel; Silva-Arias, Gustavo Adolfo; Segatto, Ana Lúcia Anversa; Mäder, Geraldo; Bonatto, Sandro Luis; de Freitas, Loreta Brandão

2014-12-01

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae).

PubMed

Sanabria-Urbán, Salomón; Song, Hojun; Oyama, Ken; González-Rodríguez, Antonio; Castillo, Raúl Cueva Del

2017-06-08

The genus Sphenarium Charpentier, 1842 comprises the most diverse group of the New World Pyrgomorphidae. These grasshoppers show an extensive variation in external morphology, and are culturally and economically important for Mexican people since pre-Hispanic times. Nevertheless, the taxonomy of Sphenarium has been chaotic and remained incompletely resolved until now. Following an integrative taxonomic framework, we infer the number of species in this genus by species delimitation based on morphological, phylogenetic, and geographic information. Based on our results, we revise the genus and redefine 9 species and describe 8 new species (S. adelinae sp.n., S. crypticum sp.n., S. infernalis sp.n., S. miztecum sp.n., S. occidentalis sp.n., S. tarascum sp.n., S. totonacum sp.n. and S. zapotecum sp.n.). Moreover, we update the knowledge of the evolutionary relationships and biogeographic patterns of Sphenarium species. Our results also demonstrate the importance of historic geological and climatic events on the lineage diversification of this genus. Different levels of morphological and genetic differentiation among species suggest a complex interplay between evolutionary forces during the evolution of these neotropical grasshoppers.

Evolutionary history of genus Macrobrachium inferred from mitochondrial markers: a molecular clock approach.

PubMed

Jose, Deepak; Harikrishnan, Mahadevan

2018-04-17

Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers. Previous studies on Macrobrachium relied on the highly variable morphological characters which were insufficient for accurate diagnosis of natural species groups. Present study focuses on the utility of molecular markers (viz. COI and 16S rRNA) for resolving the evolutionary history of genus Macrobrachium using a combination of phylogeny and timescale components. It is for the first time a molecular clock approach had been carried out towards genus Macrobrachium in a broad aspect with the incorporation of congeners inhabiting diverse geographical realms including endemic species M. striatum from South West coast of India. Molecular results obtained revealed the phylogenetic relationships between congeners of genus Macrobrachium at intra/inter-continental level along with the corresponding evolutionary time estimates.

A polyphasic approach for characterization of a collection of cereal isolates of the Fusarium incarnatum-equiseti species complex

USDA-ARS?s Scientific Manuscript database

DNA-based phylogenetic analyses have resolved the fungal genus Fusarium into multiple species complexes. The F. incarnatum-equiseti species complex (FIESC) includes fusaria associated with several diseases of agriculturally important crops, including cereals. Although members of FIESC are considered...

PHYLOGENETIC ANALYSIS OF CRYPTOSPORIDIUM PARASITES BASED ON THE SMALL SUBUNIT RIBOSOMAL RNA GENE LOCUS

EPA Science Inventory

ABSTRACT
Biologic data support the presence of multiple species in the genus Cryptosporidium, but
a recent analysis of the available genetic data has suggested that there is insufficient evidence for species differentiation. In order to resolve the controversy in the taxono...

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.

PubMed

Krause, Johannes; Unger, Tina; Noçon, Aline; Malaspinas, Anna-Sapfo; Kolokotronis, Sergios-Orestis; Stiller, Mathias; Soibelzon, Leopoldo; Spriggs, Helen; Dear, Paul H; Briggs, Adrian W; Bray, Sarah C E; O'Brien, Stephen J; Rabeder, Gernot; Matheus, Paul; Cooper, Alan; Slatkin, Montgomery; Pääbo, Svante; Hofreiter, Michael

2008-07-28

Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.

Molecular phylogeny of porcelain crabs (Porcellanidae: Petrolisthes and allies) from the south eastern Pacific: the genera Allopetrolisthes and Liopetrolisthes are not natural entities

PubMed Central

2016-01-01

Porcelain crabs from the closely related genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes are known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the genera Allopetrolisthes and Liopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species from Petrolisthes (6 species), Liopetrolisthes (2 species), and Allopetrolisthes (3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species: L. mitra + L. patagonicus, P. tuberculatus + P. tuberculosus, and A. angulosus + A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the genera Liopetrolisthes and Allopetrolisthes, and to transfer their members to the genus Petrolisthes. PMID:26989636

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

PubMed Central

2008-01-01

Background Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. Results We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Conclusion Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations. PMID:18662376

Resolving species delimitation within the genus Bunopus Blanford, 1874 (Squamata: Gekkonidae) in Iran using DNA barcoding approach.

PubMed

Khosravani, Azar; Rastegar-Pouyani, Eskandar; Rastegar-Pouyani, Nasrullah; Oraie, Hamzeh; Papenfuss, Theodore J

2017-12-19

Mitochondrial COI sequences were used to investigate species delimitation within the genus Bunopus in Iran. A dataset with a final sequence length of 633 nucleotides including 100 specimens from 31 geographically distant localities across Iran were generated. The result demonstrated that two major clades with strong support can be identified within the genus Bunopus in Iran. Clade A includes Bunopus crassicaudus and two new entities, eastern populations (subclade A2,1) and Shahdad populations (subclade A2,2). The second clade comprises western and southwestern populations (subclade B1,1), Arabian populations (subclade B1,2) and south and southeast populations in Iran, to which Bunopus tuberculatus (subclade B2) is assigned. In addition to Bunopus crassicaudus and B. tuberculatus, three new candidate species in Iran can easily be identified based on the DNA barcoding approach.

Oberholzeria (Fabaceae subfam. Faboideae), a New Monotypic Legume Genus from Namibia

PubMed Central

Swanepoel, Wessel; le Roux, M. Marianne; Wojciechowski, Martin F.; van Wyk, Abraham E.

2015-01-01

Oberholzeria etendekaensis, a succulent biennial or short-lived perennial shrublet is described as a new species, and a new monotypic genus. Discovered in 2012, it is a rare species known only from a single locality in the Kaokoveld Centre of Plant Endemism, north-western Namibia. Phylogenetic analyses of molecular sequence data from the plastid matK gene resolves Oberholzeria as the sister group to the Genisteae clade while data from the nuclear rDNA ITS region showed that it is sister to a clade comprising both the Crotalarieae and Genisteae clades. Morphological characters diagnostic of the new genus include: 1) succulent stems with woody remains; 2) pinnately trifoliolate, fleshy leaves; 3) monadelphous stamens in a sheath that is fused above; 4) dimorphic anthers with five long, basifixed anthers alternating with five short, dorsifixed anthers, and 5) pendent, membranous, one-seeded, laterally flattened, slightly inflated but indehiscent fruits. PMID:25816251

Oberholzeria (Fabaceae subfam. Faboideae), a new monotypic legume genus from Namibia.

PubMed

Swanepoel, Wessel; le Roux, M Marianne; Wojciechowski, Martin F; van Wyk, Abraham E

2015-01-01

Oberholzeria etendekaensis, a succulent biennial or short-lived perennial shrublet is described as a new species, and a new monotypic genus. Discovered in 2012, it is a rare species known only from a single locality in the Kaokoveld Centre of Plant Endemism, north-western Namibia. Phylogenetic analyses of molecular sequence data from the plastid matK gene resolves Oberholzeria as the sister group to the Genisteae clade while data from the nuclear rDNA ITS region showed that it is sister to a clade comprising both the Crotalarieae and Genisteae clades. Morphological characters diagnostic of the new genus include: 1) succulent stems with woody remains; 2) pinnately trifoliolate, fleshy leaves; 3) monadelphous stamens in a sheath that is fused above; 4) dimorphic anthers with five long, basifixed anthers alternating with five short, dorsifixed anthers, and 5) pendent, membranous, one-seeded, laterally flattened, slightly inflated but indehiscent fruits.

A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae).

PubMed

Ramírez, Santiago R; Nieh, James C; Quental, Tiago B; Roubik, David W; Imperatriz-Fonseca, Vera L; Pierce, Naomi E

2010-08-01

Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least approximately 14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae. Copyright 2010 Elsevier Inc. All rights reserved.

A remarkable new genus and a new species of chewing louse (Phthiraptera, Ischnocera, Philopteridae) from Brazil

PubMed Central

Valim, Michel P.; Cicchino, Armando C.

2015-01-01

Abstract A new genus of chewing louse as Bobdalgleishia, and its type species Bobdalgleishia stephanophallus sp. n. (Phthiraptera) belonging to the Brueelia-complex (Ischnocera: Philopteridae) are described. Adults of the new species are fully described, illustrated and compared morphologically with the type species of Motmotnirmus Mey & Barker, 2014, which is its closest relative. The type host of Bobdalgleishia stephanophallus is a subspecies of the great jacamar Jacamerops aureus ridgwayi Todd, 1943, an endemic Amazonian bird distributed in northern Brazil, and the type locality is the State of Pará. Bobdalgleishia is a remarkable genus with unique morphological and chaetotaxic characters which readily separate it from other members of the Brueelia-complex, in particular by having the first two marginal temporal and ocular setae very long. PMID:26798280

Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

PubMed Central

Zhou, Shi-Liang; Zou, Xin-Hui; Zhou, Zhi-Qin; Liu, Jing; Xu, Chao; Yu, Jing; Wang, Qiang; Zhang, Da-Ming; Wang, Xiao-Quan; Ge, Song; Sang, Tao; Pan, Kai-Yu; Hong, De-Yuan

2014-01-01

The origin of cultivated tree peonies, known as the ‘king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication. PMID:25377453

A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

PubMed

Takahashi, Tetsumi; Moreno, Edmundo

2015-12-01

The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships. Copyright © 2015 Elsevier Inc. All rights reserved.

Importance of resolving fungal nomenclature: the case of multiple pathogenic species in the Cryptococcus genus

USDA-ARS?s Scientific Manuscript database

Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoform...

Phylogenetic Relationships of American Willows (Salix L., Salicaceae)

PubMed Central

Lauron-Moreau, Aurélien; Pitre, Frédéric E.; Argus, George W.; Labrecque, Michel; Brouillet, Luc

2015-01-01

Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns. PMID:25880993

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.

PubMed

Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z

2017-01-01

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae).

PubMed

Perfectti, Francisco; Gómez, José M; González-Megías, Adela; Abdelaziz, Mohamed; Lorite, Juan

2017-01-01

The phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established. Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trn T- trn F region). We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca . The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia . The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis . We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic analyses, M. foleyi appeared outside the Moricandia lineage but within the genus Eruca . Therefore, M. foleyi should be excluded from the genus Moricandia and be ascribed, at least provisionally, to the genus Eruca .

Strategy for the elucidation of elemental compositions of trace analytes based on a mass resolution of 100,000 full width at half maximum.

PubMed

Kaufmann, Anton

2010-07-30

Elemental compositions (ECs) can be elucidated by evaluating the high-resolution mass spectra of unknown or suspected unfragmented analyte ions. Classical approaches utilize the exact mass of the monoisotopic peak (M + 0) and the relative abundance of isotope peaks (M + 1 and M + 2). The availability of high-resolution instruments like the Orbitrap currently permits mass resolutions up to 100,000 full width at half maximum. This not only allows the determination of relative isotopic abundances (RIAs), but also the extraction of other diagnostic information from the spectra, such as fully resolved signals originating from (34)S isotopes and fully or partially resolved signals related to (15)N isotopes (isotopic fine structure). Fully and partially resolved peaks can be evaluated by visual inspection of the measured peak profiles. This approach is shown to be capable of correctly discarding many of the EC candidates which were proposed by commercial EC calculating algorithms. Using this intuitive strategy significantly extends the upper mass range for the successful elucidation of ECs. Copyright 2010 John Wiley & Sons, Ltd.

Non-Intrusive, Time-Resolved Hall Thruster Near-Field Electron Temperature Measurements

DTIC Science & Technology

2011-08-01

With the growing interest in Hall thruster technology, comes the need to fully characterize the plasma dynamics that determine performance. Of...instabilities characteristic of Hall thruster behavior, time resolved techniques must be developed. This study presents a non-intrusive method of

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE PAGES

Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

2016-10-19

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edlund, Petra; Takala, Heikki; Claesson, Elin

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

Two-color vibrational, femtosecond, fully resonant electronically enhanced CARS (FREE-CARS) of gas-phase nitric oxide.

PubMed

Stauffer, Hans U; Roy, Sukesh; Schmidt, Jacob B; Wrzesinski, Paul J; Gord, James R

2016-09-28

A resonantly enhanced, two-color, femtosecond time-resolved coherent anti-Stokes Raman scattering (CARS) approach is demonstrated and used to explore the nature of the frequency- and time-dependent signals produced by gas-phase nitric oxide (NO). Through careful selection of the input pulse wavelengths, this fully resonant electronically enhanced CARS (FREE-CARS) scheme allows rovibronic-state-resolved observation of time-dependent rovibrational wavepackets propagating on the vibrationally excited ground-state potential energy surface of this diatomic species. Despite the use of broadband, ultrafast time-resolved input pulses, high spectral resolution of gas-phase rovibronic transitions is observed in the FREE-CARS signal, dictated by the electronic dephasing timescales of these states. Analysis and computational simulation of the time-dependent spectra observed as a function of pump-Stokes and Stokes-probe delays provide insight into the rotationally resolved wavepacket motion observed on the excited-state and vibrationally excited ground-state potential energy surfaces of NO, respectively.

Revision of Massylaea Möllendorff, 1898 (Stylommatophora, Helicidae).

PubMed

Bouaziz-Yahiatene, Houria; Pfarrer, Beat; Medjdoub-Bensaad, Ferroudja; Eike Neubert

2017-01-01

In this paper some helicoid species from eastern Algeria are investigated using a morphological and molecular approach. The investigation of the genital organs of M. massylaea (Morelet, 1851), the type species of the genus Massylaea Möllendorff, 1898, showed the same autapomorphic character states as are considered typical for Eobania P. Hesse, 1913. These findings are fully supported by the genetic analysis using two mitochondrial and three nuclear markers. Thus, the latter genus has to be considered a synonym of the former. Currently, three species are known to comprise the genus, viz. M. massylaea , M. constantina (E. Forbes, 1838), and M. vermiculata (O. F. Müller, 1774). Several nominal taxa from northern Africa are synonymised with one of the species mentioned here under Massylaea . The generic position of the so-called " Massylaea " species from the High Atlas Mountains in southern Morocco remains unresolved.

Myrtoessa hyas, a new valvatiform genus and a new species of the Hydrobiidae (Caenogastropoda, Truncatelloidea) from Greece

PubMed Central

Radea, Canella; Parmakelis, Aristeidis; Giokas, Sinos

2016-01-01

Abstract A new to science valvatiform hydrobiid, Myrtoessa hyas Radea, gen. n. & sp. n., from southern Greece, is described and illustrated. The new genus is a tiny gastropod thriving in a stream and is differentiated from the other known European and circum-Mediterranean valvatiform hydrobiid genera by a unique combination of the male and female genitalia features i.e. penis long, flat, blunt, with wide wrinkled proximal part and narrow distal part with a sub-terminal eversible papilla on its left side, bursa copulatrix well-developed, pyriform, fully protruding from the posterior end of the albumen gland and two seminal receptacles respectively. The new monotypic and locally endemic genus is narrowly distributed and its single known population nearby a coastal bustling village is vulnerable to anthropogenic stressors. PMID:28138282

Resolving cryptic species with morphology and DNA; thrips as a potential biocontrol agent of Brazilian peppertree, with a new species and overview of Pseudophilothrips (Thysanoptera)

USDA-ARS?s Scientific Manuscript database

Molecular and morphological evidence is presented to support the description of a second species of Pseudophilothrips in Brazil in association with Schinus terebinthifolius, an invasive weedy tree in North America. Pseudophilothrips is here recognized as a weakly defined genus comprising 13 describe...

Wood anatomy of the neotropical Sapotaceae : XVII. Gambeya

Treesearch

Bohumil Francis Kukachka

1980-01-01

Gambeya is an African genus to which Aubréville added Gambeya excelsa (Huber) Aubr., based on the Amazonian Chrysophyllum excelsum Huber. Whether Gambeya is the appropriate taxon for the American species remains to be resolved. Wood specimens indicate that several species occur in the Americas ranging from Southern Mexico to the Peruvian Amazon. The woods of the...

Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes

PubMed Central

McCarthy, Charley G. P.

2017-01-01

ABSTRACT The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus. Genome-scale phylogenetic studies have successfully resolved many eukaryotic relationships by using supertree methods, which combine large numbers of potentially disparate trees to determine evolutionary relationships that cannot be inferred from individual phylogenies alone. With a sufficient amount of genomic data now available, we have undertaken the first whole-genome phylogenetic analysis of the oomycetes using data from 37 oomycete species and 6 SAR species. In our analysis, we used established supertree methods to generate phylogenies from 8,355 homologous oomycete and SAR gene families and have complemented those analyses with both phylogenomic network and concatenated supermatrix analyses. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and individual clades within the problematic Phytophthora genus. Support for the resolution of the inferred relationships between individual Phytophthora clades varies depending on the methodology used. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. IMPORTANCE The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. PMID:28435885

A simultaneous multi-slice selective J-resolved experiment for fully resolved scalar coupling information

NASA Astrophysics Data System (ADS)

Zeng, Qing; Lin, Liangjie; Chen, Jinyong; Lin, Yanqin; Barker, Peter B.; Chen, Zhong

2017-09-01

Proton-proton scalar coupling plays an important role in molecular structure elucidation. Many methods have been proposed for revealing scalar coupling networks involving chosen protons. However, determining all JHH values within a fully coupled network remains as a tedious process. Here, we propose a method termed as simultaneous multi-slice selective J-resolved spectroscopy (SMS-SEJRES) for simultaneously measuring JHH values out of all coupling networks in a sample within one experiment. In this work, gradient-encoded selective refocusing, PSYCHE decoupling and echo planar spectroscopic imaging (EPSI) detection module are adopted, resulting in different selective J-edited spectra extracted from different spatial positions. The proposed pulse sequence can facilitate the analysis of molecular structures. Therefore, it will interest scientists who would like to efficiently address the structural analysis of molecules.

DNA barcoding of Rhodiola (crassulaceae): a case study on a group of recently diversified medicinal plants from the Qinghai-Tibetan Plateau.

PubMed

Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan

2015-01-01

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau.

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

PubMed

Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

2017-04-01

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. Copyright © 2016 Elsevier GmbH. All rights reserved.

Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes.

Treesearch

Richard C. Cronn; Randall L. Small; Tamara Hanselkorn; Jonathan F. Wendel

2002-01-01

Previous molecular phylogenetic studies have failed to resolve the branching order among the major cotton (Gossypium) lineages, and it has been unclear whether this reflects actual history (rapid radiation) or sampling properties of the genes evaluated. In this paper, we reconsider the phylogenetic relationships of diploid cotton genome groups using DNA sequences from...

Genetic structure of Eurasian and North American Leymus (Triticeae) wildryes assessed by chloroplast DNA sequences and AFLP profiles

Treesearch

C. Mae Culumber; Steve R. Larson; Kevin B. Jensen; Thomas A. Jones

2011-01-01

Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve...

Revision of Massylaea Möllendorff, 1898 (Stylommatophora, Helicidae)

PubMed Central

Bouaziz-Yahiatene, Houria; Pfarrer, Beat; Medjdoub-Bensaad, Ferroudja; Eike Neubert

2017-01-01

Abstract In this paper some helicoid species from eastern Algeria are investigated using a morphological and molecular approach. The investigation of the genital organs of M. massylaea (Morelet, 1851), the type species of the genus Massylaea Möllendorff, 1898, showed the same autapomorphic character states as are considered typical for Eobania P. Hesse, 1913. These findings are fully supported by the genetic analysis using two mitochondrial and three nuclear markers. Thus, the latter genus has to be considered a synonym of the former. Currently, three species are known to comprise the genus, viz. M. massylaea, M. constantina (E. Forbes, 1838), and M. vermiculata (O. F. Müller, 1774). Several nominal taxa from northern Africa are synonymised with one of the species mentioned here under Massylaea. The generic position of the so-called “Massylaea” species from the High Atlas Mountains in southern Morocco remains unresolved. PMID:29134002

A new genus and species of Platyischnopidae (Amphipoda: Gammaridea) from the Argentine sea, South-West Atlantic ocean.

PubMed

Chiesa, Ignacio L; Alonso, Gloria M

2014-05-30

The family Platyischnopidae is herein reported for the first time in the Argentine Sea, South-West Atlantic Ocean. A new genus and species, Platyisao holodividum gen. et. sp. nov., collected off the coast of Buenos Aires and Río Negro provinces, is fully described and illustrated. Platyisao gen. nov. is distinguished from the eight other genera of Platyischnopidae by the gnathopods subchelate, and the telson elongate, completely cleft. In addition, the distribution of Tiburonella viscana (Barnard J.L., 1964), up to now known in the South-West Atlantic Ocean from Brazilian waters, is extended to the coast off Buenos Aires province, Argentina.

Fully resolved simulations of expansion waves propagating into particle beds

NASA Astrophysics Data System (ADS)

Marjanovic, Goran; Hackl, Jason; Annamalai, Subramanian; Jackson, Thomas; Balachandar, S.

2017-11-01

There is a tremendous amount of research that has been done on compression waves and shock waves moving over particles but very little concerning expansion waves. Using 3-D direct numerical simulations, this study will explore expansion waves propagating into fully resolved particle beds of varying volume fractions and geometric arrangements. The objectives of these simulations are as follows: 1) To fully resolve all (1-way coupled) forces on the particles in a time varying flow and 2) to verify state-of-the-art drag models for such complex flows. We will explore a range of volume fractions, from very low ones that are similar to single particle flows, to higher ones where nozzling effects are observed between neighboring particles. Further, we will explore two geometric arrangements: body centered cubic and face centered cubic. We will quantify the effects that volume fraction and geometric arrangement plays on the drag forces and flow fields experienced by the particles. These results will then be compared to theoretical predictions from a model based on the generalized Faxen's theorem. This work was supported in part by the U.S. Department of Energy under the Predictive Science Academic Alliance Program, under Contract No. DE-NA0002378.

A molecular phylogeny for Cercocarpus H.B.K. (Rosaceae) using the external transcribed spacer of the nuclear ribosomal repeat

Treesearch

Brian D. Vanden Heuvel; C. Randal Linder

2001-01-01

Cercocarpus H.B.K. (Rosaceae) taxa are important members of the plant communities of the western states and Mexico, yet the systematics of this genus are unknown primarily from lack of clear morphological delimitations between taxa. In recent years, molecular data have proven useful for resolving relationships among species and the diversity within species that have...

DNA Barcoding of Rhodiola (Crassulaceae): A Case Study on a Group of Recently Diversified Medicinal Plants from the Qinghai-Tibetan Plateau

PubMed Central

Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan

2015-01-01

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences — rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) — for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau. PMID:25774915

Hidden diversity within the lizard genus Liolaemus: Genetic vs morphological divergence in the L. rothi complex (Squamata:Liolaeminae).

PubMed

Olave, Melisa; Avila, Luciano J; Sites, Jack W; Morando, Mariana

2017-02-01

Currently, Liolaemus is the second most species-rich reptile genus in the world (257 species), and predictions of its real diversity suggest that it may be the most diverse genus. Originally, Liolaemus species were described as widely distributed and morphologically variable taxa, but extensive sampling in previously unexplored geographic areas, coupled with molecular and more extensive morphological studies, have discovered an unexpectedly high number of previously undetected species. Here, we study the level of molecular vs. morphological divergence within the L. rothi complex, combining a total of 14 loci (2 mitochondrial and 12 nuclear loci) for 97 individuals, as well as morphological data (nine morphometric and 15 color pattern variables), that represent all six described species of the L. rothi complex, plus two candidate species. We use the multi-coalescent species delimitation program iBPP and resolve strong differences in molecular divergence; and each species is inferred as an independent lineage supported by high posterior probabilities. However, morphological differences are not that clear, and our modeling of morphological characters suggests differential selection pressures implying some level of morphological stasis. We discuss the role of natural selection on phenotypic traits, which may be an important factor in "hiding" the real diversity of the genus. Copyright © 2016. Published by Elsevier Inc.

Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species.

PubMed

Poyarkov, Nikolay A; Duong, Tang Van; Orlov, Nikolai L; Gogoleva, Svetlana S; Vassilieva, Anna B; Nguyen, Luan Thanh; Nguyen, Vu Dang Hoang; Nguyen, Sang Ngoc; Che, Jing; Mahony, Stephen

2017-01-01

Asian Mountain Toads ( Ophryophryne ) are a poorly known genus of mostly small-sized anurans from southeastern China and Indochina. To shed light on the systematics within this group, the most comprehensive mitochondrial DNA phylogeny for the genus to date is presented, and the taxonomy and biogeography of this group is discussed. Complimented with extensive morphological data (including associated statistical analyses), molecular data indicates that the Langbian Plateau, in the southern Annamite Mountains, Vietnam, is one of the diversity centres of this genus where three often sympatric species of Ophryophryne are found, O. gerti , O. synoria and an undescribed species. To help resolve outstanding taxonomic confusion evident in literature (reviewed herein), an expanded redescription of O. gerti is provided based on the examination of type material, and the distributions of both O. gerti and O. synoria are considerably revised based on new locality records. We provide the first descriptions of male mating calls for all three species, permitting a detailed bioacoustics comparison of the species. We describe the new species from highlands of the northern and eastern Langbian Plateau, and distinguish it from its congeners by a combination of morphological, molecular and acoustic characters. The new species represents one of the smallest known members of the genus Ophryophryne . At present, the new species is known from montane evergreen forest between 700-2200 m a.s.l. We suggest the species should be considered Data Deficient following IUCN's Red List categories.

Two new species of Piaroa (Arachnida: Schizomida, Hubbardiidae) from Colombia, with comments on the genus taxonomy and the flagellar setae pattern of Hubbardiinae.

PubMed

Moreno-González, Jairo A; Delgado-Santa, Leonardo; De Armas, Luis F

2014-08-14

Two new species of the genus Piaroa Villarreal, Tourinho & Giupponi, 2008, P. escalerete sp. nov. and P. bacata sp. nov. are described from Valle del Cauca, and Cundinamarca departments, Colombia, respectively. The female flagellum is fully illustrated for a Piaroa species for the first time; the generic diagnosis is also emended and the relationships of the new species with those previously described are discussed. New characters for Piaroa species, a new nomenclature for the chitinized arch and a reinterpretation of the Hubbardiinae flagellar setae pattern are proposed. A distribution map of the known species of Piaroa is provided. 

Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding

PubMed Central

2012-01-01

Background The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylogeny within the flowering plants are quite intriguing as several systems (Thorne system, Dahlgren system, Cronquist system, Takhtajan system and APG III system (Angiosperm Phylogeny Group III system) have attempted to redefine the Nymphaeales taxonomy. There have been also fossil records consisting especially of seeds, pollen, stems, leaves and flowers as early as the lower Cretaceous. Here we present an in silico study of the order Nymphaeales taking maturaseK (matK) and internal transcribed spacer (ITS2) as biomarkers for phylogeny reconstruction (using character-based methods and Bayesian approach) and identification of motifs for DNA barcoding. Results The Maximum Likelihood (ML) and Bayesian approach yielded congruent fully resolved and well-supported trees using a concatenated (ITS2+ matK) supermatrix aligned dataset. The taxon sampling corroborates the monophyly of Cabombaceae. Nuphar emerges as a monophyletic clade in the family Nymphaeaceae while there are slight discrepancies in the monophyletic nature of the genera Nymphaea owing to Victoria-Euryale and Ondinea grouping in the same node of Nymphaeaceae. ITS2 secondary structures alignment corroborate the primary sequence analysis. Hydatellaceae emerged as a sister clade to Nymphaeaceae and had a basal lineage amongst the water lilly clades. Species from Cycas and Ginkgo were taken as outgroups and were rooted in the overall tree topology from various methods. Conclusions MatK genes are fast evolving highly variant regions of plant chloroplast DNA that can serve as potential biomarkers for DNA barcoding and also in generating primers for angiosperms with identification of unique motif regions. We have reported unique genus specific motif regions in the Order Nymphaeles from matK dataset which can be further validated for barcoding and designing of PCR primers. Our analysis using a novel approach of sequence-structure alignment and phylogenetic reconstruction using molecular morphometrics congrue with the current placement of Hydatellaceae within the early-divergent angiosperm order Nymphaeales. The results underscore the fact that more diverse genera, if not fully resolved to be monophyletic, should be represented by all major lineages. PMID:23282079

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

PubMed Central

Schuster, Tanja M.; Setaro, Sabrina D.; Tibbits, Josquin F. G.; Batty, Erin L.; Fowler, Rachael M.; McLay, Todd G. B.; Wilcox, Stephen; Ades, Peter K.

2018-01-01

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9–10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes. PMID:29668710

Phylogeny and chromosomal diversification in the Dichroplus elongatus species group (Orthoptera, Melanoplinae).

PubMed

Castillo, Elio R D; Taffarel, Alberto; Maronna, Maximiliano M; Cigliano, María Marta; Palacios-Gimenez, Octavio M; Cabral-de-Mello, Diogo C; Martí, Dardo A

2017-01-01

In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus. However, we recovered several stable clades within the genus, including the D. elongatus species group, under the different strategies of tree analyses (Maximum Parsimony and Maximum Likelihood). The chromosomal data revealed minor variation in the D. elongatus species group's karyotypes caused by chromosome rearrangements compared to the phylogenetically related D. maculipennis species group. The karyotypes of D. intermedius and D. exilis described herein showed the standard characteristics found in most Dichroplini, 2n = 23/24, X0♂ XX♀, Fundamental number (FN) = 23/24. However, we noticed two established pericentric inversions in D. intermedius karyotype, raising the FN to 27♂/28♀. A strong variation in the heterochromatic blocks distribution was evidenced at interespecific level. The multigene families' mapping revealed significant variation, mainly in rDNA clusters. These variations are probably caused by micro chromosomal changes, such as movement of transposable elements (TEs) and ectopic recombination. These observations suggest a high genomic dynamism for these repetitive DNA sequences in related species. The reconstruction of the chromosome character "variation in the FN" posits the FN = 23/24 as the ancestral state, and it is hypothesized that variations due to pericentric inversions has arisen independently three times in the evolutionary history of Dichroplus. One of these independent events occurred in the D. elongatus species group, where D. intermedius is the unique case with the highest FN described in the tribe Dichroplini.

The cicada genus Guyalna Boulard & Martinelli, 1996 (Hemiptera: Cicadidae: Cicadinae: Fidicinini): generic description, twelve new combinations, and a key to species.

PubMed

Sanborn, Allen F

2016-04-25

The cicada genus Guyalna Boulard and Martinelli, 1996 is described fully for the first time. Dorisiana bogotana (Distant, 1892), Dorisiana brisa (Walker, 1850), Fidicinoides coffea Sanborn, Moore & Young, 2008, Fidicinoides distanti (Goding, 1925), Fidicinoides flavipronotum Sanborn, 2007, Dorisiana glauca (Goding, 1925), Dorisiana panamensis (Davis, 1939), Fidicinoides variegata (Sanborn, 2005), and Dorisiana viridifemur (Walker, 1850) are transferred to the genus Guyalna to become Guyalna bogotana (Distant, 1892) n. comb., Guyalna brisa (Walker, 1850) n. comb., Guyalna coffea (Sanborn, Moore & Young, 2008) n. comb., Guyalna distanti (Goding, 1925) n. comb., Guyalna flavipronotum (Sanborn, 2007) n. comb., Guyalna glauca (Goding, 1925) n. comb., Guyalna panamensis (Davis, 1939) n. comb., Guyalna variegata (Sanborn, 2005) n. comb., and Guyalna viridifemur (Walker, 1850) n. comb., respectively. Fidicinoides cachla (Distant, 1899), Fidicinoides compostela (Davis, 1934), Fidicinoides guayabana Sanborn, Moore & Young, 2008, are transferred to Dorisiana Metcalf, 1952 to become Dorisiana cachla (Distant, 1899) n. comb., Dorisiana compostela (Davis, 1934) n. comb., and Dorisiana guayabana (Sanborn, Moore & Young, 2008) n. comb., respectively. The current 25 species of the genus are listed along with their synonymies and known distribution of each species. Finally, a key to the species of Guyalna is provided.

Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae).

PubMed

Chen, Jin-Min; Poyarkov, Nikolay A; Suwannapoom, Chatmongkon; Lathrop, Amy; Wu, Yun-He; Zhou, Wei-Wei; Yuan, Zhi-Yong; Jin, Jie-Qiong; Chen, Hong-Man; Liu, He-Qun; Nguyen, Truong Quang; Nguyen, Sang Ngoc; Duong, Tang Van; Eto, Koshiro; Nishikawa, Kanto; Matsui, Masafumi; Orlov, Nikolai L; Stuart, Bryan L; Brown, Rafe M; Rowley, Jodi J L; Murphy, Robert W; Wang, Ying-Yong; Che, Jing

2018-07-01

Southeast Asia and southern China (SEA-SC) harbor a highly diverse and endemic flora and fauna that is under increasing threat. An understanding of the biogeographical history and drivers of this diversity is lacking, especially in some of the most diverse and threatened groups. The Asian leaf-litter frog genus Leptolalax Dubois 1980 is a forest-dependent genus distributed throughout SEA-SC, making it an ideal study group to examine specific biogeographic hypotheses. In addition, the diversity of this genus remains poorly understood, and the phylogenetic relationships among species of Leptolalax and closely related Leptobrachella Smith 1928 remain unclear. Herein, we evaluate species-level diversity based on 48 of the 53 described species from throughout the distribution of Leptolalax. Molecular analyses reveal many undescribed species, mostly in southern China and Indochina. Our well-resolved phylogeny based on multiple nuclear DNA markers shows that Leptolalax is not monophyletic with respect to Leptobrachella and, thus, we assign the former to being a junior synonym of the latter. Similarly, analyses reject monophyly of the two subgenera of Leptolalax. The diversification pattern of the group is complex, involving a high degree of sympatry and prevalence of microendemic species. Northern Sundaland (Borneo) and eastern Indochina (Vietnam) appear to have played pivotal roles as geographical centers of diversification, and paleoclimatic changes and tectonic movements seem to have driven the major divergence of clades. Analyses fail to reject an "upstream" colonization hypothesis, and, thus, the genus appears to have originated in Sundaland and then colonized mainland Asia. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns in the genus. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli▿

PubMed Central

Saffert, Ryan T.; Cunningham, Scott A.; Ihde, Sherry M.; Monson Jobe, Kristine E.; Mandrekar, Jayawant; Patel, Robin

2011-01-01

We compared the BD Phoenix automated microbiology system to the Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) system for identification of Gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. The BD Phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. The Bruker Biotyper correctly identified 408 (93%) and 360 (82%) isolates to the genus and species level, respectively. The 440 isolates were grouped into common (308) and infrequent (132) isolates in the clinical laboratory. For the 308 common isolates, the BD Phoenix and Bruker Biotyper correctly identified 294 (95%) and 296 (96%) of the isolates to the genus level, respectively. For species identification, the BD Phoenix and Bruker Biotyper correctly identified 93% of the common isolates (285 and 286, respectively). In contrast, for the 132 infrequent isolates, the Bruker Biotyper correctly identified 112 (85%) and 74 (56%) isolates to the genus and species level, respectively, compared to the BD Phoenix, which identified only 69 (52%) and 45 (34%) isolates to the genus and species level, respectively. Statistically, the Bruker Biotyper overall outperformed the BD Phoenix for identification of Gram-negative bacilli to the genus (P < 0.0001) and species (P = 0.0005) level in this sample set. When isolates were categorized as common or infrequent isolates, there was statistically no difference between the instruments for identification of common Gram-negative bacilli (P > 0.05). However, the Bruker Biotyper outperformed the BD Phoenix for identification of infrequently isolated Gram-negative bacilli (P < 0.0001). PMID:21209160

Three new species of blood flukes (Digenea: Aporocotylidae) infecting pufferfishes (Teleostei: Tetraodontidae) from off Bali, Indonesia.

PubMed

Yong, R Q-Y; Cutmore, S C; Bray, R A; Miller, T L; Semarariana, I W Y; Palm, H W; Cribb, T H

2016-10-01

We describe three new species of blood flukes (Aporocotylidae) and propose their classification within the genus Psettarium Goto & Ozaki, 1929. All three species were collected from the circulatory systems of pufferfishes caught off Bali, central Indonesia. Psettarium pulchellum n. sp. was found in the gills of both the narrow-lined puffer (Arothron manilensis de Procé) and the spiny blaasop (Tylerius spinosissimus Regan), while P. ogawai n. sp. and P. jimbaranense n. sp. were found in the gills of the reticulated puffer (Arothron reticularis Bloch & Schneider). The morphological characteristics of these taxa necessitated emendation of the diagnosis for the genus Psettarium, to accommodate the presence of an oral sucker, multiple or entirely post-caecal testes and a degenerate posterior testis. Features such as proportion of body length occupied by the oesophagus, and posterior caeca being ≥7× the length of anterior caeca, are no longer regarded as useful genus-level characters. Additionally, Sasala nolani is reassigned to this genus as Psettarium nolani n. comb. In phylogenetic analyses of the 28S and ITS2 rDNA regions, all three new taxa form a well-supported clade, together with Psettarium sinense and Psettarium nolani n. comb., the two other species of tetraodontid-infecting aporocotylids for which comparative rDNA data were available. The short branch lengths within this clade, despite dramatic morphological differences between the five species, suggest that rapid morphological diversification has occurred among the tetraodontid-infecting aporocotylids. The genus Psettarium has long been considered problematic. Further commentary is given on the history of this genus and how the issues presented might be resolved. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Revision of the Nearctic species of Nepalomyia Hollis (= Neurigonella Robinson) (Diptera: Dolichopodidae: Peloropeodinae) with a world catalog

Treesearch

Justin B. Runyon; Richard L. Hurley

2003-01-01

Nepalomyia Hollis and Neurigonella Robinson are synonymized. The genus Nepalomyia is more fully characterized and the Nearctic species are revised. Nepalomyia nigricornis (Van Duzee) and N. sombrea (Harmston & Knowlton) are reassigned and redescribed. Two new species, N. dilaticosta Runyon & Hurley and N. hesperia Runyon & Hurley, are described. New...

The second species of Phanoperla (Plecoptera: Perlidae) from China, P. hainana sp. nov., from Hainan Island.

PubMed

Li, Weihai; Qin, Xuefeng

2016-09-08

The genus Phanoperla Banks was originally established as a subgenus of Neoperla and its genus delimitation was not fully clear until the revisionary work by Zwick (1982). It currently contains 49 known species from the Oriental region (Banks 1938, 1939, Cao & Bae 2009, Cao et al. 2007, DeWalt et al. 2016, Jewett 1975, Kawai 1968, Stark 1983, 1987, Stark & Sheldon 2009, Sivec & Stark 2010, 2011, Stark & Sivec 2007, Sivec et al. 1988, Zwick 1982, Zwick 1986, Zwick & Sivec 1985). Although species of Phanoperla are not rare in many areas of Southeast Asia bordering China, especially Vietnam and India (Cao & Bae 2009, Mason & Stark 2015), P. pallipennis Banks, 1938 is the only known species of the genus known from China. In this paper, we describe a new species of Phanoperla from Hainan Island of the southernmost province of China. The northern portion of the island has a humid subtropical climate, whereas the remainder of the island has tropical monsoon climate.

Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species

PubMed Central

Jr., Nikolay A. Poyarkov; Duong, Tang Van; Orlov, Nikolai L.; Gogoleva, Svetlana S.; Vassilieva, Anna B.; Nguyen, Luan Thanh; Nguyen, Vu Dang Hoang; Nguyen, Sang Ngoc; Che, Jing; Mahony, Stephen

2017-01-01

Abstract Asian Mountain Toads (Ophryophryne) are a poorly known genus of mostly small-sized anurans from southeastern China and Indochina. To shed light on the systematics within this group, the most comprehensive mitochondrial DNA phylogeny for the genus to date is presented, and the taxonomy and biogeography of this group is discussed. Complimented with extensive morphological data (including associated statistical analyses), molecular data indicates that the Langbian Plateau, in the southern Annamite Mountains, Vietnam, is one of the diversity centres of this genus where three often sympatric species of Ophryophryne are found, O. gerti, O. synoria and an undescribed species. To help resolve outstanding taxonomic confusion evident in literature (reviewed herein), an expanded redescription of O. gerti is provided based on the examination of type material, and the distributions of both O. gerti and O. synoria are considerably revised based on new locality records. We provide the first descriptions of male mating calls for all three species, permitting a detailed bioacoustics comparison of the species. We describe the new species from highlands of the northern and eastern Langbian Plateau, and distinguish it from its congeners by a combination of morphological, molecular and acoustic characters. The new species represents one of the smallest known members of the genus Ophryophryne. At present, the new species is known from montane evergreen forest between 700–2200 m a.s.l. We suggest the species should be considered Data Deficient following IUCN’s Red List categories. PMID:28769667

Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.

PubMed

Kreipe, Victoria; Corral-Hernández, Elena; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

2015-06-01

Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

A dated phylogeny of the papilionoid legume genus Canavalia reveals recent diversification by a pantropical liana lineage.

PubMed

Snak, Cristiane; Vatanparast, Mohammad; Silva, Christian; Lewis, Gwilym Peter; Lavin, Matt; Kajita, Tadashi; Queiroz, Luciano Paganucci de

2016-05-01

Canavalia is a pantropical legume genus of lianas comprising approximately 60 species distributed in a wide range of habitats. In the last taxonomic revision, the genus was divided into four subgenera: Canavalia (Pantropical), Catodonia (Neotropical, excepting one species also found in the Old World), Maunaloa (Hawaiian), and Wenderothia (Neotropical). In this study, we reconstructed the phylogeny of Canavalia using a broad taxon sampling and analyses of nuclear (ETS and ITS) and plastid markers (trnK/matK). We evaluated the infrageneric classification of the genus and investigated its biogeographical history using molecular dating analyses and ancestral area reconstructions. The phylogenetic analyses resolved subgenus Wenderothia as monophyletic. Subgenus Catodonia needs to be recircumscribed and the relationships between subgenera Canavalia and Maunaloa remain unclear. Canavalia arose during the Miocene with a mean stem age estimate of 13.8Ma and mean crown age estimate of 8.7Ma, and most extant species evolved during the Pleistocene. Several climatic and geological events are chronologically coincident with the divergence of the major clades of Canavalia (glacial/interglacial periods, Andes uplift and the formation of Pebas and post-Pebas systems, closure of the Isthmus of Panama, and change in the direction of ocean currents). Ancestral area reconstructions for the early divergence of the genus are equivocal, although, some evidence suggests Canavalia originated in the wet forests of South America and achieved its current pantropical distribution through recent transoceanic dispersal. The evolution of Canavalia is better explained by a series of several processes than by discrete historical events. Copyright © 2016 Elsevier Inc. All rights reserved.

The Evolution of SINEs and LINEs in the genus Chironomus (Diptera).

PubMed

Papusheva, Ekaterina; Gruhl, Mary C; Berezikov, Eugene; Groudieva, Tatiana; Scherbik, Svetlana V; Martin, Jon; Blinov, Alexander; Bergtrom, Gerald

2004-03-01

Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.

Comparing Molecular Variation to Morphological Species Designations in the Deep-Sea Coral Narella Reveals New Insights into Seamount Coral Ranges

PubMed Central

Baco, Amy R.; Cairns, Stephen D.

2012-01-01

Recent studies have countered the paradigm of seamount isolation, confounding conservation efforts at a critical time. Efforts to study deep-sea corals, one of the dominant taxa on seamounts, to understand seamount connectivity, are hampered by a lack of taxonomic keys. A prerequisite for connectivity is species overlap. Attempts to better understand species overlap using DNA barcoding methods suggest coral species are widely distributed on seamounts and nearby features. However, no baseline has been established for variation in these genetic markers relative to morphological species designations for deep-sea octocoral families. Here we assess levels of genetic variation in potential octocoral mitochondrial barcode markers relative to thoroughly examined morphological species in the genus Narella. The combination of six markers used here, approximately 3350 bp of the mitochondrial genome, resolved 83% of the morphological species. Our results show that two of the markers, ND2 and NCR1, are not sufficient to resolve genera within Primnoidae, let alone species. Re-evaluation of previous studies of seamount octocorals based on these results suggest that those studies were looking at distributions at a level higher than species, possibly even genus or subfamily. Results for Narella show that using more markers provides haplotypes with relatively narrow depth ranges on the seamounts studied. Given the lack of 100% resolution of species with such a large portion of the mitochondrial genome, we argue that previous genetic studies have not resolved the degree of species overlap on seamounts and that we may not have the power to even test the hypothesis of seamount isolation using mitochondrial markers, let alone refute it. Thus a precautionary approach is advocated in seamount conservation and management, and the potential for depth structuring should be considered. PMID:23029093

What are the evolutionary mechanisms explaining the similar species richness patterns in tropical mosses? Insights from the phylogeny of the pantropical genus Pelekium.

PubMed

Norhazrina, Nik; Vanderpoorten, Alain; Hedenäs, Lars; Patiño, Jairo

2016-12-01

As opposed to angiosperms, moss species richness is similar among tropical regions of the world, in line with the hypothesis that tropical bryophytes are extremely good dispersers. Here, we reconstructed the phylogeny of the pantropical moss genus Pelekium to test the hypothesis that high migration rates erase any difference in species richness among tropical regions. In contrast with this hypothesis, several species considered to have a pantropical range were resolved as a complex of species with a strong geographic structure. Consequently, a significant phylogeographical signal was found in the data, evidencing that cladogenetic diversification within regions takes place at a faster rate than intercontinental migration. The shape of the Pelekium phylogeny, along with the selection of a constant-rate model of diversification among species in the genus, suggests, however, that the cladogenetic speciation patterns observed in Pelekium are not comparable to some of the spectacular examples of tropical radiations reported in angiosperms. Rather, the results presented here point to the constant accumulation of diversity through time in Pelekium. This, combined with evidence for long-distance dispersal limitations in the genus, suggests that the similar patterns of species richness among tropical areas are better explained in terms of comparable rates of diversification across tropical regions than by the homogenization of species richness by recurrent migrations. Copyright © 2016 Elsevier Inc. All rights reserved.

Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions.

PubMed

Fior, Simone; Li, Mingai; Oxelman, Bengt; Viola, Roberto; Hodges, Scott A; Ometto, Lino; Varotto, Claudio

2013-04-01

Aquilegia is a well-known model system in the field of evolutionary biology, but obtaining a resolved and well-supported phylogenetic reconstruction for the genus has been hindered by its recent and rapid diversification. Here, we applied 454 next-generation sequencing to PCR amplicons of 21 of the most rapidly evolving regions of the plastome to generate c. 24 kb of sequences from each of 84 individuals from throughout the genus. The resulting phylogeny has well-supported resolution of the main lineages of the genus, although recent diversification such as in the European taxa remains unresolved. By producing a chronogram of the whole Ranunculaceae family based on published data, we inferred calibration points for dating the Aquilegia radiation. The genus originated in the upper Miocene c. 6.9 million yr ago (Ma) in Eastern Asia, and diversification occurred c. 4.8 Ma with the split of two main clades, one colonizing North America, and the other Western Eurasia through the mountains of Central Asia. This was followed by a back-to-Asia migration, originating from the European stock using a North Asian route. These results provide the first backbone phylogeny and spatiotemporal reconstruction of the Aquilegia radiation, and constitute a robust framework to address the adaptative nature of speciation within the group. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

First South American Agathis (Araucariaceae), Eocene of Patagonia.

PubMed

Wilf, Peter; Escapa, Ignacio H; Cúneo, N Rubén; Kooyman, Robert M; Johnson, Kirk R; Iglesias, Ari

2014-01-01

Agathis is an iconic genus of large, ecologically important, and economically valuable conifers that range over lowland to upper montane rainforests from New Zealand to Sumatra. Exploitation of its timber and copal has greatly reduced the genus's numbers. The early fossil record of Agathis comes entirely from Australia, often presumed to be its area of origin. Agathis has no previous record from South America. We describe abundant macrofossils of Agathis vegetative and reproductive organs, from early and middle Eocene rainforest paleofloras of Patagonia, Argentina. The leaves were formerly assigned to the New World cycad genus Zamia. Agathis zamunerae sp. nov. is the first South American occurrence and the most complete representation of Agathis in the fossil record. Its morphological features are fully consistent with the living genus. The most similar living species is A. lenticula, endemic to lower montane rainforests of northern Borneo. Agathis zamunerae sp. nov. demonstrates the presence of modern-aspect Agathis by 52.2 mya and vastly increases the early range and possible areas of origin of the genus. The revision from Zamia breaks another link between the Eocene and living floras of South America. Agathis was a dominant, keystone element of the Patagonian Eocene floras, alongside numerous other plant taxa that still associate with it in Australasia and Southeast Asia. Agathis extinction in South America was an integral part of the transformation of Patagonian biomes over millions of years, but the living species are disappearing from their ranges at a far greater rate.

Morphological and Molecular Discrimination of Fasciola Species Isolated From Domestic Ruminants of Urmia City, Iran

PubMed Central

YAKHCHALI, Mohammad; MALEKZADEH-VIAYEH, Reza; IMANI-BARAN, Abbas; MARDANI, Karim

2015-01-01

Background: The trematodes of the genus Fasciola (the liver flukes) are among the well-known instances of food-borne parasites worldwide. Differentiation of Fasciola species is important because of their different transmission and epidemiological characteristics. The current study was undertaken to discriminate Fasciola species in the domestic ruminants of Urmia city, Iran. Methods: Adult flukes were isolated from the naturally infected livers of the slaughtered water buffaloes and sheep. The flukes were initially identified based on morphological and morphometric parameters. A 618-bp-long fragment of the 28SrRNA gene of Fasciola was amplified by polymerase chain reaction (PCR). The amplified fragment was digested by DraII or AvaII enzymes for a restriction fragment length polymorphism (RFLP) analysis and sequenced for the phylogenetic tree construction. Results: Based on the morphometric examination, the flukes belonged to F. hepatica, F. gigantica and an intermediate Fasciola form. The PCR-RFLP analysis was able to differentiate F. hepatica from F. gigantica. While the phylogenetic reconstruction justified, to some extent, the morphological diagnosis, it failed to segregate F. hepatica from F. gigantica identified in this and the previous studies. Conclusion: To resolve fully the problem of taxonomy and evolution in Fasciola species, employing a broad range of molecular and morphological approaches is necessary. This is crucial for epidemiological surveys and successful clinical management of their infection. PMID:25904945

Biochemical acclimation, stomatal limitation and precipitation patterns underlie decreases in photosynthetic stimulation of Soybean (Glycine max) at elevated [CO2] and temperatures under fully open air field conditions

USDA-ARS?s Scientific Manuscript database

The net effect of elevated [CO2] and temperature on photosynthetic acclimation and plant productivity is poorly resolved. We assessed the effects of canopy warming and fully open air [CO2] enrichment on 1) the acclimation of two biochemical parameters that frequently limit photosynthesis (A), the ma...

Fast reconstruction of optical properties for complex segmentations in near infrared imaging

NASA Astrophysics Data System (ADS)

Jiang, Jingjing; Wolf, Martin; Sánchez Majos, Salvador

2017-04-01

The intrinsic ill-posed nature of the inverse problem in near infrared imaging makes the reconstruction of fine details of objects deeply embedded in turbid media challenging even for the large amounts of data provided by time-resolved cameras. In addition, most reconstruction algorithms for this type of measurements are only suitable for highly symmetric geometries and rely on a linear approximation to the diffusion equation since a numerical solution of the fully non-linear problem is computationally too expensive. In this paper, we will show that a problem of practical interest can be successfully addressed making efficient use of the totality of the information supplied by time-resolved cameras. We set aside the goal of achieving high spatial resolution for deep structures and focus on the reconstruction of complex arrangements of large regions. We show numerical results based on a combined approach of wavelength-normalized data and prior geometrical information, defining a fully parallelizable problem in arbitrary geometries for time-resolved measurements. Fast reconstructions are obtained using a diffusion approximation and Monte-Carlo simulations, parallelized in a multicore computer and a GPU respectively.

Using a bias aware EnKF to account for unresolved structure in an unsaturated zone model

NASA Astrophysics Data System (ADS)

Erdal, D.; Neuweiler, I.; Wollschläger, U.

2014-01-01

When predicting flow in the unsaturated zone, any method for modeling the flow will have to define how, and to what level, the subsurface structure is resolved. In this paper, we use the Ensemble Kalman Filter to assimilate local soil water content observations from both a synthetic layered lysimeter and a real field experiment in layered soil in an unsaturated water flow model. We investigate the use of colored noise bias corrections to account for unresolved subsurface layering in a homogeneous model and compare this approach with a fully resolved model. In both models, we use a simplified model parameterization in the Ensemble Kalman Filter. The results show that the use of bias corrections can increase the predictive capability of a simplified homogeneous flow model if the bias corrections are applied to the model states. If correct knowledge of the layering structure is available, the fully resolved model performs best. However, if no, or erroneous, layering is used in the model, the use of a homogeneous model with bias corrections can be the better choice for modeling the behavior of the system.

Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

PubMed Central

Ludeña, Bertha; Chabrillange, Nathalie; Aberlenc-Bertossi, Frédérique; Adam, Hélène; Tregear, James W.; Pintaud, Jean-Christophe

2011-01-01

Background and Aims Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics. Methods New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated. Key Results The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics. Conclusions AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies. PMID:21828068

Complete genome sequence of Thauera aminoaromatica strain MZ1T

PubMed Central

Jiang, Ke; Sanseverino, John; Chauhan, Archana; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Del Rio, Tijana Glavina; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Chang, Y.J.; Larimer, Frank; Land, Miriam; Hauser, Loren; Kyrpides, Nikos C.; Mikhailova, Natalia; Moser, Scott; Jegier, Patricia; Close, Dan; DeBruyn, Jennifer M.; Wang, Ying; Layton, Alice C.; Allen, Michael S.; Sayler, Gary S.

2012-01-01

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Sequencing Program CSP_776774. PMID:23407619

A new genus of horse from Pleistocene North America

PubMed Central

Zazula, Grant D; MacPhee, Ross DE; Scott, Eric; Cahill, James A; McHorse, Brianna K; Kapp, Joshua D; Stiller, Mathias; Wooller, Matthew J; Orlando, Ludovic; Southon, John; Froese, Duane G

2017-01-01

The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event. PMID:29182148

Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers.

PubMed

Sarower, Mohammed Golam; Shahriar, Sheik Istiak Md; Nakamura, Hiromasa; Rouf, Muhammad Abdur; Okada, Shigeru

2017-11-01

Taxonomy of mud crabs genus Scylla has been misidentified for several years due to their high morphological plasticity. Several reports concerning mud crab have been published with misleading identification in Bangladesh. In this study, partial fragments of nuclear and mitochondrial DNA of Scylla species obtained from four locations along the Bangladesh coast were used to resolve taxonomical ambiguity of mud crab species. A single PCR product from the nuclear first internal transcribed spacer (ITS-1) marker and phylogenetic trees constructed based on 16S rDNA sequences indicated that all Scylla species obtained in this study were S. olivacea. Both molecular data and morphological characters revealed that S. olivacea is the only major species in Bangladesh coastal waters. Further, the 16S rDNA haplotypes significantly differed with known S. serrata by 33%. From this study it is clear that 'S. serrata' commonly reported from Bangladesh should be S. olivacea.

Performance and microbial community analysis of the anaerobic reactor with coke oven gas biomethanation and in situ biogas upgrading.

PubMed

Wang, Wen; Xie, Li; Luo, Gang; Zhou, Qi; Angelidaki, Irini

2013-10-01

A new method for simultaneous coke oven gas (COG) biomethanation and in situ biogas upgrading in anaerobic reactor was developed in this study. The simulated coke oven gas (SCOG) (92% H2 and 8% CO) was injected directly into the anaerobic reactor treating sewage sludge through hollow fiber membrane (HFM). With pH control at 8.0, the added H2 and CO were fully consumed and no negative effects on the anaerobic degradation of sewage sludge were observed. The maximum CH4 content in the biogas was 99%. The addition of SCOG resulted in enrichment and dominance of homoacetogenetic genus Treponema and hydrogenotrophic genus Methanoculleus in the liquid, which indicated that H2 were converted to methane by both direct (hydrogenotrophic methanogenesis) and indirect (homoacetogenesis+aceticlastic methanogenesis) pathways in the liquid. However, the aceticlasitic genus Methanosaeta was dominant for archaea in the biofilm on the HFM, which indicated indirect (homoacetogenesis+aceticlastic methanogenesis) H2 conversion pathway on the biofilm. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evolution through cold and deep waters: the molecular phylogeny of the Lithodidae (Crustacea: Decapoda)

NASA Astrophysics Data System (ADS)

Hall, Sally; Thatje, Sven

2018-04-01

The objectives of this work are to use gene sequence data to assess the hypothesis that the Lithodinae arose from ancestors with uncalcified abdomens in shallow waters of the North-East Pacific, investigate the monophyly and interrelationships of genera within the Lithodinae and to estimate the scale and minimum number of biogeographic transitions from the shallow environment to the deep sea and vice versa. To do this, phylogenetic analysis from three mitochondrial and three nuclear markers was conducted using minimum evolution, maximum likelihood and Bayesian methods. The Lithodinae as defined to include North Pacific genus Cryptolithodes may be paraphyletic, with the Hapalogastrinae and Cryptolithodes as sister taxa. This implies that the soft-bodied abdomen of the Hapalogastrinae might not be plesiomorphic for the Lithodidae. Paralomis, Lopholithodes, Phyllolithodes, Lithodes and Neolithodes share a common ancestor, from which the North Pacific Hapalogastrinae did not descend. Lithodid ancestors are likely to have had a north Pacific, shallow water distribution and to have had planktotrophic larvae. North Pacific genus Paralithodes is paraphyletic; P. brevipes is the most basal member of the genus (as sampled) while P. camtschaticus and P. platypus are more closely related to the genera Lithodes and Neolithodes. Genera Lithodes, Neolithodes and Paralomis (as sampled) are monophyletic if Glyptolithodes is included within Paralomis. Lopholithodes is closely related to, but not included within, the Paralomis genus. Paralomis is divided into at least two major lineages: one containing South Atlantic, West African, and Indian Ocean species, and the other containing Pacific and South American species. Several species of Paralomis do not resolve consistently with any other groups sampled, implying a complex and possibly rapid global evolution early in the history of the genus. Relationships within the Lithodes genus vary between analytical methods, suggesting that conclusions may not be stable. Consistently, however, Indian Ocean and Pacific forms— L. murrayi, L. longispina and L. nintokuae form a group separated from Atlantic species such as L. santolla, L. confundens, L. maja and L. ferox.

Evolution through cold and deep waters: the molecular phylogeny of the Lithodidae (Crustacea: Decapoda).

PubMed

Hall, Sally; Thatje, Sven

2018-02-27

The objectives of this work are to use gene sequence data to assess the hypothesis that the Lithodinae arose from ancestors with uncalcified abdomens in shallow waters of the North-East Pacific, investigate the monophyly and interrelationships of genera within the Lithodinae and to estimate the scale and minimum number of biogeographic transitions from the shallow environment to the deep sea and vice versa. To do this, phylogenetic analysis from three mitochondrial and three nuclear markers was conducted using minimum evolution, maximum likelihood and Bayesian methods. The Lithodinae as defined to include North Pacific genus Cryptolithodes may be paraphyletic, with the Hapalogastrinae and Cryptolithodes as sister taxa. This implies that the soft-bodied abdomen of the Hapalogastrinae might not be plesiomorphic for the Lithodidae. Paralomis, Lopholithodes, Phyllolithodes, Lithodes and Neolithodes share a common ancestor, from which the North Pacific Hapalogastrinae did not descend. Lithodid ancestors are likely to have had a north Pacific, shallow water distribution and to have had planktotrophic larvae. North Pacific genus Paralithodes is paraphyletic; P. brevipes is the most basal member of the genus (as sampled) while P. camtschaticus and P. platypus are more closely related to the genera Lithodes and Neolithodes. Genera Lithodes, Neolithodes and Paralomis (as sampled) are monophyletic if Glyptolithodes is included within Paralomis. Lopholithodes is closely related to, but not included within, the Paralomis genus. Paralomis is divided into at least two major lineages: one containing South Atlantic, West African, and Indian Ocean species, and the other containing Pacific and South American species. Several species of Paralomis do not resolve consistently with any other groups sampled, implying a complex and possibly rapid global evolution early in the history of the genus. Relationships within the Lithodes genus vary between analytical methods, suggesting that conclusions may not be stable. Consistently, however, Indian Ocean and Pacific forms-L. murrayi, L. longispina and L. nintokuae form a group separated from Atlantic species such as L. santolla, L. confundens, L. maja and L. ferox.

Towards a Fine-Resolution Global Coupled Climate System for Prediction on Decadal/Centennial Scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

McClean, Julie L.

The over-arching goal of this project was to contribute to the realization of a fully coupled fine resolution Earth System Model simulation in which a weather-scale atmosphere is coupled to an ocean in which mesoscale eddies are largely resolved. Both a prototype fine-resolution fully coupled ESM simulation and a first-ever multi-decadal forced fine-resolution global coupled ocean/ice simulation were configured, tested, run, and analyzed as part of this grant. Science questions focused on the gains from the use of high horizontal resolution, particularly in the ocean and sea-ice, with respect to climatically important processes. Both these fine resolution coupled ocean/sea icemore » and fully-coupled simulations and precedent stand-alone eddy-resolving ocean and eddy-permitting coupled ocean/ice simulations were used to explore the high resolution regime. Overall, these studies showed that the presence of mesoscale eddies significantly impacted mixing processes and the global meridional overturning circulation in the ocean simulations. Fourteen refereed publications and a Ph.D. dissertation resulted from this grant.« less

ELF communications system ecological monitoring program: Pollinating insect studies

NASA Astrophysics Data System (ADS)

Strickler, Karen; Schriber, J. Mark

1994-11-01

High voltage transmission lines and the earth's and other magnetic fields have been shown to affect honeybee reproduction, survival, orientation, and nest structure. ELY EM fields could have similar effects on native megachilid bees. Two species in the genus Megachile were abundant in artificial nests at experimental and control areas in Dickinson and Iron Counties in Michigan. Data on their nest architecture, nest activity, and emergence/mortality were collected between 1983 and 1993. Eight hypotheses concerning the possible effects of ELY EM fields were considered using these data. The ELY antenna has been fully operational since the summer of 1989. Tests of the hypotheses compare control vs. experimental areas before and after the ELY antenna became fully operational.

Optimizing identification of clinically relevant Gram-positive organisms by use of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

PubMed

McElvania Tekippe, Erin; Shuey, Sunni; Winkler, David W; Butler, Meghan A; Burnham, Carey-Ann D

2013-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including "heavy" (H) and "light" (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or "score." We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS.

Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum

PubMed Central

Hawkins, Jennifer S.; Ramachandran, Dhanushya; Henderson, Ashley; Freeman, Jasmine; Carlise, Michael; Harris, Alex; Willison-Headley, Zachary

2015-01-01

Background and Aims Sorghum is an essential grain crop whose evolutionary placement within the Andropogoneae has been the subject of scrutiny for decades. Early studies using cytogenetic and morphological data point to a poly- or paraphyletic origin of the genus; however, acceptance of poly- or paraphyly has been met with resistance. This study aimed to address the species relationships within Sorghum, in addition to the placement of Sorghum within the tribe, using a phylogenetic approach and employing broad taxon sampling. Methods From 16 diverse Sorghum species, eight low-copy nuclear loci were sequenced that are known to play a role in morphological diversity and have been previously used to study evolutionary relationships in grasses. Further, the data for four of these loci were combined with those from 57 members of the Andropogoneae in order to determine the placement of Sorghum within the tribe. Both maximum likelihood and Bayesian analyses were performed on multilocus concatenated data matrices. Key Results The Sorghum-specific topology provides strong support for two major lineages, in alignment with earlier studies employing chloroplast and internal transcribed spacer (ITS) markers. Clade I is composed of the Eu-, Chaeto- and Heterosorghum, while clade II contains the Stipo- and Parasorghum. When combined with data from the Andropogoneae, Clade II resolves as sister to a clade containing Miscanthus and Saccharum with high posterior probability and bootstrap support, and to the exclusion of Clade I. Conclusions The results provide compelling evidence for a two-lineage polyphyletic ancestry of Sorghum within the larger Andropogoneae, i.e. the derivation of the two major Sorghum clades from a unique common ancestor. Rejection of monophyly in previous molecular studies is probably due to limited taxon sampling outside of the genus. The clade consisting of Para- and Stiposorghum resolves as sister to Miscanthus and Saccharum with strong node support. PMID:26141132

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae)

PubMed Central

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x–18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System

PubMed Central

McElvania TeKippe, Erin; Shuey, Sunni; Winkler, David W.; Butler, Meghan A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS. PMID:23426925

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

PubMed

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

Morphological and Molecular Revision of the Genus Ozirhincus (Diptera: Cecidomyiidae)—Long-Snouted Seed-Feeding Gall Midges on Asteraceae

PubMed Central

Dorchin, Netta; Astrin, Jonas J.; Bodner, Levona; Harris, Keith M.

2015-01-01

The Palaearctic gall-midge genus Ozirhincus is unique among the Cecidomyiidae for its morphology and biology. Unlike most other phytophagous gall midges, species in this genus do not induce galls but develop inside achenes of Asteraceae plants. The heads of adults are characterized by an unusually elongate proboscis, the function of which is unclear. Despite a lot of attention from taxonomists in the 19th and early 20th century, a proper revision of the genus has been hindered by complex host associations, the loss of most relevant type material, and the lack of a thorough comparative study of all life stages. The present revision integrated morphological, molecular, and life-history data to clearly define species boundaries within Ozirhincus, and delimit host-plant ranges for each of them. A phylogenetic analysis based on the mitochondrial COI and 16S genes confirmed the validity of four distinct species but did not resolve the relationships among them. All species are oligophages, and some may occur together on the same host plant. Species with wider host-plant ranges have wider European and circum-Mediterranean distribution ranges, whereas species with narrower host ranges are limited to Europe and the Russian Far East. As part of the present work, O. hungaricus is reinstated from synonymy, O. tanaceti is synonymized under O. longicollis, neotypes are designated for O. longicollis and O. millefolii, and a lectotype is designated for O. anthemidis. PMID:26134526

Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

PubMed

Leaché, Adam D; Banbury, Barbara L; Linkem, Charles W; de Oca, Adrián Nieto-Montes

2016-03-22

Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20-25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

Prediction of the thermal imaging minimum resolvable (circle) temperature difference with neural network application.

PubMed

Fang, Yi-Chin; Wu, Bo-Wen

2008-12-01

Thermal imaging is an important technology in both national defense and the private sector. An advantage of thermal imaging is its ability to be deployed while fully engaged in duties, not limited by weather or the brightness of indoor or outdoor conditions. However, in an outdoor environment, many factors, including atmospheric decay, target shape, great distance, fog, temperature out of range and diffraction limits can lead to bad image formation, which directly affects the accuracy of object recognition. The visual characteristics of the human eye mean that it has a much better capacity for picture recognition under normal conditions than artificial intelligence does. However, conditions of interference significantly reduce this capacity for picture recognition for instance, fatigue impairs human eyesight. Hence, psychological and physiological factors can affect the result when the human eye is adopted to measure MRTD (minimum resolvable temperature difference) and MRCTD (minimum resolvable circle temperature difference). This study explores thermal imaging recognition, and presents a method for effectively choosing the characteristic values and processing the images fully. Neural network technology is successfully applied to recognize thermal imaging and predict MRTD and MRCTD (Appendix A), exceeding thermal imaging recognition under fatigue and the limits of the human eye.

Understanding Unimer Exchange Processes in Block Copolymer Micelles using NMR Diffusometry, Time-Resolved NMR, and SANS

NASA Astrophysics Data System (ADS)

Madsen, Louis; Kidd, Bryce; Li, Xiuli; Miller, Katherine; Cooksey, Tyler; Robertson, Megan

Our team seeks to understand dynamic behaviors of block copolymer micelles and their interplay with encapsulated cargo molecules. Quantifying unimer and cargo exchange rates micelles can provide critical information for determining mechanisms of unimer exchange as well as designing systems for specific cargo release dynamics. We are exploring the utility of NMR spectroscopy and diffusometry techniques as complements to existing SANS and fluorescence methods. One promising new method involves time-resolved NMR spin relaxation measurements, wherein mixing of fully protonated and 2H-labeled PEO-b-PCL micelles solutions shows an increase in spin-lattice relaxation time (T1) with time after mixing. This is due to a weakening in magnetic environment surrounding 1H spins as 2H-bearing unimers join fully protonated micelles. We are measuring time constants for unimer exchange of minutes to hours, and we expect to resolve times of <1 min. This method can work on any solution NMR spectrometer and with minimal perturbation to chemical structure (as in dye-labelled fluorescence methods). Multimodal NMR can complement existing characterization tools, expanding and accelerating dynamics measurements for polymer micelle, nanogel, and nanoparticle developers.

Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists.

PubMed

Zhao, Yan; Yi, Zhenzhen; Gentekaki, Eleni; Zhan, Aibin; Al-Farraj, Saleh A; Song, Weibo

2016-01-01

Ciliates comprise a highly diverse protozoan lineage inhabiting all biotopes and playing crucial roles in regulating microbial food webs. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. Here, we use the species-rich taxon Frontonia and employ both nuclear and mitochondrial loci. We attempt to assess the level of genetic diversity and evaluate the potential of each marker in delineating species of Frontonia. Morphological features and ecological characteristics are also integrated into genetic results, in an attempt to resolve conflicts of species identification based on morphological and molecular methods. Our studies reveal: (1) the mitochondrial cox1 gene, nuclear ITS1 and ITS2 as well as the hypervariable D2 region of LSU rDNA are promising candidates for species delineation; (2) the cox1 gene provides the best resolution for analyses below the species level; (3) the V2 and V4 hypervariable regions of SSU rDNA, and D1 of LSU rDNA as well as the 5.8S rDNA gene do not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences; (4) morphological character-based analysis shows promise for delimitation of Frontonia species; and (5) all gene markers and character-based analyses demonstrate that the genus Frontonia consists of three groups and monophyly of the genus Frontonia is questionable. Copyright © 2015 Elsevier Inc. All rights reserved.

Gene structure and evolution of transthyretin in the order Chiroptera.

PubMed

Khwanmunee, Jiraporn; Leelawatwattana, Ladda; Prapunpoj, Porntip

2016-02-01

Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested.

Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora

PubMed Central

Choudhury, Robin A.; Mehl, Heather K.; Blomquist, Cheryl L.; McRoberts, Neil; Rizzo, David M.

2018-01-01

Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the “subgeneric” clades of Phytophthora, which include twenty downy mildew genera and hundreds of species. PMID:29529094

Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora.

PubMed

Bourret, Tyler B; Choudhury, Robin A; Mehl, Heather K; Blomquist, Cheryl L; McRoberts, Neil; Rizzo, David M

2018-01-01

Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.

Fictitious domain method for fully resolved reacting gas-solid flow simulation

NASA Astrophysics Data System (ADS)

Zhang, Longhui; Liu, Kai; You, Changfu

2015-10-01

Fully resolved simulation (FRS) for gas-solid multiphase flow considers solid objects as finite sized regions in flow fields and their behaviours are predicted by solving equations in both fluid and solid regions directly. Fixed mesh numerical methods, such as fictitious domain method, are preferred in solving FRS problems and have been widely researched. However, for reacting gas-solid flows no suitable fictitious domain numerical method has been developed. This work presents a new fictitious domain finite element method for FRS of reacting particulate flows. Low Mach number reacting flow governing equations are solved sequentially on a regular background mesh. Particles are immersed in the mesh and driven by their surface forces and torques integrated on immersed interfaces. Additional treatments on energy and surface reactions are developed. Several numerical test cases validated the method and a burning carbon particles array falling simulation proved the capability for solving moving reacting particle cluster problems.

Three computational mise-en-scènes of red- and blue-shifted hydrogen bonding motifs: Concept of negative intramolecular coupling-What else?

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.

This work is a kind of attempt to rethink some problems which are related to the blue-shifted "hydrogen bonds" and which have been left in the past decade as not yet fully resolved. The impetus for such rethink is originated from the three computational mise-en-scènes on red- and blue-shifted hydrogen bonding motifs, which are aimed to be thoroughly studied in this work, thus resolving the above problems.

Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean.

PubMed

Divya, P R; Mohitha, C; Rahul, G Kumar; Rajool Shanis, C P; Basheer, V S; Gopalakrishnan, A

2017-04-01

Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence. Copyright © 2017 Elsevier Inc. All rights reserved.

TOWARD A MOLECULAR PHYLOGENY FOR PEROMYSCUS: EVIDENCE FROM MITOCHONDRIAL CYTOCHROME-b SEQUENCES

PubMed Central

Bradley, Robert D.; Durish, Nevin D.; Rogers, Duke S.; Miller, Jacqueline R.; Engstrom, Mark D.; Kilpatrick, C. William

2009-01-01

One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data. PMID:19924266

The topology of galaxy clustering.

NASA Astrophysics Data System (ADS)

Coles, P.; Plionis, M.

The authors discuss an objective method for quantifying the topology of the galaxy distribution using only projected galaxy counts. The method is a useful complement to fully three-dimensional studies of topology based on the genus by virtue of the enormous projected data sets available. Applying the method to the Lick counts they find no evidence for large-scale non-gaussian behaviour, whereas the small-scale distribution is strongly non-gaussian, with a shift in the meatball direction.

From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides

PubMed Central

2011-01-01

Background Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some microhylid subfamilies, and therefore subfamilial affiliations of some genera are still unclear. To elucidate the phylogenetic positions of two mysterious Asian genera, Gastrophrynoides and Phrynella, and to better understand the trans-continental distributions of microhylid taxa, we performed molecular phylogenetic and dating analyses using the largest molecular dataset applied to these taxa to date. Results Six nuclear and two mitochondrial genes (approx. 8 kbp) were sequenced from 22 microhylid frog species representing eight subfamilies. The maximum likelihood and Bayesian analyses could not fully elucidate the subfamilial relationships, suggesting a rapid radiation of these taxa between 85 and 66 million years ago. In contrast, generic relationships of Asian microhylines were generally well resolved. Conclusion Our results clearly showed that one of two problematic Asian genera, Phrynella, was nested in the clade of the Asian subfamily Microhylinae. By contrast, Gastrophrynoides occupied the most basal position of the Australian-New Guinean subfamily Asterophryinae. The estimated divergence of Gastrophrynoides from other asterophryine was unexpectedly around 48 million years ago. Although a colonization scenario via Antarctica to the Australian-New Guinean landmass has been suggested for Asterophryinae, our finding suggested a novel colonization route via Indo-Eurasia. PMID:21689462

From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides.

PubMed

Kurabayashi, Atsushi; Matsui, Masafumi; Belabut, Daicus M; Yong, Hoi-Sen; Ahmad, Norhayati; Sudin, Ahmad; Kuramoto, Mitsuru; Hamidy, Amir; Sumida, Masayuki

2011-06-21

Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some microhylid subfamilies, and therefore subfamilial affiliations of some genera are still unclear. To elucidate the phylogenetic positions of two mysterious Asian genera, Gastrophrynoides and Phrynella, and to better understand the trans-continental distributions of microhylid taxa, we performed molecular phylogenetic and dating analyses using the largest molecular dataset applied to these taxa to date. Six nuclear and two mitochondrial genes (approx. 8 kbp) were sequenced from 22 microhylid frog species representing eight subfamilies. The maximum likelihood and Bayesian analyses could not fully elucidate the subfamilial relationships, suggesting a rapid radiation of these taxa between 85 and 66 million years ago. In contrast, generic relationships of Asian microhylines were generally well resolved. Our results clearly showed that one of two problematic Asian genera, Phrynella, was nested in the clade of the Asian subfamily Microhylinae. By contrast, Gastrophrynoides occupied the most basal position of the Australian-New Guinean subfamily Asterophryinae. The estimated divergence of Gastrophrynoides from other asterophryine was unexpectedly around 48 million years ago. Although a colonization scenario via Antarctica to the Australian-New Guinean landmass has been suggested for Asterophryinae, our finding suggested a novel colonization route via Indo-Eurasia.

Medicinal chemistry and pharmacology of genus Tripterygium (Celastraceae)

PubMed Central

Brinker, Anita M.; Ma, Jun; Lipsky, Peter E.; Raskin, Ilya

2013-01-01

Plants in the genus Tripterygium, such as Tripterygium wilfordii Hook. f., have a long history of use in traditional Chinese medicine. In recent years there has been considerable interest in the use of Tripterygium extracts and of the main bioactive constituent, the diterpene triepoxide triptolide (1), to treat a variety of autoimmune and inflammation-related conditions. The main mode of action of the Tripterygium extracts and triptolide (1) is the inhibition of expression of proinflammatory genes such as those for interleukin-2 (IL-2), inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX-2) and interferon-gamma (IFN-γ). The efficacy and safety of certain types of Tripterygium extracts were confirmed in human clinical trials in the US and abroad. Over 300 compounds have been identified in the genus Tripterygium, and many of these have been evaluated for biological activity. The overall activity of the extract is based on the interaction between its components. Therefore, the safety and efficacy of the extract cannot be fully mimicked by any individual constituent. This review discusses the biochemical composition and biological and pharmacological activities of Tripterygium extracts, and their main bioactive components. PMID:17250858

Medicinal chemistry and pharmacology of genus Tripterygium (Celastraceae).

PubMed

Brinker, Anita M; Ma, Jun; Lipsky, Peter E; Raskin, Ilya

2007-03-01

Plants in the genus Tripterygium, such as Tripterygium wilfordii Hook.f., have a long history of use in traditional Chinese medicine. In recent years there has been considerable interest in the use of Tripterygium extracts and of the main bioactive constituent, the diterpene triepoxide triptolide (1), to treat a variety of autoimmune and inflammation-related conditions. The main mode of action of the Tripterygium extracts and triptolide (1) is the inhibition of expression of proinflammatory genes such as those for interleukin-2 (IL-2), inducible nitric oxide synthase (iNOS), tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase-2 (COX-2) and interferon-gamma (IFN-gamma). The efficacy and safety of certain types of Tripterygium extracts were confirmed in human clinical trials in the US and abroad. Over 300 compounds have been identified in the genus Tripterygium, and many of these have been evaluated for biological activity. The overall activity of the extract is based on the interaction between its components. Therefore, the safety and efficacy of the extract cannot be fully mimicked by any individual constituent. This review discusses the biochemical composition and biological and pharmacological activities of Tripterygium extracts, and their main bioactive components.

Fully digital routing logic for single-photon avalanche diode arrays in highly efficient time-resolved imaging

NASA Astrophysics Data System (ADS)

Cominelli, Alessandro; Acconcia, Giulia; Ghioni, Massimo; Rech, Ivan

2018-03-01

Time-correlated single-photon counting (TCSPC) is a powerful optical technique, which permits recording fast luminous signals with picosecond precision. Unfortunately, given its repetitive nature, TCSPC is recognized as a relatively slow technique, especially when a large time-resolved image has to be recorded. In recent years, there has been a fast trend toward the development of TCPSC imagers. Unfortunately, present systems still suffer from a trade-off between number of channels and performance. Even worse, the overall measurement speed is still limited well below the saturation of the transfer bandwidth toward the external processor. We present a routing algorithm that enables a smart connection between a 32×32 detector array and five shared high-performance converters able to provide an overall conversion rate up to 10 Gbit/s. The proposed solution exploits a fully digital logic circuit distributed in a tree structure to limit the number and length of interconnections, which is a major issue in densely integrated circuits. The behavior of the logic has been validated by means of a field-programmable gate array, while a fully integrated prototype has been designed in 180-nm technology and analyzed by means of postlayout simulations.

Development of a fully implicit particle-in-cell scheme for gyrokinetic electromagnetic turbulence simulation in XGC1

NASA Astrophysics Data System (ADS)

Ku, Seung-Hoe; Hager, R.; Chang, C. S.; Chacon, L.; Chen, G.; EPSI Team

2016-10-01

The cancelation problem has been a long-standing issue for long wavelengths modes in electromagnetic gyrokinetic PIC simulations in toroidal geometry. As an attempt of resolving this issue, we implemented a fully implicit time integration scheme in the full-f, gyrokinetic PIC code XGC1. The new scheme - based on the implicit Vlasov-Darwin PIC algorithm by G. Chen and L. Chacon - can potentially resolve cancelation problem. The time advance for the field and the particle equations is space-time-centered, with particle sub-cycling. The resulting system of equations is solved by a Picard iteration solver with fixed-point accelerator. The algorithm is implemented in the parallel velocity formalism instead of the canonical parallel momentum formalism. XGC1 specializes in simulating the tokamak edge plasma with magnetic separatrix geometry. A fully implicit scheme could be a way to accurate and efficient gyrokinetic simulations. We will test if this numerical scheme overcomes the cancelation problem, and reproduces the dispersion relation of Alfven waves and tearing modes in cylindrical geometry. Funded by US DOE FES and ASCR, and computing resources provided by OLCF through ALCC.

A quantification method for numerical dissipation in quasi-DNS and under-resolved DNS, and effects of numerical dissipation in quasi-DNS and under-resolved DNS of turbulent channel flows

NASA Astrophysics Data System (ADS)

Komen, E. M. J.; Camilo, L. H.; Shams, A.; Geurts, B. J.; Koren, B.

2017-09-01

LES for industrial applications with complex geometries is mostly characterised by: a) a finite volume CFD method using a non-staggered arrangement of the flow variables and second order accurate spatial and temporal discretisation schemes, b) an implicit top-hat filter, where the filter length is equal to the local computational cell size, and c) eddy-viscosity type LES models. LES based on these three main characteristics is indicated as industrial LES in this paper. It becomes increasingly clear that the numerical dissipation in CFD codes typically used in industrial applications with complex geometries may inhibit the predictive capabilities of explicit LES. Therefore, there is a need to quantify the numerical dissipation rate in such CFD codes. In this paper, we quantify the numerical dissipation rate in physical space based on an analysis of the transport equation for the mean turbulent kinetic energy. Using this method, we quantify the numerical dissipation rate in a quasi-Direct Numerical Simulation (DNS) and in under-resolved DNS of, as a basic demonstration case, fully-developed turbulent channel flow. With quasi-DNS, we indicate a DNS performed using a second order accurate finite volume method typically used in industrial applications. Furthermore, we determine and explain the trends in the performance of industrial LES for fully-developed turbulent channel flow for four different Reynolds numbers for three different LES mesh resolutions. The presented explanation of the mechanisms behind the observed trends is based on an analysis of the turbulent kinetic energy budgets. The presented quantitative analyses demonstrate that the numerical errors in the industrial LES computations of the considered turbulent channel flows result in a net numerical dissipation rate which is larger than the subgrid-scale dissipation rate. No new computational methods are presented in this paper. Instead, the main new elements in this paper are our detailed quantification method for the numerical dissipation rate, the application of this method to a quasi-DNS and under-resolved DNS of fully-developed turbulent channel flow, and the explanation of the effects of the numerical dissipation on the observed trends in the performance of industrial LES for fully-developed turbulent channel flows.

Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Y., E-mail: ybao@sjtu.edu.cn; Department of Aeronautics, Imperial College London, South Kensington Campus, London; Palacios, R., E-mail: r.palacios@imperial.ac.uk

2016-09-15

We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural modelmore » of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.« less

Humpback Dolphin (Genus Sousa) Behavioural Responses to Human Activities.

PubMed

Piwetz, Sarah; Lundquist, David; Würsig, Bernd

2015-01-01

Humpback dolphins (genus Sousa) use shallow, near-shore waters throughout their range. This coastal distribution makes them vulnerable to recreational and commercial disturbances, especially near heavily populated and industrialized areas. Most research focusing on Sousa and human activities has emphasized direct impacts and threats, involving injury and death, with relatively little focus on indirect effects on dolphins, such as changes in behaviour that may lead to deleterious effects. Understanding behaviour is important in resolving human-wildlife conflict and is an important component of conservation. This chapter gives an overview of animal behavioural responses to human activity with examples from diverse taxa; reviews the scientific literature on behavioural responses of humpback dolphins to human activity throughout their range, including marine vessel traffic, dolphin tourism, cetacean-fishery interactions, noise pollution, and habitat alteration; and highlights information and data gaps for future humpback dolphin research to better inform behaviour-based management decisions that contribute to conservation efforts. © 2015 Elsevier Ltd All rights reserved.

Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.

PubMed

Cui, Rongfeng; Schumer, Molly; Kruesi, Karla; Walter, Ronald; Andolfatto, Peter; Rosenthal, Gil G

2013-08-01

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

A review of all Recent species in the genus Novocrania (Craniata, Brachiopoda).

PubMed

Robinson, Jeffrey H

2017-10-10

The Recent species in the craniid genus Novocrania are reviewed, based on the examination of actual specimens wherever possible, especially for species named from one or a few specimens. The fourteen Recent species currently in the literature are reduced to eight; five species names are synonymized. One species name was given to a specimen that is not a craniid. The wide morphological ranges of the remaining Novocrania species are described and figured and the extended geographical ranges illustrated. Diagnoses of the remaining species are provided. The long-standing debate whether Novocrania anomala and N. turbinata are separate species or synonyms is resolved; they are separate species. New molecular analyses and a relative time-tree are provided by Cohen et al. (Appendix 1), the time-tree is calibrated herein and the results of Cohen et al. (2014; Appendix 1) and the time tree are discussed. The likelihood of craniid long-distance migration based on their geographical ranges is discussed.

Pestalotioid fungi from Restionaceae in the Cape Floral Kingdom

PubMed Central

Lee, Seonju; Crous, Pedro W.; Wingfield, Michael J.

2006-01-01

Eight pestalotioid fungi were isolated from the Restionaceae growing in the Cape Floral Kingdom of South Africa. Sarcostroma restionis, Truncatella megaspora, T. restionacearum and T. spadicea are newly described. New records include Pestalotiopsis matildae, Sarcostroma lomatiae, Truncatella betulae and T. hartigii. To resolve generic affiliations, phylogenetic analyses were performed on ITS (ITS1, 5.8S, ITS2) and part of 28S rDNA. DNA data support the original generic concept of Truncatella, which encompasses Pestalotiopsis species having 3-septate conidia. The genus Sarcostroma is retained as separate from Seimatosporium. PMID:18490978

The genus Pterocaulon (Asteraceae) - A review on traditional medicinal uses, chemical constituents and biological properties.

PubMed

Medeiros-Neves, Bruna; Teixeira, Helder Ferreira; von Poser, Gilsane Lino

2018-06-15

Species of the genus Pterocaulon (Asteraceae) are used in different parts of the world for mainly to treat skin and liver diseases, as well as disorders of the respiratory system, among others. This review aims to discuss the present state of the art concerning the ethnobotanical uses, secondary metabolites and biological effects of Pterocaulon species and their chemical components. The available information on the genus Pterocaulon was gathered from scientific databases (Web of Science, Pubmed, ScienceDirect, Scopus, ChemSpider, SciFinder ACS Publications, Wiley Online Library). Information was also obtained from local publications, M.Sc. and Ph.D. dissertations. All studies on the ethnobotany, phytochemistry, pharmacology and toxicology of the plants until December 2017 were included in this review. Approximately 40 coumarins and 30 flavonoids have been isolated from Pterocaulon species. Coumarins have been considered the chemotaxonomic markers in the genus and the most active components. Pharmacological studies carried out with extracts and isolated compounds revealed in vitro bioactivities that include antifungal, antiviral, and cytotoxicity. Most of the pharmacological investigations were not correlated with traditional uses of the plants. Pterocaulon species, a rich source of coumarins, have great ethnomedical potential. Nevertheless, further studies into the pharmacological activities are necessary since none of the purported effects of these plants was fully assessed. In-depth research regarding the toxicity are also required to ensure the safety of these medicinal plants. Copyright © 2018 Elsevier Ireland Ltd. All rights reserved.

Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.

PubMed

Lee, Laura L; Blumer-Schuette, Sara E; Izquierdo, Javier A; Zurawski, Jeffrey V; Loder, Andrew J; Conway, Jonathan M; Elkins, James G; Podar, Mircea; Clum, Alicia; Jones, Piet C; Piatek, Marek J; Weighill, Deborah A; Jacobson, Daniel A; Adams, Michael W W; Kelly, Robert M

2018-05-01

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii ), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis ), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii ), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis , but there was also evidence for other thermophilic fermentative anaerobes ( Caldanaerobacter , Fervidobacterium , Caloramator , and Clostridium ). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator , had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic. Copyright © 2018 American Society for Microbiology.

Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly.

PubMed

Hopple, J S; Vilgalys, R

1999-10-01

Phylogenetic relationships were investigated in the mushroom genus Coprinus based on sequence data from the nuclear encoded large-subunit rDNA gene. Forty-seven species of Coprinus and 19 additional species from the families Coprinaceae, Strophariaceae, Bolbitiaceae, Agaricaceae, Podaxaceae, and Montagneaceae were studied. A total of 1360 sites was sequenced across seven divergent domains and intervening sequences. A total of 302 phylogenetically informative characters was found. Ninety-eight percent of the average divergence between taxa was located within the divergent domains, with domains D2 and D8 being most divergent and domains D7 and D10 the least divergent. An empirical test of phylogenetic signal among divergent domains also showed that domains D2 and D3 had the lowest levels of homoplasy. Two equally most parsimonious trees were resolved using Wagner parsimony. A character-state weighted analysis produced 12 equally most parsimonious trees similar to those generated by Wagner parsimony. Phylogenetic analyses employing topological constraints suggest that none of the major taxonomic systems proposed for subgeneric classification is able to completely reflect phylogenetic relationships in Coprinus. A strict consensus integration of the two Wagner trees demonstrates the problematic nature of choosing outgroups within dark-spored mushrooms. The genus Coprinus is found to be polyphyletic and is separated into three distinct clades. Most Coprinus taxa belong to the first two clades, which together form a larger monophyletic group with Lacrymaria and Psathyrella in basal positions. A third clade contains members of Coprinus section Comati as well as the genus Leucocoprinus, Podaxis pistillaris, Montagnea arenaria, and Agaricus pocillator. This third clade is separated from the other species of Coprinus by members of the families Strophariaceae and Bolbitiaceae and the genus Panaeolus. Copyright 1999 Academic Press.

Phylogenetic analysis of Saccharum s.l. (Poaceae; Andropogoneae), with emphasis on the circumscription of the South American species.

PubMed

Welker, Cassiano A D; Souza-Chies, Tatiana T; Longhi-Wagner, Hilda M; Peichoto, Myriam Carolina; McKain, Michael R; Kellogg, Elizabeth A

2015-02-01

Polyploidy and reticulate evolution are often a complication for discovering phylogenetic relationships between genera and species. Despite the huge economic importance of sugarcane (Saccharum officinarum-Poaceae, Andropogoneae), the limits of the genus Saccharum and its species are complex and largely unresolved, involving both polyploidy and reticulate evolution. This study aimed to assess the phylogenetic relationships of Saccharum s.l., including Erianthus and Tripidium, as well as investigate the taxonomic circumscription of the South American species of the genus. Molecular cloning and sequencing of five regions of four low-copy nuclear loci were performed, including Aberrant panicle organization1 (apo1), Dwarf8 (d8), two exons of Erect panicle2 (ep2-ex7 and ep2-ex8), and Retarded palea1 (rep1). Concatenated trees were reconstructed using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference analyses. The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. The samples of Saccharum s.l. grouped in two distinct clades, with S. arundinaceum and S. ravennae (= Tripidium, or Erianthus sect. Ripidium) apart from all other species analyzed of the genus. Saccharum angustifolium, S. asperum, and S. villosum correspond to distinct clades (different species). The plants with intermediate morphology between S. angustifolium and S. villosum presented a pattern of paralogues consistent with a hybrid origin. Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. However, no strong evidence was found to support the segregation of Erianthus. The taxonomic circumscription of the South American species of the genus was resolved and the occurrence of natural hybrids was documented. Better understanding of the phylogenetic relationships of Saccharum and relatives may be useful for sugarcane breeders to identify potential taxa for interspecific and intergeneric crosses in the genetic improvement of sugarcane. © 2015 Botanical Society of America, Inc.

High-resolution hard x-ray spectroscopy of high-temperature plasmas using an array of quantum microcalorimeters.

PubMed

Thorn, Daniel B; Gu, Ming F; Brown, Greg V; Beiersdorfer, Peter; Porter, F Scott; Kilbourne, Caroline A; Kelley, Richard L

2008-10-01

Quantum microcalorimeters show promise in being able to fully resolve x-ray spectra from heavy highly charged ions, such as would be found in hot plasmas with temperatures in excess of 50 keV. Quantum microcalorimeter arrays are able to achieve this as they have a high-resolving power and good effective quantum efficiency for hard x-ray photons up to 60 keV. To demonstrate this, we present a measurement using an array of thin HgTe quantum microcalorimeters to measure the K-shell spectrum of hydrogenlike through carbonlike praseodymium (Z=57). With this device we are able to attain a resolving power, E/DeltaE, of 1000 at a photon energy of 37 keV.

Determining the orientation of a chiral substrate using full-hemisphere angle-resolved photoelectron spectroscopy.

PubMed

Tadich, A; Riley, J; Thomsen, L; Cowie, B C C; Gladys, M J

2011-10-21

Chiral interfaces and substrates are of increasing importance in the field of enantioselective chemistry. To fully understand the enantiospecific interactions between chiral adsorbate molecules and the chiral substrate, it is vital that the chiral orientation of the substrate is known. In this Letter we demonstrate that full-hemisphere angle-resolved photoemission permits straightforward identification of the orientation of a chiral surface. The technique can be applied to any solid state system for which photoemission measurements are possible. © 2011 American Physical Society

Higher Education Quality and Work-Based Learning: Two Concepts Not yet Fully Integrated

ERIC Educational Resources Information Center

Gibbs, Paul; Armsby, Pauline

2010-01-01

This short paper recognises the growth in emphasis in work-based learning as Europe moves forward on economically driven life-long learning. We support such a move and point to issues which still need to be resolved.

The fifth electron in the fully reduced caa(3) from Thermus thermophilus is competent in proton pumping.

PubMed

Siletsky, Sergey A; Belevich, Ilya; Soulimane, Tewfik; Verkhovsky, Michael I; Wikström, Mårten

2013-01-01

The time-resolved kinetics of membrane potential generation coupled to oxidation of the fully reduced (five-electron) caa(3) cytochrome oxidase from Thermus thermophilus by oxygen was studied in a single-turnover regime. In order to calibrate the number of charges that move across the vesicle membrane in the different reaction steps, the reverse electron transfer from heme a(3) to heme a and further to the cytochrome c/Cu(A) has been resolved upon photodissociation of CO from the mixed valence enzyme in the absence of oxygen. The reverse electron transfer from heme a(3) to heme a and further to the cytochrome c/Cu(A) pair is resolved as a single transition with τ~40 μs. In the reaction of the fully reduced cytochrome caa(3) with oxygen, the first electrogenic phase (τ~30 μs) is linked to OO bond cleavage and generation of the P(R) state. The next electrogenic component (τ~50 μs) is associated with the P(R)→F transition and together with the previous reaction step it is coupled to translocation of about two charges across the membrane. The three subsequent electrogenic phases, with time constants of ~0.25 ms, ~1.4 ms and ~4 ms, are linked to the conversion of the binuclear center through the F→O(H)→E(H) transitions, and result in additional transfer of four charges through the membrane dielectric. This indicates that the delivery of the fifth electron from heme c to the binuclear center is coupled to pumping of an additional proton across the membrane. Copyright © 2012 Elsevier B.V. All rights reserved.

DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia.

PubMed

Nevill, Paul G; Wallace, Mark J; Miller, Joseph T; Krauss, Siegfried L

2013-11-01

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology. © 2013 John Wiley & Sons Ltd.

Study of Pure Proteins, Nucleic Acids and Their Complexes from Halobacteria of the Dead Sea: RNA Polymerase-DNA Interaction.

DTIC Science & Technology

1987-09-21

objectives of our program are to isolate and characterize a fully active DNA dependent RNA polymerase from the extremely halophilic archaebacteria of the genus...operons in II. Marismortui. The halobacteriaceae are extreme halophiles . They require 3.5 M NaCI for optimal growth an(l no growth is observed below 2...was difficutlt to perform due to the extreme genetic instability in this strain (6). In contrast, the genoine of the extreme halophilic and prototrophic

First record of the African-Indian centipede genus Digitipes Attems, 1930 (Scolopendromorpha: Otostigminae) from Myanmar, and the systematic position of a new species based on molecular phylogenetics.

PubMed

Siriwut, Warut; Edgecombe, Gregory D; Sutcharit, Chirasak; Tongkerd, Piyoros; Panha, Somsak

2015-03-11

The first Southeast Asian record of the scolopendrid centipede Digitipes Attems, 1930, has been collected and analyzed based on a new species from Myanmar, males possessing a distomedial process on the ultimate leg femur that is diagnostic of the genus. Digitipes kalewaensis n. sp., described herein, is distinguished from other members of Digitipes by its 2.5 to 2.7 dorsally glabrous antennal articles, an unusually long basal suture on the tooth-plates, absence of a lateral spine on the coxopleural process, and a lack of median and dorso-median spines on the ultimate leg prefemur. Maximum likelihood and Bayesian analyses of two molecular markers (mitochondrial COI and 16S rRNA) supported the proposal of a new species from Myanmar. The phylogenetic tree identifies Digitipes barnabasi from the Western Ghats, India, in a polytomy with members of other genera of Otostigminae (Otostigmus, Ethmostigmus and Rhysida) and a robust Indian-Burmese Digitipes clade in which D. kalewaensis n. sp. is resolved as sister group to a clade composed of most Indian species. Available molecular dates for the diversification of Indian Digitipes are consistent with introduction of the genus into SE Asia when the Indian subcontinent made contact with Myanmar in the early Palaeogene.

Phylogeny and dating of divergences within the genus Thymallus (Salmonidae: Thymallinae) using complete mitochondrial genomes.

PubMed

Ma, Bo; Jiang, Haiying; Sun, Peng; Chen, Jinping; Li, Linmiao; Zhang, Xiujuan; Yuan, Lihong

2016-09-01

The genus Thymallus has attracted increasing attention in recent years because of its sharp demographic decline. In this study, we reported four complete mitochondrial genomes in the Thymallus genus: Baikal-Lena grayling (T. arcticus baicalolenensis), lower Amur grayling (T. tugarinae), Yalu grayling (T. a. yaluensis), and Mongolian grayling (T. brevirostris). The total length of the four new grayling mtDNAs ranged from 16 658 to 16 663 bp, all of which contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny within Thymallinae. Our study validated that the Yalu grayling should be a synonym of the Amur grayling (T. grubii) at the whole mitogenome level. The phylogenetic and dating analyses placed the Amur grayling at the deepest divergence node within Thymallus, diverging at ∼14.95 Ma. The lower Amur grayling diverged at the next deepest node (∼12.14 Ma). This was followed by T. thymallus, which diverged at ∼9.27 Ma. The Mongolian grayling and the ancestor of the sister species, T. arcticus and T. arcticus baicalolenensis, diverged at ∼7.79 Ma, with T. arcticus and T. arcticus baicalolenensis separating at ∼6.64 Ma. Our study provides far better resolution of the phylogenetic relationships and divergence dates of graylings than previous studies.

Revision of the genus Hydroides (Annelida: Serpulidae) from Australia.

PubMed

Sun, Yanan; Wong, Eunice; ten Hove, Harry A; Hutchings, Pat A; Williamson, Jane E; Kupriyanova, Elena K

2015-09-01

Hydroides Gunnerus, 1768 is the largest and one of the economically most important genera of calcareous tubeworms (Serpulidae, Annelida) that includes a number of notorious fouling and bioinvading species. Although the representatives of the genus are typically found in shallow waters of tropical and subtropical areas worldwide, the species composition of the genus in Australia has never been revised. We conducted the first detailed regional taxonomic revision of Hydroides species based both on the historical collections from Australian museums (Australian Museum, Museum Victoria, South Australian Museum, Western Australian Museum, Queensland Museum, and Museum and Art Gallery of Northern Territory) and newly collected material from New South Wales, Victoria, Queensland, Northern Territory, and Western Australia. In total, 25 species are currently considered valid in Australia, including three new species: H. amri n. sp. from NSW, SA, and Vic (previously referred to as H. cf. brachyacantha), as well as H. glasbyi n. sp. and H. qiui n. sp., both from NT, and two new records of H. furcifera and H. multispinosa for Australia. We have synonymised H. spiratubus with H. albiceps, and H. spiculitubus with H. tambalagamensis in this study. The status of the taxon H. cf. recta remains undecided. An identification key and diagnoses accompanied by original high-quality photographs for all species recorded in Australia are provided. Application of molecular genetics is needed to resolve the status of some problematic species.

Taxonomy and phylogeny of two species of the genus Deviata (Protista, Ciliophora) from China, with description of a new soil form, Deviata parabacilliformis sp. nov.

PubMed

Li, Fengchao; Lv, Zhao; Yi, Zhenzhen; Al-Farraj, Saleh A; Al-Rasheid, Khaled A S; Shao, Chen

2014-11-01

The morphology and morphogenesis of a soil hypotrichous ciliate, Deviata parabacilliformis sp. nov., isolated from northern China, were investigated. D. parabacilliformis measures about 75-210 × 25-60 µm in vivo, with an elongate and flexible body. It possesses one right marginal row, two to four left marginal rows and three dorsal kineties. The main morphogenetic features of D. parabacilliformis are: (i) the oral primordium originates de novo; (ii) anlage IV of the opisthe originates from parental frontoventral row V, anlage V originates de novo, and anlage VI forms from frontoventral row VI; and (iii) anlage I of the proter originates from the anterior portion of the parental paroral, anlage II originates from the buccal cirrus, anlage III originates from the parabuccal cirri, anlage IV originates from parental frontoventral row IV and anlage V forms from the anterior of parental frontoventral row VI. The morphology of an edaphic population of another species of the genus Deviata, Deviata bacilliformis (Gelei 1954) Eigner 1995, was also investigated. This work also provides the first record of SSU rRNA gene sequences for species of the genus Deviata. Molecular phylogenetic analysis suggests that Deviata is not monophyletic, and its position is poorly resolved due to weak phylogenetic signal of the 18S marker in the Stichotrichida. © 2014 IUMS.

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.

PubMed

Wan, Yizhen; Schwaninger, Heidi R; Baldo, Angela M; Labate, Joanne A; Zhong, Gan-Yuan; Simon, Charles J

2013-07-05

Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

Anopheles salivary gland proteomes from major malaria vectors

PubMed Central

2012-01-01

Background Antibody responses against Anopheles salivary proteins can indicate individual exposure to bites of malaria vectors. The extent to which these salivary proteins are species-specific is not entirely resolved. Thus, a better knowledge of the diversity among salivary protein repertoires from various malaria vector species is necessary to select relevant genus-, subgenus- and/or species-specific salivary antigens. Such antigens could be used for quantitative (mosquito density) and qualitative (mosquito species) immunological evaluation of malaria vectors/host contact. In this study, salivary gland protein repertoires (sialomes) from several Anopheles species were compared using in silico analysis and proteomics. The antigenic diversity of salivary gland proteins among different Anopheles species was also examined. Results In silico analysis of secreted salivary gland protein sequences retrieved from an NCBInr database of six Anopheles species belonging to the Cellia subgenus (An. gambiae, An. arabiensis, An. stephensi and An. funestus) and Nyssorhynchus subgenus (An. albimanus and An. darlingi) displayed a higher degree of similarity compared to salivary proteins from closely related Anopheles species. Additionally, computational hierarchical clustering allowed identification of genus-, subgenus- and species-specific salivary proteins. Proteomic and immunoblot analyses performed on salivary gland extracts from four Anopheles species (An. gambiae, An. arabiensis, An. stephensi and An. albimanus) indicated that heterogeneity of the salivary proteome and antigenic proteins was lower among closely related anopheline species and increased with phylogenetic distance. Conclusion This is the first report on the diversity of the salivary protein repertoire among species from the Anopheles genus at the protein level. This work demonstrates that a molecular diversity is exhibited among salivary proteins from closely related species despite their common pharmacological activities. The involvement of these proteins as antigenic candidates for genus-, subgenus- or species-specific immunological evaluation of individual exposure to Anopheles bites is discussed. PMID:23148599

Phytochemical, phylogenetic, and anti-inflammatory evaluation of 43 Urtica accessions (stinging nettle) based on UPLC-Q-TOF-MS metabolomic profiles.

PubMed

Farag, Mohamed A; Weigend, Maximilian; Luebert, Federico; Brokamp, Grischa; Wessjohann, Ludger A

2013-12-01

Several species of the genus Urtica (especially Urtica dioica, Urticaceae), are used medicinally to treat a variety of ailments. To better understand the chemical diversity of the genus and to compare different accessions and different taxa of Urtica, 63 leaf samples representing a broad geographical, taxonomical and morphological diversity were evaluated under controlled conditions. A molecular phylogeny for all taxa investigated was prepared to compare phytochemical similarity with phylogenetic relatedness. Metabolites were analyzed via UPLC-PDA-MS and multivariate data analyses. In total, 43 metabolites were identified, with phenolic compounds and hydroxy fatty acids as the dominant substance groups. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) provides a first structured chemotaxonomy of the genus. The molecular data present a highly resolved phylogeny with well-supported clades and subclades. U. dioica is retrieved as both para- and polyphyletic. European members of the U. dioica group and the North American subspecies share a rather similar metabolite profile and were largely retrieved as one, nearly exclusive cluster by metabolite data. This latter cluster also includes - remotely related - Urtica urens, which is pharmaceutically used in the same way as U. dioica. However, most highly supported phylogenetic clades were not retrieved in the metabolite cluster analyses. Overall, metabolite profiles indicate considerable phytochemical diversity in the genus, which largely falls into a group characterized by high contents of hydroxy fatty acids (e.g., most Andean-American taxa) and another group characterized by high contents of phenolic acids (especially the U. dioica-clade). Anti-inflammatory in vitro COX1 enzyme inhibition assays suggest that bioactivity may be predicted by gross metabolic profiling in Urtica. Copyright © 2013. Published by Elsevier Ltd.

Complex species status for extinct moa (Aves: Dinornithiformes) from the genus Euryapteryx.

PubMed

Huynen, Leon; Lambert, David M

2014-01-01

The exact species status of New Zealand's extinct moa remains unknown. In particular, moa belonging to the genus Euryapteryx have been difficult to classify. We use the DNA barcoding sequence on a range of Euryapteryx samples in an attempt to resolve the species status for this genus. We obtained mitochondrial control region and the barcoding region from Cytochrome Oxidase Subunit I (COI) from a number of new moa samples and use available sequences from previous moa phylogenies and eggshell data to try and clarify the species status of Euryapteryx. Using the COI barcoding region we show that species status in Euryapteryx is complex with no clear separation between various individuals. Eggshell, soil, and bone data suggests that a Euryapteryx subspecies likely exists on New Zealand's North Island and can be characterized by a single mitochondrial control region SNP. COI divergences between Euryapteryx individuals from the south of New Zealand's South Island and those from the Far North of the North Island exceed 1.6% and are likely to represent separate species. Individuals from other areas of New Zealand were unable to be clearly separated based on COI differences possibly as a result of repeated hybridisation events. Despite the accuracy of the COI barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus Euryapteryx, COI barcoding fails to provide a clear result, possibly as a consequence of repeated hybridisation events between these moa. A single control region SNP was identified however that segregates with the two general morphological variants determined for Euryapteryx; a smaller subspecies restricted to the North Island of New Zealand, and a larger subspecies, found on both New Zealand's North and South Island.

New phylogenetic insights toward developing a natural generic classification of African angraecoid orchids (Vandeae, Orchidaceae).

PubMed

Simo-Droissart, Murielle; Plunkett, Gregory M; Droissart, Vincent; Edwards, Molly B; Farminhão, João N M; Ječmenica, Vladimir; D'haijère, Tania; Lowry, Porter P; Sonké, Bonaventure; Micheneau, Claire; Carlsward, Barbara S; Azandi, Laura; Verlynde, Simon; Hardy, Olivier J; Martos, Florent; Bytebier, Benny; Fischer, Eberhard; Stévart, Tariq

2018-09-01

Despite significant progress made in recent years toward developing an infrafamilial classification of Orchidaceae, our understanding of relationships among and within tribal and subtribal groups of epidendroid orchids remains incomplete. To reassess generic delimitation among one group of these epidendroids, the African angraecoids, phylogenetic relationships were inferred from DNA sequence data from three regions, ITS, matK, and the trnL-trnF intergenic spacer, obtained from a broadly representative sample of taxa. Parsimony and Bayesian analyses yielded highly resolved trees that are in clear agreement and show significant support for many key clades within subtribe Angraecinae s.l. Angraecoid orchids comprise two well-supported clades: an African/American group and an Indian Ocean group. Molecular results also support many previously proposed relationships among genera, but also reveal some unexpected relationships. The genera Aerangis, Ancistrorhynchus, Bolusiella, Campylocentrum, Cyrtorchis, Dendrophylax, Eurychone, Microcoelia, Nephrangis, Podangis and Solenangis are all shown to be monophyletic, but Angraecopsis, Diaphananthe and Margelliantha are polyphyletic. Diaphananthe forms three well-supported clades, one of which might represent a new genus, and Rhipidoglossum is paraphyletic with respect to Cribbia and Rhaesteria, and also includes taxa currently assigned to Margelliantha. Tridactyle too is paraphyletic as Eggelingia is embedded within it. The large genus Angraecum is confirmed to be polyphyletic and several groups will have to be recognized as separate genera, including sections Dolabrifolia and Hadrangis. The recently segregated genus Pectinariella (previously recognized as A. sect. Pectinaria) is polyphyletic and its Continental African species will have to be removed. Similarly, some of the species recently transferred to Angraecoides that were previously placed in Angraecum sects. Afrangraecum and Conchoglossum will have to be moved and described as a new genus. Copyright © 2018 Elsevier Inc. All rights reserved.

Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae).

PubMed

Prebus, Matthew

2017-12-13

Temnothorax (Formicidae: Myrmicinae) is a diverse genus of ants found in a broad spectrum of ecosystems across the northern hemisphere. These diminutive ants have long served as models for social insect behavior, leading to discoveries about social learning and inspiring hypotheses about the process of speciation and the evolution of social parasitism. This genus is highly morphologically and behaviorally diverse, and this has caused a great deal of taxonomic confusion in recent years. Past efforts to estimate the phylogeny of this genus have been limited in taxonomic scope, leaving the broader evolutionary patterns in Temnothorax unclear. To establish the monophyly of Temnothorax, resolve the evolutionary relationships, reconstruct the historical biogeography and investigate trends in the evolution of key traits, I generated, assembled, and analyzed two molecular datasets: a traditional multi-locus Sanger sequencing dataset, and an ultra-conserved element (UCE) dataset. Using maximum likelihood, Bayesian, and summary-coalescent based approaches, I analyzed 22 data subsets consisting of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2485 loci. The results of this study suggest an origin of Temnothorax at the Eocene-Oligocene transition, concerted transitions to arboreal nesting habits in several clades during the Oligocene, coinciding with ancient global cooling, and several convergent origins of social parasitism in the Miocene and Pliocene. As with other Holarctic taxa, Temnothorax has a history of migration across Beringia during the Miocene. Temnothorax is corroborated as a natural group, and the notion that many of the historical subgeneric and species group concepts are artificial is reinforced. The strict form of Emery's Rule, in which a socially parasitic species is sister to its host species, is not well supported in Temnothorax.

High-order Two-Fluid Plasma Solver for Direct Numerical Simulations of Magnetic Flows with Realistic Transport Phenomena

NASA Astrophysics Data System (ADS)

Li, Zhaorui; Livescu, Daniel

2017-11-01

The two-fluid plasma equations with full transport terms, including temperature and magnetic field dependent ion and electron viscous stresses and heat fluxes, frictional drag force, and ohmic heating term have been solved by using the sixth-order non-dissipative compact scheme for plasma flows in several different regimes. In order to be able to fully resolve all the dynamically relevant time and length scales while maintaining computational feasibility, the assumptions of infinite speed of light and negligible electron inertia have been made. The accuracy and robustness of this two-fluid plasma solver in handling plasma flows have been tested against a series of canonical problems, such as Alfven-Whistler dispersion relation, electromagnetic plasma shock, magnetic reconnection, etc. For all test cases, grid convergence tests have been conducted to achieve fully resolved results. The roles of heat flux, viscosity, resistivity, Hall and Biermann battery effects, are investigated for the canonical flows studied.

Localized oscillatory states in magnetoconvection.

PubMed

Buckley, Matthew C; Bushby, Paul J

2013-02-01

Localized states are found in many pattern forming systems. The aim of this paper is to investigate the occurrence of oscillatory localized states in two-dimensional Boussinesq magnetoconvection. Initially considering an idealized model, in which the vertical structure of the system has been simplified by a projection onto a small number of Fourier modes, we find that these states are restricted to the low ζ regime (where ζ represents the ratio of the magnetic to thermal diffusivities). These states always exhibit bistability with another nontrivial solution branch; in other words, they show no evidence of subcritical behavior. This is due to the weak flux expulsion that is exhibited by these time-dependent solutions. Using the results of this parameter survey, we locate corresponding states in a fully resolved two-dimensional system, although the mode of oscillation is more complex in this case. This is the first time that a localized oscillatory state, of this kind, has been found in a fully resolved magnetoconvection simulation.

Upscaling of dilution and mixing using a trajectory based Spatial Markov random walk model in a periodic flow domain

NASA Astrophysics Data System (ADS)

Sund, Nicole L.; Porta, Giovanni M.; Bolster, Diogo

2017-05-01

The Spatial Markov Model (SMM) is an upscaled model that has been used successfully to predict effective mean transport across a broad range of hydrologic settings. Here we propose a novel variant of the SMM, applicable to spatially periodic systems. This SMM is built using particle trajectories, rather than travel times. By applying the proposed SMM to a simple benchmark problem we demonstrate that it can predict mean effective transport, when compared to data from fully resolved direct numerical simulations. Next we propose a methodology for using this SMM framework to predict measures of mixing and dilution, that do not just depend on mean concentrations, but are strongly impacted by pore-scale concentration fluctuations. We use information from trajectories of particles to downscale and reconstruct pore-scale approximate concentration fields from which mixing and dilution measures are then calculated. The comparison between measurements from fully resolved simulations and predictions with the SMM agree very favorably.

Exploring the neural bases of goal-directed motor behavior using fully resolved simulations

NASA Astrophysics Data System (ADS)

Patel, Namu; Patankar, Neelesh A.

2016-11-01

Undulatory swimming is an ideal problem for understanding the neural architecture for motor control and movement; a vertebrate's robust morphology and adaptive locomotive gait allows the swimmer to navigate complex environments. Simple mathematical models for neurally activated muscle contractions have been incorporated into a swimmer immersed in fluid. Muscle contractions produce bending moments which determine the swimming kinematics. The neurobiology of goal-directed locomotion is explored using fast, efficient, and fully resolved constraint-based immersed boundary simulations. Hierarchical control systems tune the strength, frequency, and duty cycle for neural activation waves to produce multifarious swimming gaits or synergies. Simulation results are used to investigate why the basal ganglia and other control systems may command a particular neural pattern to accomplish a task. Using simple neural models, the effect of proprioceptive feedback on refining the body motion is demonstrated. Lastly, the ability for a learned swimmer to successfully navigate a complex environment is tested. This work is supported by NSF CBET 1066575 and NSF CMMI 0941674.

Catalog to families, genera, and species of orders Actiniaria and Corallimorpharia (Cnidaria: Anthozoa).

PubMed

Fautin, Daphne Gail

2016-08-01

This book inventories all available (and some unavailable) names in the family, genus, and species groups of extant members of orders Actiniaria and Corallimorpharia [cnidarian subclass Hexacorallia (Zoantharia) of class Anthozoa], providing a benchmark of names, their status, and taxon membership. I have attempted to make the compilation complete as of 2010; some names created after 2010 are included. The book is derived from a database I compiled that was available through a website. Most of the book is from the literature that defines taxa and documents their geographic distribution-primarily publications on nomenclature, taxonomy, and biogeography, but also some on ecology, pharmacology, reproductive biology, physiology, etc. of anemones (the common name for these groups); the reference section comprises 845 entries. As for previous anemone catalogs, this contains taxonomic as well as nomenclatural information,  the former based on subjective opinion of working biologists, the latter objectively verifiable and unchanging (except by action of the International Commission on Zoological Nomenclature).        Each family-group name, genus-group name, and original combination for species-group names has an entry. The entry contains the bibliographic reference to the publication in which each name was made available. This book contains for Corallimorpharia seven family names (four considered valid [57%]), 20 generic names (10 considered valid [50%] and one unavailable), and 65 species names (46 considered valid [70%]). It contains for Actiniaria 86 family names (50 considered valid [58%] and three unavailable), 447 generic names (264 considered valid [59%] and two unavailable), and 1427 species names (1101 considered valid [77%] and nine unavailable). Type specimens are inventoried from more than 50 natural history museums in Africa, Australia, Europe, New Zealand, and North America, including those with the largest collections of anemones; the geographic sources of specimens that were the bases of new names are identified. I resolve some nomenclatural issues, acting as First Reviser. A few taxonomic opinions are published for the first time. I have been unable to resolve a small number of problematic names having both nomenclatural and taxonomic problems. Molecular phylogenetic analyses are changing assignment of genera to families and species to genera. Systematics may change, but the basics of nomenclature remain unchanged in face of such alterations.        All actions are in accord with the principles of nomenclature enunciated in the International Code of Zoological Nomenclature. These include the type concept, the Principle of Coordination, and the Principle of Priority. Nomenclatural acts include the creation of new replacement names; seven actiniarian generic names and one species name that are junior homonyms but have been treated as valid are replaced and an eighth new genus name is created. I designate type species for two genera. Except for published misspellings, names are rendered correctly according to the International Code of Zoological Nomenclature; I have altered spelling of some species names to conform to orthographic regulations. I place several species that had been assigned to genera now considered junior synonyms in the genus to which the type species was moved; experts on these anemones should determine whether those generic placements, which follow the nomenclatural rules, are taxonomically appropriate.        This inventory can be a useful starting point in assembling the literature and trying to understand the rationale for the creation and use of names for the taxonomic matters yet to be resolved.  Some nomenclatural conundra will not be resolved until taxonomic uncertainties are. A taxonomist familiar with the animals needs to ascertain whether the published synonymies are justified. If so, the senior synonym should be used, which, in many instances, will involve determining the proper generic assignment of the species and the correct rendering of the name; if changing the name would be disruptive, retaining the junior name would require an appeal to the Commission (Code Article 23.11).

The Width Distribution of Loops and Strands in the Solar Corona—Are We Hitting Rock Bottom?

NASA Astrophysics Data System (ADS)

Aschwanden, Markus J.; Peter, Hardi

2017-05-01

In this study, we analyze Atmospheric Imaging Assembly (AIA) and Hi-C images in order to investigate absolute limits for the finest loop strands. We develop a model of the occurrence-size distribution function of coronal loop widths, characterized by the lower limit of widths w min, the peak (or most frequent) width w p , the peak occurrence number n p , and a power-law slope a. Our data analysis includes automated tracing of curvilinear features with the OCCULT-2 code, automated sampling of the cross-sectional widths of coronal loops, and fitting of the theoretical size distribution to the observed distribution. With Monte Carlo simulations and variable pixel sizes {{Δ }}x, we derive a first diagnostic criterion to discriminate whether the loop widths are unresolved ({w}p/{{Δ }}x≈ 2.5+/- 0.2) or fully resolved (if {w}p/{{Δ }}x≳ 2.7). For images with resolved loop widths, we can apply a second diagnostic criterion that predicts the lower limit of loop widths as a function of the spatial resolution. We find that the loop widths are marginally resolved in AIA images but are fully resolved in Hi-C images, where our model predicts a most frequent (peak) value at {w}p≈ 550 {km}, in agreement with recent results of Brooks et al. This result agrees with the statistics of photospheric granulation sizes and thus supports coronal heating mechanisms operating on the macroscopic scale of photospheric magneto-convection, rather than nanoflare braiding models on unresolved microscopic scales.

Electrocotyle whittingtoni n. gen., n. sp. (Monogenea: Monocotylidae: Heterocotylinae) from the gills of a captive onefin electric ray, Narke capensis (Narkidae) at Two Oceans Aquarium, Cape Town, South Africa.

PubMed

Vaughan, David B; Chisholm, Leslie A; Hansen, Haakon

2016-09-01

Electrocotyle whittingtoni n. gen., n. sp. (Monogenea: Monocotylidae) is described from the gills of a captive female onefin electric ray, Narke capensis, collected for exhibition at Two Oceans Aquarium in Cape Town, South Africa. Electrocotyle n. gen. is most similar to the heterocotyline genera Heterocotyle and Potamotrygonocotyle but could not be accommodated easily in either of these groups. The new genus is characterised by a haptor with one central and eight peripheral loculi, four unsclerotised structures on the dorsal surface of the haptor, a single unsclerotised non-sinous ridge on the ventral surface of the haptoral septa, large hamuli with a long handle and reduced guard, a vagina with sclerotised walls, and tetrahedral eggs. Molecular phylogenetic analyses based on 28S sequences strongly support the separate genus status of Electrocotyle n. gen and thus support our morphological conclusion. The Heterocotylinae is amended to accommodate the new genus, and the new species is fully described and illustrated herein. This is the first record of a monocotylid from the Narkidae. Electrocotyle whittingtoni n. gen. n. sp. is considered potentially pathogenic given its negative impact on the health of its captive host kept in the quarantine facility at Two Oceans Aquarium.

Fully compressible solutions for early stage Richtmyer–Meshkov instability

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael

2016-10-27

Here, we will consider the effects of compressibility and viscosity on the early dynamics of the Richtmyer–Meshkov instability (RMI). In particular, we will combine theory, scaling, and high resolution simulation of RMI to probe the details of the initial compression and the subsequent viscous damping as a shock interacts with a density discontinuity. We will propose a refinement of the classic 1D model for the linear regime of RMI that, for small initial perturbation wavelengths, more accurately reproduces the 2D dynamics of a fully resolved numerical simulation.

A craniometric study of the black and white Colobus Illiger 1811 (Primates: Ceropithecoidea).

PubMed

Hull, D B

1979-08-01

This study examines the craniometry of Black and White Colobus monkeys using 1072 specimens representing all the recognized subspecies (after Rahm, '70) of the genus. Seventy-six measurements were taken on each individual, and examined using canonical variates analysis and clustering by Ward's Error Sum method. The assumptions of the analytical techniques are shown to be met, and the results demonstrated to be stable. Examination of the populations for statistical difference and taxonomic distinctiveness using a multivariate extension of Mayr's Rule indicates that the taxonomy presented by Rahm ('70) is essentially correct, except that the subspecies of guereza across the northern part of Central Africa should be lumped into a single group--C. g. occidentalis--and the subspecies of montane angolan colobus in Eastern Zaire should all be lumped into C. a. ruwenzorii. The systematic patterns of the genus illustrate the whole range of the process of speciation, from barely distinct subspecies, to subspecies almost as distinct as allopatric species of the genus, and on the fully sympatric species Three major zoogeographic areas may be delineated: an East African area dominated by the effects of the Rift Valley, with a large number of subspecies isolated in forest islands; a Central African area with little subspeciation and sympatric overlap of the major species of Colobus; and a West African area with a clinal pattern of distribution of subspecies, and secondary intergradation. The arbitrary nature of Mary's Rule is also apparent. Lastly, the CVA indicated major differences across the genus to be located in the teeth and jaws, suggesting diet might be an important distinguishing feature in Colobus.

Exactly energy conserving semi-implicit particle in cell formulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapenta, Giovanni, E-mail: giovanni.lapenta@kuleuven.be

We report a new particle in cell (PIC) method based on the semi-implicit approach. The novelty of the new method is that unlike any of its semi-implicit predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non-linear iteration procedure. The new method (referred to as Energy Conserving Semi-Implicit Method, ECSIM), instead, does not require any non-linear iteration and its computational cycle is similar to that of explicit PIC. The properties of the new method are: i) it conservesmore » energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length; iv) the particle mover has a computational complexity identical to that of the explicit PIC, only the field solver has an increased computational cost. The new ECSIM is tested in a number of benchmarks where accuracy and computational performance are tested. - Highlights: • We present a new fully energy conserving semi-implicit particle in cell (PIC) method based on the implicit moment method (IMM). The new method is called Energy Conserving Implicit Moment Method (ECIMM). • The novelty of the new method is that unlike any of its predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. • The new method is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency. • The new method eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length. • These features are achieved at a reduced cost compared with either previous IMM or fully implicit implementation of PIC.« less

Preparation and characterization of ultraflat Pt facets by atom-height-resolved differential optical microscopy

NASA Astrophysics Data System (ADS)

Azhagurajan, M.; Wen, R.; Kim, Y. G.; Itoh, T.; Sashikata, K.; Itaya, K.

2015-01-01

We recently demonstrated that improvements to our technique, laser confocal microscopy with differential interference microscopy (LCM-DIM), has rendered it fully capable of resolving monatomic steps with heights of ca. 0.25 nm on Au(111) and Pd(111) surfaces, even as low as 0.14 nm on Si(100), in aqueous solution. In this paper, we describe in detail a method to prepare and characterize, via atomic-layer-resolved LCM-DIM, ultraflat Pt(111) and Pt(100) facets over a wide surface area. The preparation of ultraflat surfaces is important in the characterization at the atomic scale of electrochemical processes under reaction conditions. To showcase the elegance of LCM-DIM, the anodic dissolution of Pt in aqueous HCl is briefly recounted.

Comparisons of angularly and spectrally resolved Bremsstrahlung measurements to two-dimensional multi-stage simulations of short-pulse laser-plasma interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, C. D.; Kemp, A. J.; Pérez, F.

2013-05-15

A 2-D multi-stage simulation model incorporating realistic laser conditions and a fully resolved electron distribution handoff has been developed and compared to angularly and spectrally resolved Bremsstrahlung measurements from high-Z planar targets. For near-normal incidence and 0.5-1 × 10{sup 20} W/cm{sup 2} intensity, particle-in-cell (PIC) simulations predict the existence of a high energy electron component consistently directed away from the laser axis, in contrast with previous expectations for oblique irradiation. Measurements of the angular distribution are consistent with a high energy component when directed along the PIC predicted direction, as opposed to between the target normal and laser axis asmore » previously measured.« less

Digital resolver for helicopter model blade motion analysis

NASA Technical Reports Server (NTRS)

Daniels, T. S.; Berry, J. D.; Park, S.

1992-01-01

The paper reports the development and initial testing of a digital resolver to replace existing analog signal processing instrumentation. Radiometers, mounted directly on one of the fully articulated blades, are electrically connected through a slip ring to analog signal processing circuitry. The measured signals are periodic with azimuth angle and are resolved into harmonic components, with 0 deg over the tail. The periodic nature of the helicopter blade motion restricts the frequency content of each flapping and yaw signal to the fundamental and harmonics of the rotor rotational frequency. A minicomputer is employed to collect these data and then plot them graphically in real time. With this and other information generated by the instrumentation, a helicopter test pilot can then adjust the helicopter model's controls to achieve the desired aerodynamic test conditions.

Velocity-Resolved LES (VR-LES) technique for simulating turbulent transport of high Schmidt number passive scalars

NASA Astrophysics Data System (ADS)

Verma, Siddhartha; Blanquart, Guillaume; P. K. Yeung Collaboration

2011-11-01

Accurate simulation of high Schmidt number scalar transport in turbulent flows is essential to studying pollutant dispersion, weather, and several oceanic phenomena. Batchelor's theory governs scalar transport in such flows, but requires further validation at high Schmidt and high Reynolds numbers. To this end, we use a new approach with the velocity field fully resolved, but the scalar field only partially resolved. The grid used is fine enough to resolve scales up to the viscous-convective subrange where the decaying slope of the scalar spectrum becomes constant. This places the cutoff wavenumber between the Kolmogorov scale and the Batchelor scale. The subgrid scale terms, which affect transport at the supergrid scales, are modeled under the assumption that velocity fluctuations are negligible beyond this cutoff wavenumber. To ascertain the validity of this technique, we performed a-priori testing on existing DNS data. This Velocity-Resolved LES (VR-LES) technique significantly reduces the computational cost of turbulent simulations of high Schmidt number scalars, and yet provides valuable information of the scalar spectrum in the viscous-convective subrange.

Structure-Preserving Variational Multiscale Modeling of Turbulent Incompressible Flow with Subgrid Vortices

NASA Astrophysics Data System (ADS)

Evans, John; Coley, Christopher; Aronson, Ryan; Nelson, Corey

2017-11-01

In this talk, a large eddy simulation methodology for turbulent incompressible flow will be presented which combines the best features of divergence-conforming discretizations and the residual-based variational multiscale approach to large eddy simulation. In this method, the resolved motion is represented using a divergence-conforming discretization, that is, a discretization that preserves the incompressibility constraint in a pointwise manner, and the unresolved fluid motion is explicitly modeled by subgrid vortices that lie within individual grid cells. The evolution of the subgrid vortices is governed by dynamical model equations driven by the residual of the resolved motion. Consequently, the subgrid vortices appropriately vanish for laminar flow and fully resolved turbulent flow. As the resolved velocity field and subgrid vortices are both divergence-free, the methodology conserves mass in a pointwise sense and admits discrete balance laws for energy, enstrophy, and helicity. Numerical results demonstrate the methodology yields improved results versus state-of-the-art eddy viscosity models in the context of transitional, wall-bounded, and rotational flow when a divergence-conforming B-spline discretization is utilized to represent the resolved motion.

A replacement name for Thomasella Santos-Silva, Bezark Martins (Coleoptera, Cerambycidae, Cerambycinae).

PubMed

Santos-Silva, Antonio; Bezark, Larry G

2018-03-14

        Santos-Silva et al. (2012) described Thomasella as a new genus of Rhinotragini to include a single species from Panama: Ommata (Eclipta) igniventris Giesbert, 1991. However, Thomasella is a junior homonym of Thomasella Fredericks, 1928 (Brachiopoda). To resolve this homonym, in accordance with the International Code of Zoological Nomenclature, we are proposing Neothomasella as a new replacement name (nomen novum) for Thomasella Santos-Silva et al. (2012). The new name is a compound of the prefix "neo-" (from Greek νεο-, meaning "new") + Thomasella; feminine gender.

Limnodrilus sulphurensis n. sp., from a sulfur cave in Colorado, USA, with notes on the morphologically similar L. profundicola (Clitellata, Naididae, Tubificinae).

PubMed

Fend, Steven V; Liu, Yingkui; Steinmann, David; Giere, Olav; Barton, Hazel A; Luiszer, Fred; Erséus, Christer

2016-01-18

A new species of the tubificine genus Limnodrilus is described and COI barcoded from Sulphur Cave and associated springs in Colorado, USA. The habitats are characterized by high sulfide concentrations. The new species, L. sulphurensis, is distinguished from all congeners by the elongate, nearly parallel teeth of chaetae in its anterior segments. It has a penis sheath resembling that of L. profundicola; consequently, museum specimens and new collections are examined here to resolve some of the taxonomic confusion surrounding that widespread, but uncommon species.

Lipid Bilayer Vesicles with Numbers of Membrane-Linking Pores

NASA Astrophysics Data System (ADS)

Ken-ichirou Akashi,; Hidetake Miyata,

2010-06-01

We report that phospholipid membranes spontaneously formed in aqueous medium giant unilamellar vesicles (GUVs) possessing many membranous wormhole-like structures (membrane-linking pores, MLPs). By phase contract microscopy and confocal fluorescence microscopy, the structures of the MLPs, consisting of lipid bilayer, were resolvable, and a variety of vesicular shapes having many MLPs (a high genus topology) were found. These vesicles were stable but easily deformed by micromanipulation with a microneedle. We also observed the size reduction of the MLPs with the increase in membrane tension, which was qualitatively consistent with a prediction from a simple dynamical model.

Communication—indentation of Li-ion pouch cell: Effect of material homogenization on prediction of internal short circuit

DOE PAGES

Kumar, A.; Kalnaus, Sergiy; Simunovic, Srdjan; ...

2016-09-12

We performed finite element simulations of spherical indentation of Li-ion pouch cells. Our model fully resolves different layers in the cell. The results of the layer resolved models were compared to the models available in the literature that treat the cell as an equivalent homogenized continuum material. Simulations were carried out for different sizes of the spherical indenter. Here, we show that calibration of a failure criterion for the cell in the homogenized model depends on the indenter size, whereas in the layer-resoled model, such dependency is greatly diminished.

Biexciton Auger Recombination Differs in Hybrid and Inorganic Halide Perovskite Quantum Dots.

PubMed

Eperon, Giles E; Jedlicka, Erin; Ginger, David S

2018-01-04

We use time-resolved photoluminescence measurements to determine the biexciton Auger recombination rate in both hybrid organic-inorganic and fully inorganic halide perovskite nanocrystals as a function of nanocrystal volume. We find that the volume scaling of the biexciton Auger rate in the hybrid perovskites, containing a polar organic A-site cation, is significantly shallower than in the fully inorganic Cs-based nanocrystals. As the nanocrystals become smaller, the Auger rate in the hybrid nanocrystals increases even less than expected, compared to the fully inorganic nanocrystals, which already show a shallower volume dependence than other material systems such as chalcogenide quantum dots. This finding suggests there may be differences in the strength of Coulombic interactions between the fully inorganic and hybrid perovskites, which may prove to be crucial in selecting materials to obtain the highest performing devices in the future, and hints that there could be something "special" about the hybrid materials.

Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Laura L.; Blumer-Schuette, Sara E.; Izquierdo, Javier A.

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and thirteen genome sequences were used to re-assess genus-wide biodiversity for the extremely thermophilicCaldicellulosiruptor. The updated core-genome contains 1,401 ortholog groups (average genome size for thirteen species = 2,516 genes). The pan-genome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multi-domain glycoside hydrolases (GH). These include three cellulases with GH48 domains that are co-located in the Glucan Degradation Locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species,Caldicellulosiruptorsp. str. Rt8.B8 (re-named hereCaldicellulosiruptor morganii),Thermoanaerobacter cellulolyticusstr. NA10 (re-named hereCaldicellulosiruptor naganoensisNA10), andCaldicellulosiruptorsp. str.more » Wai35.B1 (re-named hereCaldicellulosiruptor danielii) degraded Avicel and lignocellulose (switchgrass).C. morganiiwas more efficient thanC. besciiin this regard and differed from the other twelve species examined here, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related toCaldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter,Fervidobacterium,Caloramator, andClostridium). One enrichment, containing 89.7%Caldicellulosiruptorand 9.7%Caloramator, had a capacity for switchgrass solubilization comparable toC. bescii. These results refine the known biodiversity ofCaldicellulosiruptorand indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. The genusCaldicellulosiruptorcontains the most thermophilic bacteria capable of lignocellulose deconstruction and are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pan-genomes, based on analysis of thirteen species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the Glucan Degradation Locus (GDL), a set of genes encoding glycoside hydrolases (GH), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic« less

Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis

DOE PAGES

Lee, Laura L.; Blumer-Schuette, Sara E.; Izquierdo, Javier A.; ...

2018-02-23

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and thirteen genome sequences were used to re-assess genus-wide biodiversity for the extremely thermophilicCaldicellulosiruptor. The updated core-genome contains 1,401 ortholog groups (average genome size for thirteen species = 2,516 genes). The pan-genome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multi-domain glycoside hydrolases (GH). These include three cellulases with GH48 domains that are co-located in the Glucan Degradation Locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species,Caldicellulosiruptorsp. str. Rt8.B8 (re-named hereCaldicellulosiruptor morganii),Thermoanaerobacter cellulolyticusstr. NA10 (re-named hereCaldicellulosiruptor naganoensisNA10), andCaldicellulosiruptorsp. str.more » Wai35.B1 (re-named hereCaldicellulosiruptor danielii) degraded Avicel and lignocellulose (switchgrass).C. morganiiwas more efficient thanC. besciiin this regard and differed from the other twelve species examined here, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related toCaldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter,Fervidobacterium,Caloramator, andClostridium). One enrichment, containing 89.7%Caldicellulosiruptorand 9.7%Caloramator, had a capacity for switchgrass solubilization comparable toC. bescii. These results refine the known biodiversity ofCaldicellulosiruptorand indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. The genusCaldicellulosiruptorcontains the most thermophilic bacteria capable of lignocellulose deconstruction and are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pan-genomes, based on analysis of thirteen species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the Glucan Degradation Locus (GDL), a set of genes encoding glycoside hydrolases (GH), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic« less

Characterization of novel human papillomavirus types 157, 158 and 205 from healthy skin and recombination analysis in genus γ-Papillomavirus.

PubMed

Bolatti, Elisa M; Chouhy, Diego; Casal, Pablo E; Pérez, Germán R; Stella, Emma J; Sanchez, Adriana; Gorosito, Mario; Bussy, Ramón Fernandez; Giri, Adriana A

2016-08-01

Gammapapillomavirus (γ-PV) is a diverse and rapidly expanding genus, currently consisting of 79 fully characterized human PV (HPV) types. In this study, three novel types, HPV157, HPV158 and HPV205, obtained from healthy sun-exposed skin of two immunocompetent individuals, were amplified by the "Hanging droplet" long PCR technique, cloned, sequenced and characterized. HPV157, HPV158 and HPV205 genomes comprise 7154-bp, 7192-bp and 7298-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2). Phylogenetic analysis of the L1 ORF placed all novel types within the γ-PV genus: HPV157 was classified as a new member of species γ-12 while HPV158 and HPV205 belong to species γ-1. We then explored potential recombination events in genus γ-PV with the RDP4 program in a dataset of 74 viruses (71 HPV types with available full-length genomes and the 3 novel types). Two events, both located in the E1 ORF, met the inclusion criterion (p-values <0.05 with at least four methods) and persisted in different ORF combinations: an inter-species recombination in species γ-8 (major and minor parents: species γ-24 and γ-11, respectively), and an intra-species recombination in species γ-7 (recombinant strain: HPV170; major and minor parents: HPV-109 and HPV-149, respectively). These findings were confirmed by phylogenetic tree incongruence analysis. An additional incongruence was found in members of species γ-9 but it was not detected by the RDP4. This report expands our knowledge of the family Papillomaviridae and provides for the first time in silico evidence of recombination in genus γ-PV. Copyright © 2016 Elsevier B.V. All rights reserved.

A molecular phylogeny of Alpine subterranean Trechini (Coleoptera: Carabidae)

PubMed Central

2013-01-01

Background The Alpine region harbours one of the most diverse subterranean faunas in the world, with many species showing extreme morphological modifications. The ground beetles of tribe Trechini (Coleoptera, Carabidae) are among the best studied and widespread groups with abundance of troglobionts, but their origin and evolution is largely unknown. Results We sequenced 3.4 Kb of mitochondrial (cox1, rrnL, trnL, nad1) and nuclear (SSU, LSU) genes of 207 specimens of 173 mostly Alpine species, including examples of all subterranean genera but two plus a representation of epigean taxa. We applied Bayesian methods and maximum likelihood to reconstruct the topology and to estimate divergence times using a priori rates obtained for a related ground beetle genus. We found three main clades of late Eocene-early Oligocene origin: (1) the genus Doderotrechus and relatives; (2) the genus Trechus sensu lato, with most anisotopic subterranean genera, including the Pyrenean lineage and taxa from the Dinaric Alps; and (3) the genus Duvalius sensu lato, diversifying during the late Miocene and including all subterranean isotopic taxa. Most of the subterranean genera had an independent origin and were related to epigean taxa of the same geographical area, but there were three large monophyletic clades of exclusively subterranean species: the Pyrenean lineage, a lineage including subterranean taxa from the eastern Alps and the Dinarides, and the genus Anophthalmus from the northeastern Alps. Many lineages have developed similar phenotypes independently, showing extensive morphological convergence or parallelism. Conclusions The Alpine Trechini do not form a homogeneous fauna, in contrast with the Pyrenees, and show a complex scenario of multiple colonisations of the subterranean environment at different geological periods and through different processes. Examples go from populations of an epigean widespread species going underground with little morphological modifications to ancient, geographically widespread lineages of exclusively subterranean species likely to have diversified once fully adapted to the subterranean environment. PMID:24225133

Language Assessment Literacy: Implications for Language Teachers

ERIC Educational Resources Information Center

Giraldo, Frank

2018-01-01

Recently, the applied linguistics field has examined the knowledge, skills, and principles needed for assessment, defined as language assessment literacy. Two major issues in language assessment literacy have been addressed but not fully resolved--what exactly language assessment literacy is and how it differs among stakeholders (e.g., students…

Multiple Systems for Cognitive Control: Evidence from a Hybrid Prime-Simon Task

ERIC Educational Resources Information Center

Schlaghecken, Friederike; Refaat, Malik; Maylor, Elizabeth A.

2011-01-01

Cognitive control resolves conflicts between appropriate and inappropriate response tendencies. Is this achieved by a unitary all-purpose conflict control system, or do independent subsystems deal with different aspects of conflicting information? In a fully factorial hybrid prime-Simon task, participants responded to the identity of targets…

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.

PubMed

Hamilton, Chris A; Lemmon, Alan R; Lemmon, Emily Moriarty; Bond, Jason E

2016-10-13

Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.

A new concept of Absoloniella (=Ruffodytes syn. n.) for five blind Mediterranean species (Coleoptera: Brachyceridae: Erirhininae).

PubMed

Grebennikov, Vasily V

2014-09-22

A hundred year-long taxonomic ambiguity surrounding two mysterious species originally described as Caulomorphus reitteri Müller, 1912 and Absoloniella cylindrica Formánek, 1913, both known from single specimens believed to be lost, is resolved. This is achieved by designation of their neotypes based on the same specimen collected together, and considered conspecific, with the holotype of Ruffodytes hellenicus Osella, 1973, the latter the type of the genus Ruffodytes Osella, 1973. This action triggers the following nomenclatorial and taxonomic changes: (1) the generic name Ruffodytes Osella, 1973 syn. n. is a junior subjective synonym of Absoloniella Formánek, 1913; (2) the names cylindrica syn. n. and hellenica syn. n. are junior objective and subjective synonyms, respectively, of the name reitteri for the species Absoloniella reitteri (Müller, 1912); (3) the genus Absoloniella currently comprises five species: A. reitteri (Müller, 1912), A. italica (Osella, 1976) comb. n., A. pacei (Osella, 1976) comb. n., A. servadeii (Osella, 1982) and A. nitidipennis (Osella, 1989) comb. n. Puzzling distribution of blind and wingless Mediterranean Absoloniella is briefly discussed.

Common but different: The expanding realm of Cladosporium

PubMed Central

Bensch, K.; Groenewald, J.Z.; Braun, U.; Dijksterhuis, J.; de Jesús Yáñez-Morales, M.; Crous, P.W.

2015-01-01

The genus Cladosporium (Cladosporiaceae, Dothideomycetes), which represents one of the largest genera of dematiaceous hyphomycetes, has been intensively investigated during the past decade. In the process, three major species complexes (C. cladosporioides, C. herbarum and C. sphaerospermum) were resolved based on morphology and DNA phylogeny, and a monographic revision of the genus (s. lat.) published reflecting the current taxonomic status quo. In the present study a further 19 new species are described based on phylogenetic characters (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, as well as partial actin and translation elongation factor 1-α gene sequences) and morphological differences. For a selection of the species with ornamented conidia, scanning electron microscopic photos were prepared to illustrate the different types of surface ornamentation. Surprisingly, during this study Cladosporium ramotenellum was found to be a quite common saprobic species, being widely distributed and occurring on various substrates. Therefore, an emended species description is provided. Furthermore, the host range and distribution data for several previously described species are also expanded. PMID:26955200

Phylogeny of the Genus Flavivirus

PubMed Central

Kuno, Goro; Chang, Gwong-Jen J.; Tsuchiya, K. Richard; Karabatsos, Nick; Cropp, C. Bruce

1998-01-01

We undertook a comprehensive phylogenetic study to establish the genetic relationship among the viruses of the genus Flavivirus and to compare the classification based on molecular phylogeny with the existing serologic method. By using a combination of quantitative definitions (bootstrap support level and the pairwise nucleotide sequence identity), the viruses could be classified into clusters, clades, and species. Our phylogenetic study revealed for the first time that from the putative ancestor two branches, non-vector and vector-borne virus clusters, evolved and from the latter cluster emerged tick-borne and mosquito-borne virus clusters. Provided that the theory of arthropod association being an acquired trait was correct, pairwise nucleotide sequence identity among these three clusters provided supporting data for a possibility that the non-vector cluster evolved first, followed by the separation of tick-borne and mosquito-borne virus clusters in that order. Clades established in our study correlated significantly with existing antigenic complexes. We also resolved many of the past taxonomic problems by establishing phylogenetic relationships of the antigenically unclassified viruses with the well-established viruses and by identifying synonymous viruses. PMID:9420202

Phylogeny of the genus Flavivirus.

PubMed

Kuno, G; Chang, G J; Tsuchiya, K R; Karabatsos, N; Cropp, C B

1998-01-01

We undertook a comprehensive phylogenetic study to establish the genetic relationship among the viruses of the genus Flavivirus and to compare the classification based on molecular phylogeny with the existing serologic method. By using a combination of quantitative definitions (bootstrap support level and the pairwise nucleotide sequence identity), the viruses could be classified into clusters, clades, and species. Our phylogenetic study revealed for the first time that from the putative ancestor two branches, non-vector and vector-borne virus clusters, evolved and from the latter cluster emerged tick-borne and mosquito-borne virus clusters. Provided that the theory of arthropod association being an acquired trait was correct, pairwise nucleotide sequence identity among these three clusters provided supporting data for a possibility that the non-vector cluster evolved first, followed by the separation of tick-borne and mosquito-borne virus clusters in that order. Clades established in our study correlated significantly with existing antigenic complexes. We also resolved many of the past taxonomic problems by establishing phylogenetic relationships of the antigenically unclassified viruses with the well-established viruses and by identifying synonymous viruses.

Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants

PubMed Central

Kaiser, Bettina; Vogg, Gerd; Fürst, Ursula B.; Albert, Markus

2015-01-01

By comparison with plant–microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant–plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato. PMID:25699071

Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants.

PubMed

Kaiser, Bettina; Vogg, Gerd; Fürst, Ursula B; Albert, Markus

2015-01-01

By comparison with plant-microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant-plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato.

Molecular diversification of Trichuris spp. from Sigmodontinae (Cricetidae) rodents from Argentina based on mitochondrial DNA sequences.

PubMed

Callejón, Rocío; Robles, María Del Rosario; Panei, Carlos Javier; Cutillas, Cristina

2016-08-01

A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob). The taxa consisted of nine populations of whipworm from five species of Sigmodontinae rodents from Argentina. Bayesian Inference, Maximum Parsimony, and Maximum Likelihood methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data and the combined mitochondrial and nuclear dataset. Phylogenetic results based on cox1 and cob mitochondrial DNA (mtDNA) revealed three clades strongly resolved corresponding to three different species (Trichuris navonae, Trichuris bainae, and Trichuris pardinasi) showing phylogeographic variation, but relationships among Trichuris species were poorly resolved. Phylogenetic reconstruction based on concatenated sequences had greater phylogenetic resolution for delimiting species and populations intra-specific of Trichuris than those based on partitioned genes. Thus, populations of T. bainae and T. pardinasi could be affected by geographical factors and co-divergence parasite-host.

The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

PubMed Central

2011-01-01

Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups. PMID:21745361

Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies.

PubMed

Carlson, Alexis; Justo, Alfredo; Hibbett, David S

2014-01-01

Trametes is a cosmopolitan genus of white rot polypores, including the "turkey tail" fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus. © 2014 by The Mycological Society of America.

Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs

PubMed Central

Horvath, Julie E.; Weisrock, David W.; Embry, Stephanie L.; Fiorentino, Isabella; Balhoff, James P.; Kappeler, Peter; Wray, Gregory A.; Willard, Huntington F.; Yoder, Anne D.

2008-01-01

Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing ∼9 kb of nuclear sequence data. In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds ∼275 kb of DNA sequence to current databases. Our phylogenetic analyses confirm hypotheses of lemuriform monophyly and provide robust resolution of the phylogenetic relationships among the five lemuriform families. We verify that the genus Daubentonia is the sister lineage to all other lemurs. The Cheirogaleidae and Lepilemuridae are sister taxa and together form the sister lineage to the Indriidae; this clade is the sister lineage to the Lemuridae. Divergence time estimates indicate that lemurs are an ancient group, with their initial diversification occurring around the Cretaceous-Tertiary boundary. Given the power of this data set to resolve branches in a notoriously problematic area of primate phylogeny, we anticipate that our phylogenomic toolkit will be of value to other studies of primate phylogeny and diversification. Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve. PMID:18245770

Convergence behavior of idealized convection-resolving simulations of summertime deep moist convection over land

NASA Astrophysics Data System (ADS)

Panosetti, Davide; Schlemmer, Linda; Schär, Christoph

2018-05-01

Convection-resolving models (CRMs) can explicitly simulate deep convection and resolve interactions between convective updrafts. They are thus increasingly used in numerous weather and climate applications. However, the truncation of the continuous energy cascade at scales of O (1 km) poses a serious challenge, as in kilometer-scale simulations the size and properties of the simulated convective cells are often determined by the horizontal grid spacing (Δ x ).In this study, idealized simulations of deep moist convection over land are performed to assess the convergence behavior of a CRM at Δ x = 8, 4, 2, 1 km and 500 m. Two types of convergence estimates are investigated: bulk convergence addressing domain-averaged and integrated variables related to the water and energy budgets, and structural convergence addressing the statistics and scales of individual clouds and updrafts. Results show that bulk convergence generally begins at Δ x =4 km, while structural convergence is not yet fully achieved at the kilometer scale, despite some evidence that the resolution sensitivity of updraft velocities and convective mass fluxes decreases at finer resolution. In particular, at finer grid spacings the maximum updraft velocity generally increases, and the size of the smallest clouds is mostly determined by Δ x . A number of different experiments are conducted, and it is found that the presence of orography and environmental vertical wind shear yields more energetic structures at scales much larger than Δ x , sometimes reducing the resolution sensitivity. Overall the results lend support to the use of kilometer-scale resolutions in CRMs, despite the inability of these models to fully resolve the associated cloud field.

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution.

PubMed

Fu, Chao-Nan; Li, Hong-Tao; Milne, Richard; Zhang, Ting; Ma, Peng-Fei; Yang, Jing; Li, De-Zhu; Gao, Lian-Ming

2017-12-08

The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified. Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.

Resolvent analysis of exact coherent solutions

NASA Astrophysics Data System (ADS)

Rosenberg, Kevin; McKeon, Beverley

2017-11-01

Exact coherent solutions have been hypothesized to constitute the state-space skeleton of turbulent trajectories and thus are of interest as a means to better understand the underlying dynamics of turbulent flows. An asymptotic description of how these types of solutions self-sustain was provided by Hall & Sherwin. Here we offer a fully-nonlinear perspective on the self-sustainment of these solutions in terms of triadic scale interactions and use the resolvent framework of McKeon & Sharma to interpret these results from an input/output point of view. We analyze traveling wave solutions and periodic orbits in channel flow, and demonstrate how resolvent analysis can be used to obtain low-dimensional representations of these flows. We gratefully acknowledge funding from the AFOSR (FA9550-16-1-0361) and J.S. Park, M.D. Graham, and J.F. Gibson for providing data for the ECS solutions.

Coarse Grid CFD for underresolved simulation

NASA Astrophysics Data System (ADS)

Class, Andreas G.; Viellieber, Mathias O.; Himmel, Steffen R.

2010-11-01

CFD simulation of the complete reactor core of a nuclear power plant requires exceedingly huge computational resources so that this crude power approach has not been pursued yet. The traditional approach is 1D subchannel analysis employing calibrated transport models. Coarse grid CFD is an attractive alternative technique based on strongly under-resolved CFD and the inviscid Euler equations. Obviously, using inviscid equations and coarse grids does not resolve all the physics requiring additional volumetric source terms modelling viscosity and other sub-grid effects. The source terms are implemented via correlations derived from fully resolved representative simulations which can be tabulated or computed on the fly. The technique is demonstrated for a Carnot diffusor and a wire-wrap fuel assembly [1]. [4pt] [1] Himmel, S.R. phd thesis, Stuttgart University, Germany 2009, http://bibliothek.fzk.de/zb/berichte/FZKA7468.pdf

Translational control of a graphically simulated robot arm by kinematic rate equations that overcome elbow joint singularity

NASA Technical Reports Server (NTRS)

Barker, L. K.; Houck, J. A.; Carzoo, S. W.

1984-01-01

An operator commands a robot hand to move in a certain direction relative to its own axis system by specifying a velocity in that direction. This velocity command is then resolved into individual joint rotational velocities in the robot arm to effect the motion. However, the usual resolved-rate equations become singular when the robot arm is straightened. To overcome this elbow joint singularity, equations were developed which allow continued translational control of the robot hand even though the robot arm is (or is nearly) fully extended. A feature of the equations near full arm extension is that an operator simply extends and retracts the robot arm to reverse the direction of the elbow bend (difficult maneuver for the usual resolved-rate equations). Results show successful movement of a graphically simulated robot arm.

A lower Cretaceous (Valanginian) seed cone provides the earliest fossil record for Picea (Pinaceae).

PubMed

Klymiuk, Ashley A; Stockey, Ruth A

2012-06-01

Sequence analyses for Pinaceae have suggested that extant genera diverged in the late Mesozoic. While the fossil record indicates that Pinaceae was highly diverse during the Cretaceous, there are few records of living genera. This description of an anatomically preserved seed cone extends the fossil record for Picea A. Dietrich (Pinaceae) by ∼75 Ma. The specimen was collected from the Apple Bay locality of Vancouver Island (Lower Cretaceous, Valanginian) and is described from anatomical sections prepared using cellulose acetate peels. Cladistic analyses of fossil and extant pinaceous seed cones employed parsimony ratchet searches of an anatomical and morphological matrix. This new seed cone has a combination of characters shared only with the genus Picea A. Dietr. and is thus described as Picea burtonii Klymiuk et Stockey sp. nov. Bisaccate pollen attributable to Picea is found in the micropyles of several ovules, corroborating the designation of this cone as an early spruce. Cladistic analyses place P. burtonii with extant Picea and an Oligocene representative of the genus. Furthermore, our analyses indicate that Picea is sister to Cathaya Chun et Kuang, and P. burtonii helps to establish a minimum date for this node in hypotheses of conifer phylogeny. As an early member of the extant genus Picea, this seed cone extends the fossil record of Picea to the Valanginian Stage of the Early Cretaceous, ca. 136 Ma, thereby resolving a ghost lineage predicted by molecular divergence analyses, and offers new insight into the evolution of Pinaceae.

Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume.

PubMed

Yang, Shuyi; Grall, Aurélie; Chapman, Mark A

2018-05-01

For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop. © 2018 Botanical Society of America.

Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

PubMed

García, Miguel A; Costea, Mihai; Kuzmina, Maria; Stefanović, Saša

2014-04-01

The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.

Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence.

PubMed

Friis, Guillermo; Aleixandre, Pau; Rodríguez-Estrella, Ricardo; Navarro-Sigüenza, Adolfo G; Milá, Borja

2016-12-01

Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates. © 2016 John Wiley & Sons Ltd.

The discovery of Halictivirus resolves the Sinaivirus phylogeny.

PubMed

Bigot, Diane; Dalmon, Anne; Roy, Bronwen; Hou, Chunsheng; Germain, Michèle; Romary, Manon; Deng, Shuai; Diao, Qingyun; Weinert, Lucy A; Cook, James M; Herniou, Elisabeth A; Gayral, Philippe

2017-11-01

By providing pollination services, bees are among the most important insects, both in ecological and economical terms. Combined next-generation and classical sequencing approaches were applied to discover and study new insect viruses potentially harmful to bees. A bioinformatics virus discovery pipeline was used on individual Illumina transcriptomes of 13 wild bees from three species from the genus Halictus and 30 ants from six species of the genera Messor and Aphaenogaster. This allowed the discovery and description of three sequences of a new virus termed Halictus scabiosae Adlikon virus (HsAV). Phylogenetic analyses of ORF1, RNA-dependent RNA-polymerase (RdRp) and capsid genes showed that HsAV is closely related to (+)ssRNA viruses of the unassigned Sinaivirus genus but distant enough to belong to a different new genus we called Halictivirus. In addition, our study of ant transcriptomes revealed the first four sinaivirus sequences from ants (Messor barbarus, M. capitatus and M. concolor). Maximum likelihood phylogenetic analyses were performed on a 594 nt fragment of the ORF1/RdRp region from 84 sinaivirus sequences, including 31 new Lake Sinai viruses (LSVs) from honey bees collected in five countries across the globe and the four ant viral sequences. The phylogeny revealed four main clades potentially representing different viral species infecting honey bees. Moreover, the ant viruses belonged to the LSV4 clade, suggesting a possible cross-species transmission between bees and ants. Lastly, wide honey bee screening showed that all four LSV clades have worldwide distributions with no obvious geographical segregation.

Molecular phylogenetic evidence supports a new family of octocorals and a new genus of Alcyoniidae (Octocorallia, Alcyonacea)

PubMed Central

McFadden, Catherine S.; van Ofwegen, Leen P.

2013-01-01

Abstract Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n., and family, Parasphaerascleridae fam. n., of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites in the polyps, and have radiates or spheroidal sclerites in the colony surface and interior. Parasphaerascleridae fam. n. constitutes a well-supported clade that is phylogenetically distinct from all other octocoral taxa. We also describe a new genus of Alcyoniidae, Sphaerasclera gen. n., for a species of Eleutherobia with a unique capitate growth form. Sphaerasclera gen. n. is a member of the Anthomastus–Corallium clade of octocorals, but is morphologically and genetically distinct from Anthomastus Verrill, 1878 and Paraminabea Williams & Alderslade, 1999, two similar but dimorphic genera of Alcyoniidae that are its sister taxa. In addition, we have re-assigned two species of Eleutherobia that have clavate to capitate growth forms, polyp sclerites arranged to form a collaret and points, and spindles in the colony interior to Alcyonium, a move that is supported by both morphological and molecular phylogenetic evidence. PMID:24223488

Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae).

PubMed

Ghosh, S; Majumder, P B; Sen Mandi, S

2011-02-08

The Zingiber genus, which includes the herbs known as gingers, commonly used in cooking, is well known for its medicinal properties, as described in the Indian pharmacopoeia. Different members of this genus, although somewhat similar in morphology, differ widely in their pharmacological and therapeutic properties. The most important species of this genus, with maximal therapeutic properties, is Zingiber officinale (garden ginger), which is often adulterated with other less-potent Zingiber sp. There is an existing demand in the herbal drug industry for an authentication system for the Zingiber sp in order to facilitate their commercial use as genuine phytoceuticals. To this end, we used amplified fragment length polymorphism (AFLP) to produce DNA fingerprints for three Zingiber species. Sixteen collections (six of Z. officinale, five of Z. montanum, and five of Z. zerumbet) were used in the study. Seven selective primer pairs were found to be useful for all the accessions. A total of 837 fragments were produced by these primer pairs. Species-specific markers were identified for all three Zingiber species (91 for Z. officinale, 82 for Z. montanum, and 55 for Z. zerumbet). The dendogram analysis generated from AFLP patterns showed that Z. montanum and Z. zerumbet are phylogenetically closer to each other than to Z. officinale. The AFLP fingerprints of the Zingiber species could be used to authenticate Zingiber sp-derived drugs and to resolve adulteration-related problems faced by the commercial users of these herbs.

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

PubMed Central

Marcussen, Thomas; Heier, Lise; Brysting, Anne K.; Oxelman, Bengt; Jakobsen, Kjetill S.

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage—between 67% and 88%—of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. PMID:25281848

Pulling the sting out of nettle systematics - A comprehensive phylogeny of the genus Urtica L. (Urticaceae).

PubMed

Grosse-Veldmann, Bernadette; Nürk, Nicolai M; Smissen, Rob; Breitwieser, Ilse; Quandt, Dietmar; Weigend, Maximilian

2016-09-01

The genus Urtica L. is subcosmopolitan, found on all continents (except Antarctica) and most extratropical islands and ranges from Alaska to Patagonia, Spitzbergen to the Cape and Camtschatka to the subantarctic islands. However, throughout its geographical range morphologically nearly indistinguishable species are found alongside morphologically quite disparate species, with the overall diversity of morphological characters extremely limited. The systematics of Urtica have puzzled scientists for the past 200years and no single comprehensive attempt at understanding infrageneric relationships has been published in the past, nor are species delimitations unequivocally established. We here provide the first comprehensive phylogeny of the genus including 61 of the 63 species recognized, represented by 144 ingroup accessions and 14 outgroup taxa. The markers ITS1-5.8S-ITS2, psbA-trnH intergenic spacer, trnL-trnF and trnS-trnG are used. The phylogeny is well resolved. The eastern Asian Zhengyia shennongensis T. Deng, D.G. Zhang & H. Sun is retrieved as sister to Urtica. Within Urtica, a clade comprising the western Eurasian species U. pilulifera L. and U. neubaueri Chrtek is sister to all other species of the genus. The phylogenetic analyses retrieve numerous well-supported clades, suggesting previously unsuspected relationships and implying that classically used taxonomic characters such as leaf morphology and growth habit are highly homoplasious. Species delimitation is problematical, and several accessions assigned to Urtica dioica L. (as subspecies) are retrieved in widely different places in the phylogeny. The genus seems to have undergone numerous dispersal-establishment events both between continents and onto different islands. Three recent species radiations are inferred, one in America centered in the Andes, one in New Zealand, and one in northern Eurasia which includes Urtica dioica s.str. sensu Henning et al. (2014). The present study provides the basis of a critical re-examination of species limits and taxonomy, but also of the dispersal ecology of this widespread plant group and an in-depth study of the three clades with recent radiations. Copyright © 2016 Elsevier Inc. All rights reserved.

Micromonospora schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil.

PubMed

Vela Gurovic, Maria Soledad; Müller, Sebastian; Domin, Nicole; Seccareccia, Ivana; Nietzsche, Sandor; Martin, Karin; Nett, Markus

2013-10-01

A Gram-stain-positive, spore-forming actinomycete strain (HKI0641(T)) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus Micromonospora. The peptidoglycan of strain HKI0641(T) contained meso-diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. MK-10(H4), MK-10(H2) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641(T), we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gyrB gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus Micromonospora, but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified Micromonospora coxensis DSM 45161(T) (99.1 % sequence similarity) and Micromonospora marina DSM 45555(T) (99.0 %) as the nearest taxonomic neighbours, whereas the gyrB sequence of strain HKI0641(T) indicated a closer relationship to Micromonospora aurantiaca DSM 43813(T) (95.1 %). By means of DNA-DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641(T) from other species of the genus Micromonospora. The type strains of the aforementioned species of the genus Micromonospora could be further distinguished from strain HKI0641(T) by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus Micromonospora, for which the name Micromonospora schwarzwaldensis sp. nov. is proposed. The type strain is HKI0641(T) ( = DSM 45708(T) = CIP 110415(T)).

Molecular phylogeny and taxonomic revision of the genus Wittrockiella (Pithophoraceae, Cladophorales), including the descriptions of W. australis sp. nov. and W. zosterae sp. nov.

PubMed

Boedeker, Christian; O'Kelly, Charles J; West, John A; Hanyuda, Takeaki; Neale, Adele; Wakana, Isamu; Wilcox, Mike D; Karsten, Ulf; Zuccarello, Giuseppe C

2017-06-01

Wittrockiella is a small genus of filamentous green algae that occurs in habitats with reduced or fluctuating salinities. Many aspects of the basic biology of these algae are still unknown and the phylogenetic relationships within the genus have not been fully explored. We provide a phylogeny based on three ribosomal markers (ITS, LSU, and SSU rDNA) of the genus, including broad intraspecific sampling for W. lyallii and W. salina, recommendations for the use of existing names are made, and highlight aspects of their physiology and life cycle. Molecular data indicate that there are five species of Wittrockiella. Two new species, W. australis and W. zosterae, are described, both are endophytes. Although W. lyallii and W. salina can be identified morphologically, there are no diagnostic morphological characters to distinguish between W. amphibia, W. australis, and W. zosterae. A range of low molecular weight carbohydrates were analyzed but proved to not be taxonomically informative. The distribution range of W. salina is extended to the Northern Hemisphere as this species has been found in brackish lakes in Japan. Furthermore, it is shown that there are no grounds to recognize W. salina var. kraftii, which was described as an endemic variety from a freshwater habitat on Lord Howe Island, Australia. Culture experiments indicate that W. australis has a preference for growth in lower salinities over full seawater. For W. amphibia and W. zosterae, sexual reproduction is documented, and the split of these species is possibly attributable to polyploidization. © 2017 Phycological Society of America.

Topology Analysis of the Sloan Digital Sky Survey. I. Scale and Luminosity Dependence

NASA Astrophysics Data System (ADS)

Park, Changbom; Choi, Yun-Young; Vogeley, Michael S.; Gott, J. Richard, III; Kim, Juhan; Hikage, Chiaki; Matsubara, Takahiko; Park, Myeong-Gu; Suto, Yasushi; Weinberg, David H.; SDSS Collaboration

2005-11-01

We measure the topology of volume-limited galaxy samples selected from a parent sample of 314,050 galaxies in the Sloan Digital Sky Survey (SDSS), which is now complete enough to describe the fully three-dimensional topology and its dependence on galaxy properties. We compare the observed genus statistic G(νf) to predictions for a Gaussian random field and to the genus measured for mock surveys constructed from new large-volume simulations of the ΛCDM cosmology. In this analysis we carefully examine the dependence of the observed genus statistic on the Gaussian smoothing scale RG from 3.5 to 11 h-1 Mpc and on the luminosity of galaxies over the range -22.50

New species of aquatic insects from Europe (Insecta: Trichoptera): Alps and Pyrenees as harbours of unknown biodiversity

PubMed Central

GRAF, WOLFRAM; VITECEK, SIMON; PREVIŠIĆ, ANA; MALICKY, HANS

2016-01-01

New species are described from the following genera: Consorophylax and Anisogamus, (Trichoptera, Limnephilidae). Additionally the larvae of the genus Anisogamus, and the larval stages of Anisogamus waringeri nov. sp. and A. difformis (McLachlan 1867) are described. The new species Consorophylax vinconi sp. nov. is a microendemic from the Southern Alps and differs distinctly from its congeners in the shape of the parameres, which are distinctly straitened in the distal quarter in the new species. The new species Anisogamus waringeri sp. nov. represents the second species in the hitherto monospecific genus Anisogamus. Compared to Anisogamus difformis, A. waringeri sp. nov. develops more slender superior appendages; a more rounded basal plate of the intermediate appendages, lacking pointed protuberances; and parameres shorter than the aedaegus, proximally with one dorsal and several ventral tines. Further, the two species are disjunctly distributed in the European mountain ranges (A. difformis: Alps, A. waringeri sp. nov.: Pyrenees). Larvae of the genus Anisogamus are characterized by the lack of a dorsal protuberance on the 1st abdominal segment, a unique feature among Limnephilidae. Anisogamus difformis and A. waringeri sp. nov. larvae differ in pronotum shape. The recovery of two new species demonstrates the significance of taxonomic studies in Europe, and the importance of adequate training for young scientists in order to assess a biodiversity under threat of extinction that has yet to be fully described. PMID:25661619

EVALUATION OF THE CMAQ - AIM MODEL AGAINST SIZE AND CHEMICALLY-RESOLVED IMPACTOR DATA AT A COASTAL URBAN SITE

EPA Science Inventory

CMAQ-UCD (formerly known as CMAQ-AIM), is a fully dynamic, sectional aerosol model which has been coupled to the Community Multiscale Air Quality (CMAQ) host air quality model. Aerosol sulfate, nitrate, ammonium, sodium, and chloride model outputs are compared against MOUDI data...

Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty.

PubMed

Blomberg, S

2000-11-01

Currently available programs for the comparative analysis of phylogenetic data do not perform optimally when the phylogeny is not completely specified (i.e. the phylogeny contains polytomies). Recent literature suggests that a better way to analyse the data would be to create random trees from the known phylogeny that are fully-resolved but consistent with the known tree. A computer program is presented, Fels-Rand, that performs such analyses. A randomisation procedure is used to generate trees that are fully resolved but whose structure is consistent with the original tree. Statistics are then calculated on a large number of these randomly-generated trees. Fels-Rand uses the object-oriented features of Xlisp-Stat to manipulate internal tree representations. Xlisp-Stat's dynamic graphing features are used to provide heuristic tools to aid in analysis, particularly outlier analysis. The usefulness of Xlisp-Stat as a system for phylogenetic computation is discussed. Available from the author or at http://www.uq.edu.au/~ansblomb/Fels-Rand.sit.hqx. Xlisp-Stat is available from http://stat.umn.edu/~luke/xls/xlsinfo/xlsinfo.html. s.blomberg@abdn.ac.uk

Nonperturbative Quantum Nature of the Dislocation–Phonon Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mingda; Ding, Zhiwei; Meng, Qingping

Despite the long history of dislocation–phonon interaction studies, there are many problems that have not been fully resolved during this development. These include an incompatibility between a perturbative approach and the long-range nature of a dislocation, the relation between static and dynamic scattering, and their capability of dealing with thermal transport phenomena for bulk material only. Here in this paper, by utilizing a fully quantized dislocation field, which we called a “dislon”, a phonon interacting with a dislocation is renormalized as a quasi-phonon, with shifted quasi-phonon energy, and accompanied by a finite quasi-phonon lifetime, which are reducible to classical results.more » A series of outstanding legacy issues including those above can be directly explained within this unified phonon renormalization approach. For instance, a renormalized phonon naturally resolves the decade-long debate between dynamic and static dislocation–phonon scattering approaches, as two limiting cases. In particular, at nanoscale, both the dynamic and static approaches break down, while the present renormalization approach remains valid by capturing the size effect, showing good agreement with lattice dynamics simulations.« less

Nonperturbative Quantum Nature of the Dislocation–Phonon Interaction

DOE PAGES

Li, Mingda; Ding, Zhiwei; Meng, Qingping; ...

2017-01-31

Despite the long history of dislocation–phonon interaction studies, there are many problems that have not been fully resolved during this development. These include an incompatibility between a perturbative approach and the long-range nature of a dislocation, the relation between static and dynamic scattering, and their capability of dealing with thermal transport phenomena for bulk material only. Here in this paper, by utilizing a fully quantized dislocation field, which we called a “dislon”, a phonon interacting with a dislocation is renormalized as a quasi-phonon, with shifted quasi-phonon energy, and accompanied by a finite quasi-phonon lifetime, which are reducible to classical results.more » A series of outstanding legacy issues including those above can be directly explained within this unified phonon renormalization approach. For instance, a renormalized phonon naturally resolves the decade-long debate between dynamic and static dislocation–phonon scattering approaches, as two limiting cases. In particular, at nanoscale, both the dynamic and static approaches break down, while the present renormalization approach remains valid by capturing the size effect, showing good agreement with lattice dynamics simulations.« less

Microsphere-assisted super-resolution imaging with enlarged numerical aperture by semi-immersion

NASA Astrophysics Data System (ADS)

Wang, Fengge; Yang, Songlin; Ma, Huifeng; Shen, Ping; Wei, Nan; Wang, Meng; Xia, Yang; Deng, Yun; Ye, Yong-Hong

2018-01-01

Microsphere-assisted imaging is an extraordinary simple technology that can obtain optical super-resolution under white-light illumination. Here, we introduce a method to improve the resolution of a microsphere lens by increasing its numerical aperture. In our proposed structure, BaTiO3 glass (BTG) microsphere lenses are semi-immersed in a S1805 layer with a refractive index of 1.65, and then, the semi-immersed microspheres are fully embedded in an elastomer with an index of 1.4. We experimentally demonstrate that this structure, in combination with a conventional optical microscope, can clearly resolve a two-dimensional 200-nm-diameter hexagonally close-packed (hcp) silica microsphere array. On the contrary, the widely used structure where BTG microsphere lenses are fully immersed in a liquid or elastomer cannot even resolve a 250-nm-diameter hcp silica microsphere array. The improvement in resolution through the proposed structure is due to an increase in the effective numerical aperture by semi-immersing BTG microsphere lenses in a high-refractive-index S1805 layer. Our results will inform on the design of microsphere-based high-resolution imaging systems.

Recent Advances in Fluorescence Lifetime Analytical Microsystems: Contact Optics and CMOS Time-Resolved Electronics.

PubMed

Wei, Liping; Yan, Wenrong; Ho, Derek

2017-12-04

Fluorescence spectroscopy has become a prominent research tool with wide applications in medical diagnostics and bio-imaging. However, the realization of combined high-performance, portable, and low-cost spectroscopic sensors still remains a challenge, which has limited the technique to the laboratories. A fluorescence lifetime measurement seeks to obtain the characteristic lifetime from the fluorescence decay profile. Time-correlated single photon counting (TCSPC) and time-gated techniques are two key variations of time-resolved measurements. However, commercial time-resolved analysis systems typically contain complex optics and discrete electronic components, which lead to bulkiness and a high cost. These two limitations can be significantly mitigated using contact sensing and complementary metal-oxide-semiconductor (CMOS) implementation. Contact sensing simplifies the optics, whereas CMOS technology enables on-chip, arrayed detection and signal processing, significantly reducing size and power consumption. This paper examines recent advances in contact sensing and CMOS time-resolved circuits for the realization of fully integrated fluorescence lifetime measurement microsystems. The high level of performance from recently reported prototypes suggests that the CMOS-based contact sensing microsystems are emerging as sound technologies for application-specific, low-cost, and portable time-resolved diagnostic devices.

Recent Advances in Fluorescence Lifetime Analytical Microsystems: Contact Optics and CMOS Time-Resolved Electronics

PubMed Central

Yan, Wenrong; Ho, Derek

2017-01-01

Fluorescence spectroscopy has become a prominent research tool with wide applications in medical diagnostics and bio-imaging. However, the realization of combined high-performance, portable, and low-cost spectroscopic sensors still remains a challenge, which has limited the technique to the laboratories. A fluorescence lifetime measurement seeks to obtain the characteristic lifetime from the fluorescence decay profile. Time-correlated single photon counting (TCSPC) and time-gated techniques are two key variations of time-resolved measurements. However, commercial time-resolved analysis systems typically contain complex optics and discrete electronic components, which lead to bulkiness and a high cost. These two limitations can be significantly mitigated using contact sensing and complementary metal-oxide-semiconductor (CMOS) implementation. Contact sensing simplifies the optics, whereas CMOS technology enables on-chip, arrayed detection and signal processing, significantly reducing size and power consumption. This paper examines recent advances in contact sensing and CMOS time-resolved circuits for the realization of fully integrated fluorescence lifetime measurement microsystems. The high level of performance from recently reported prototypes suggests that the CMOS-based contact sensing microsystems are emerging as sound technologies for application-specific, low-cost, and portable time-resolved diagnostic devices. PMID:29207568

4D blood flow mapping using SPIM-microPIV in the developing zebrafish heart

NASA Astrophysics Data System (ADS)

Zickus, Vytautas; Taylor, Jonathan M.

2018-02-01

Fluid-structure interaction in the developing heart is an active area of research in developmental biology. However, investigation of heart dynamics is mostly limited to computational uid dynamics simulations using heart wall structure information only, or single plane blood ow information - so there is a need for 3D + time resolved data to fully understand cardiac function. We present an imaging platform combining selective plane illumination microscopy (SPIM) with micro particle image velocimetry (μPIV) to enable 3D-resolved flow mapping in a microscopic environment, free from many of the sources of error and bias present in traditional epi uorescence-based μPIV systems. By using our new system in conjunction with optical heart beat synchronization, we demonstrate the ability obtain non-invasive 3D + time resolved blood flow measurements in the heart of a living zebrafish embryo.

Quantitative, spectrally-resolved intraoperative fluorescence imaging

PubMed Central

Valdés, Pablo A.; Leblond, Frederic; Jacobs, Valerie L.; Wilson, Brian C.; Paulsen, Keith D.; Roberts, David W.

2012-01-01

Intraoperative visual fluorescence imaging (vFI) has emerged as a promising aid to surgical guidance, but does not fully exploit the potential of the fluorescent agents that are currently available. Here, we introduce a quantitative fluorescence imaging (qFI) approach that converts spectrally-resolved data into images of absolute fluorophore concentration pixel-by-pixel across the surgical field of view (FOV). The resulting estimates are linear, accurate, and precise relative to true values, and spectral decomposition of multiple fluorophores is also achieved. Experiments with protoporphyrin IX in a glioma rodent model demonstrate in vivo quantitative and spectrally-resolved fluorescence imaging of infiltrating tumor margins for the first time. Moreover, we present images from human surgery which detect residual tumor not evident with state-of-the-art vFI. The wide-field qFI technique has broad implications for intraoperative surgical guidance because it provides near real-time quantitative assessment of multiple fluorescent biomarkers across the operative field. PMID:23152935

Systematic status of Fejervarya ((Amphibia, Anura, Dicroglossidae) from South and SE Asia with the description of a new species from the Western Ghats of Peninsular India.

PubMed

Dinesh, K P; Vijayakumar, S P; Channakeshavamurthy, B H; Torsekar, Varun R; Kulkarni, Nirmal U; Shanker, Kartik

2015-08-07

We carried out a large-scale phylogenetic analysis of fejervaryan (dicroglossid frogs with 'Fejervaryan lines' on the ventral side of the body) frogs, distributed in South and SE Asia, using published and newly generated sequences of unidentified individuals from the northern Western Ghats. The results corroborate the presence of a larger fejervaryan clade with a sister relationship to a clade composed of Sphaerotheca. Two sister clades could be discerned within the lager fejervaryan clade. The unidentified individuals formed a monophyletic group and showed a strong support for a sister relationship with Minervarya sahyadris. The species was found to be highly divergent (16S rRNA-4% and tyr-1%) from its sister lineage Minervarya sahyadris, and the clade composed of these two lineages were found to be deeply nested within the larger clade of Fejervarya. Based on this, the genus Minervarya Dubois, Ohler and Biju, 2001 is synonymized under the genus Fejervarya Bolkay, 1915. The unidentified lineage is recognized, based on phylogenetic position, genetic divergence and morphological divergence, as a distinct species and named here as Fejervarya gomantaki sp. nov. The presence of rictal glands was observed to be a synapomorphic character shared by the nested clade members, Fejervarya sahyadris and Fejervarya gomantaki sp. nov. Based on the presence of rictal gland and small size, Minervarya chilapata, a species from a lowland region in the Eastern Himalayas, is synonymized under Fejervarya and evidence for morphological separation from the new species, Fejervarya gomantaki sp. nov. is provided. For fejervaryan frogs, three generic names (Frost, 2015) are currently in use for two phylogenetic subclades; the genus Fejervarya Bolkay, 1915 for species distributed in South East Asia; the genus Zakerana Howlader, 2011 for species distributed in South Asia and the genus Minervarya Dubois, Ohler and Biju, 2001 nested within the 'Zakerana clade'. In the phylogenetic analysis Minervarya sahyadris and the new species described herein as Fejervarya gomantaki sp. nov. are nested within the 'Zakerana clade'. If the 'Zakerana clade' for the fejervaryan frogs distributed in South Asia is assigned a generic status, the nomen 'Minervarya' should be used as per the principle of priority of the ICZN Code. Taking into consideration the overlapping distribution ranges of members of the sister clades within the larger fejervaryan clade and the absence of distinct morphological characteristics, we also synonymize the genus Zakerana Howlader, 2011, a name assigned to one of the sister clades with members predominantly distributed in South Asia, under the genus Fejervarya Bolkay, 1915. We discuss the need for additional sampling to identify additional taxa and determine the geographical ranges of the members of the sister clades within Fejervarya to resolve taxonomy within this group. [Corrected

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

PubMed Central

2013-01-01

Background Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. Results Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. Conclusions Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use. PMID:23826735

Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by nuclear introns: implications for the evolution of male tusks.

PubMed

Dalebout, Merel L; Steel, Debbie; Baker, C Scott

2008-12-01

With 14 species currently recognized, the beaked whale genus Mesoplodon (family Ziphiidae) is the most speciose in the order Cetacea. Beaked whales are widely distributed but are rarely seen at sea due to their oceanic distribution, deep-diving capacity, and apparent low abundance. Morphological differentiation among Mesoplodon species is relatively limited, with the exception of tooth form in adult males. Based on scarring patterns, males appear to use their tusk-like teeth as weapons in aggressive encounters with other males. Females are effectively toothless. We used sequences from seven nuclear introns (3348 base pairs) to construct a robust and highly resolved phylogeny, which was then used as a framework to test predictions from four hypotheses seeking to explain patterns of Mesoplodon tusk morphology and/or the processes that have driven the diversification of this genus: (1) linear progression of tusk form; (2) allopatric speciation through isolation in adjacent deep-sea canyons; (3) sympatric speciation through sexual selection on tusks; and (4) selection for species-recognition cues. Maximum-likelihood and Bayesian reconstructions confirmed the monophyly of the genus and revealed that what were considered ancestral and derived tusk forms have in fact arisen independently on several occasions, contrary to predictions from the linear-progression hypothesis. Further, none of the three well-supported species clades was confined to a single ocean basin, as might have been expected from the deep-sea canyon-isolation or sexual-selection hypotheses, and some species with similar tusks have overlapping distributions, contrary to predictions from the species-recognition hypothesis. However, the divergent tusk forms and sympatric distributions of three of the four sister-species pairs identified suggest that sexual selection on male tusks has likely played an important role in this unique radiation, although other forces are clearly also involved. To our knowledge, this is the first time that sexual selection has been explicitly implicated in the radiation of a mammalian group outside terrestrial ungulates.

Embracing Wicked Problems: The Turn to Design in Composition Studies

ERIC Educational Resources Information Center

Marback, Richard

2009-01-01

Recent appeal to the concept of design in composition studies benefits teaching writing in digital media. Yet the concept of design has not been developed enough to fully benefit composition instruction. This article develops an understanding of design as a matter of resolving wicked problems and makes a case for the advantages of this…

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala.

PubMed

Lavoué, Sébastien; Miya, Masaki; Inoue, Jun G; Saitoh, Kenji; Ishiguro, Naoya B; Nishida, Mutsumi

2005-10-01

Although the order Gonorynchiformes includes only 31 species assigned to seven genera and four families, it exhibits a large variety of anatomical structures, making difficult the reconstruction of phylogenetic relationships among its representatives. Within the basal teleosts, the Gonorynchiformes belong to the Otocephala where they have been alternatively placed as the sister group of the Otophysi and of the Clupeiformes. In this context, we investigated the phylogeny of the Gonorynchiformes using whole mitogenome sequences from 40 species (six being newly determined for this study). Our taxonomic sampling included at least one species of each gonorynchiform genus and of each other major otocephalan lineage. Unambiguously aligned, concatenated mitogenomic sequences (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd, and 3rd codon positions, tRNA genes, and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenetic trees were fully resolved, with most of the nodes well supported by the high posterior probabilities. As expected, the Otocephala were recovered as monophyletic. Within this group, the mitogenome data supported the monophyly of Alepocephaloidei, Gonorynchiformes, Otophysi, and Clupeiformes. The Gonorynchiformes and the Otophysi formed a sister group, rending the Ostariophysi monophyletic. This result conflicts with previous mitogenomic phylogenetic studies, in which a sister relationship was found between Clupeiformes and Gonorynchiformes. We discussed the possible causes of this incongruence. Within the Gonorynchiformes, the following original topology was found: (Gonorynchus (Chanos (Phractolaemus (Cromeria (Grasseichthys (Kneria, Parakneria)))))). We confirmed that the paedomorphic species Cromeria nilotica and Grasseichthys gabonensis belong to the family Kneriidae; however, the two species together did not form a monophyletic group. This result challenges the value of reductive or absent characters as synapomorphies in this group.

Osteology of the crescent gunnel Pholis laeta and the phylogeny of the family Pholidae (Cottiformes, Zoarcoidei).

PubMed

Sweetser, P W; Hilton, E J

2016-09-01

This study provides a complete description of the osteology of the crescent gunnel Pholis laeta based on cleared-and-stained specimens and X-rays to help provide sufficient morphological data to generate a robust phylogeny for the family Pholidae. Pholis laeta exhibits high variation in the structure of its caudal skeleton. The length of the preural (pu)2 neural spine is variably reduced (most common) or elongated (i.e. of similar length to that of pu3). Additionally, the neural spine of pu3 is either bifurcated or single. These results document and describe characters useful for phylogenetic inference of the family, including the insertion pattern of anal-fin pterygiophores between haemal spines. Pholidae was recovered as monophyletic (synapomorphies: ribs absent, haemonephropophyses present, gill membranes broadly joined, first neural arch fused to centrum, first anal-fin spine very robust, the dorsal fin comprises only spines and the presence of five branchiostegals), with monophyletic genera Pholis and Apodichthys (Rhodymenichthys is monotypic) and Apodichthys and Rhodymenichthys as sister taxa. The elongation of its pu2 neural spine defines Pholis and synapomorphies for Apodichthys include five infraorbital bones, no pelvic fin, a hypertrophied first anal-fin spine, the presence of two or three empty interhaemal spaces after the anteriormost anal-fin spine and having 35-46 abdominal vertebrae. Apodichthys and Rhodymenichthys are sister taxa based on the continuity of the caudal fin with the dorsal and anal fins and uniform colouration. Future study is needed to more fully resolve the interrelationships of species within Pholidae (especially the genus Pholis) and solidify the position of Pholidae within the Zoarcoidei. © 2016 The Fisheries Society of the British Isles.

A NEW AGAROPHYTE SPECIES, GELIDIUM EUCORNEUM SP. NOV. (GELIDIALES, RHODOPHYTA), BASED ON MOLECULAR AND MORPHOLOGICAL DATA(1).

PubMed

Kim, Kyeong Mi; Hwang, Il Ki; Park, Jeong Kwang; Boo, Sung Min

2011-08-01

Gelidium is an economically and ecologically important agar-producing genus. Although the taxonomy of Gelidium has been the focus of many published studies, there is still a need to reevaluate species-level diversity. Herein, we describe Gelidium eucorneum sp. nov. based on specimens collected off Geojedo on the southern coast of Korea. G. eucorneum is distinguished by cartilaginous thalli with brush-like haptera, rhizoidal filaments concentrated in the medulla, and globose cytocarps that are horned with multiple determinate branchlets. The species occurs in wave-exposed intertidal sites, sometimes in association with other mat-forming algae. Phylogenetic analyses (rbcL, psaA, and cox1) reveal that G. eucorneum is unique and clearly distinct from other species of the genus. The clade containing Gelidium vagum and Acanthopeltis longiramulosa was resolved as a sister group to G. eucorneum. We suggest that the diverse morphologies of G. eucorneum, G. vagum, and Acanthopeltis developed from a common ancestor in East Asian waters. This study shows that even in well-studied areas, more agarophyte species are to be added to the world inventory of red algae. © 2011 Phycological Society of America.

Molecular systematics and origin of sociality in mongooses (Herpestidae, Carnivora).

PubMed

Veron, Géraldine; Colyn, Marc; Dunham, Amy E; Taylor, Peter; Gaubert, Philippe

2004-03-01

The Herpestidae are small terrestrial carnivores comprising 18 African and Asian genera, currently split into two subfamilies, the Herpestinae and the Galidiinae. The aim of this work was to resolve intra-familial relationships and to test the origin of sociality in the group. For this purpose we analysed sequences of the complete cytochrome b gene for 18 species of Herpestidae. The results showed that the mongooses were split into three clades: (1) the Malagasy taxa (Galidiinae and Cryptoprocta), (2) the true social mongooses and (3) the solitary mongooses, each group being also supported by morphological and chromosomal data. Our results suggested unexpected phylogenetic relationships: (1) the genus Cynictis is included in the solitary mongoose clade, (2) the genera Liberiictis and Mungos are sister-group, and (3) the genus Herpestes is polyphyletic. We examined the evolution of the sociality in mongooses by combining behavioural traits with the cytochrome b data. Some of the behavioural traits provided good synapomorphies for characterizing the social species clade, showing the potential benefit of using such characters in phylogeny. The mapping of ecological and behavioural features resulted in hypothesizing solitary behavior and life in forest as the conditions at the base of the mongoose clade.

Acrophialophora, a Poorly Known Fungus with Clinical Significance

PubMed Central

Sandoval-Denis, Marcelo; Sutton, Deanna A.; Wiederhold, Nathan P.; Guarro, Josep

2015-01-01

Acrophialophora fusispora is an emerging opportunistic fungus capable of causing human infections. The taxonomy of the genus is not yet resolved and, in order to facilitate identification of clinical specimens, we have studied a set of clinical and environmental Acrophialophora isolates by morphological and molecular analyses. This set included the available type strains of Acrophialophora species and similar fungi, some of which were considered by various authors to be synonyms of A. fusispora. Sequence analysis of the large subunit (LSU) and internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and a fragment of the β-tubulin (Tub) gene revealed that Acrophialophora belongs in the family Chaetomiaceae and comprises three different species, i.e., A. fusispora, Acrophialophora levis, and Acrophialophora seudatica; the latter was previously included in the genus Ampullifera. The most prevalent species among clinical isolates was A. levis (72.7%), followed by A. fusispora (27.3%), both of which were isolated mostly from respiratory specimens (72.7%), as well as subcutaneous and corneal tissue samples. In general, of the eight antifungal drugs tested, voriconazole had the greatest in vitro activity, while all other agents showed poor in vitro activity against these fungi. PMID:25716450

Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870).

PubMed

Haus, Tanja; Akom, Emmanuel; Agwanda, Bernard; Hofreiter, Michael; Roos, Christian; Zinner, Dietmar

2013-04-01

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys' genetic diversity and evolution and a basis for further molecular studies on this genus. © 2013 Wiley Periodicals, Inc.

Dendrogramma, New Genus, with Two New Non-Bilaterian Species from the Marine Bathyal of Southeastern Australia (Animalia, Metazoa incertae sedis) – with Similarities to Some Medusoids from the Precambrian Ediacara

PubMed Central

Just, Jean; Kristensen, Reinhardt Møbjerg; Olesen, Jørgen

2014-01-01

A new genus, Dendrogramma, with two new species of multicellular, non-bilaterian, mesogleal animals with some bilateral aspects, D. enigmatica and D. discoides, are described from the south-east Australian bathyal (400 and 1000 metres depth). A new family, Dendrogrammatidae, is established for Dendrogramma. These mushroom-shaped organisms cannot be referred to either of the two phyla Ctenophora or Cnidaria at present, because they lack any specialised characters of these taxa. Resolving the phylogenetic position of Dendrogramma depends much on how the basal metazoan lineages (Ctenophora, Porifera, Placozoa, Cnidaria, and Bilateria) are related to each other, a question still under debate. At least Dendrogramma must have branched off before Bilateria and is possibly related to Ctenophora and/or Cnidaria. Dendrogramma, therefore, is referred to Metazoa incertae sedis. The specimens were fixed in neutral formaldehyde and stored in 80% ethanol and are not suitable for molecular analysis. We recommend, therefore, that attempts be made to secure new material for further study. Finally similarities between Dendrogramma and a group of Ediacaran (Vendian) medusoids are discussed. PMID:25184248

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

NASA Astrophysics Data System (ADS)

Sangal, Vartul; Goodfellow, Michael; Jones, Amanda L.; Schwalbe, Edward C.; Blom, Jochen; Hoskisson, Paul A.; Sutcliffe, Iain C.

2016-12-01

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

Molecular characterization of the species Salvinia (Salviniaceae) from the upper Paraná River floodplain.

PubMed

Machado, S A; Oliveira, A V; Fabrin, T M C; Prioli, S M A P; Prioli, A J

2016-08-12

The pteridophytes Salvinia minima, S. herzogii, and S. auriculata are among the most abundant aquatic macrophytes in the upper Paraná River floodplain. Since some species have highly similar morphological features, it is very difficult to identify members of this genus to the species level. An indication of this difficulty is a set of poorly differentiated taxa comprising S. auriculata and S. herzogii known as the 'S. auriculata complex', which is found in the Paraná River together with other Salvinia species such as S. biloba and S. molesta. Some authors have reported the existence of inter-species hybrids. Despite the complex Salvinia taxonomy, few genetic studies have been performed on purported species within the genus to resolve this complexity. The present study was conducted to determine useful molecular sequences for the discrimination of Salvinia species of the upper Paraná River floodplain. Molecular data were compared with data of other species of the genus to clarify phylogenetic relationships, employing the nucleotide sequence trnL-trnF from the chloroplast DNA. The results revealed that Salvinia populations in the upper Paraná River floodplain belong to different species and indicated that species of the S. auriculata complex may be distinguished from one another after the division of the S. minima group, corroborating results by other researchers. Although the taxonomic position of S. oblongifolia was clarified, as high closeness between S. oblongifolia and the S. auriculata complex was reported, Salvinia kinship is still not thoroughly established and further investigations in morphology and molecular diversity are required.

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae).

PubMed

Donkpegan, Armel S L; Doucet, Jean-Louis; Migliore, Jérémy; Duminil, Jérôme; Dainou, Kasso; Piñeiro, Rosalía; Wieringa, Jan J; Champluvier, Dominique; Hardy, Olivier J

2017-02-01

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogeny and biogeography of the amphi-Pacific genus Aphananthe

PubMed Central

Yang, Mei-Qing; Li, De-Zhu; Wen, Jun; Yi, Ting-Shuang

2017-01-01

Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS) and two plastid (psbA-trnH & trnL-trnF) regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses. Aphananthe was supported to be monophyletic, with the eastern Asian A. aspera resolved as sister to a clade of the remaining four species. Aphananthe was inferred to have originated in the Late Cretaceous (71.5 mya, with 95% HPD: 66.6–81.3 mya), and the crown age of the genus was dated to be in the early Miocene (19.1 mya, with 95% HPD: 12.4–28.9 mya). The fossil record indicates that Aphananthe was present in the high latitude thermophilic forests in the early Tertiary, and experienced extinctions from the middle Tertiary onwards. Aphananthe originated in Europe based on the inference that included fossil and extant species, but eastern Asia was estimated to be the ancestral area of the clade of the extant species of Aphananthe. Both the West Gondwanan vicariance hypothesis and the boreotropics hypothesis could be excluded as explanation for its amphi-Pacific distribution. Long-distance dispersals out of eastern Asia into North America, southern and southeastern Asia and Australia, and Madagascar during the Miocene account for its wide intercontinental disjunct distribution. PMID:28170425

Molecular phylogeny of Cyclophyllidea (Cestoda: Eucestoda): an in-silico analysis based on mtCOI gene.

PubMed

Sharma, Sunil; Lyngdoh, Damanbha; Roy, Bishnupada; Tandon, Veena

2016-09-01

Order Cyclophyllidea (of cestode platyhelminths) has a rich diversity of parasites and includes many families and species that are known to cause serious medical condition in humans and domestic and wild animals. Despite various attempts to resolve phylogenetic relationships at the inter-family level, uncertainty remains. In order to add resolution to the existing phylogeny of the order, we generated partial mtCO1 sequences for some commonly occurring cyclophyllidean cestodes and combined them with available sequences from GenBank. Phylogeny was inferred taking a total 83 representative species spanning 8 families using Bayesian analysis. The phylogenetic tree revealed Dilepididae as the most basal taxon and showed early divergence in the phylogenetic tree. Paruterinidae, Taeniidae and Anoplocephalidae showed non-monophyletic assemblage; our result suggests that the family Paruterinidae may represent a polyphyletic group. The diverse family Taeniidae appeared in two separate clades; while one of them included all the members of the genus Echinococcus and also Versteria, the representatives of the genera Taenia and Hydatigera clubbed in the other clade. A close affinity of Dipylidiidae with Taenia and Hydatigera was seen, whereas existence of a close relationship between Mesocestoididae and Echinococcus (of Taeniidae) is also demonstrated. The crown group comprised the families Anoplocephalidae, Davaineidae, Hymenolepididae and Mesocestoididae, and also all species of the genus Echinococcus and Versteria mustelae; monophyly of these families (excepting Anolplocephalidae) and the genus Echinococcus as well as its sister-taxon relation with V. mustelae is also confirmed. Furthermore, non-monophyly of Anoplocephalidae is suggested to be correlated with divergence in the host selection.

Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.

PubMed

Lymbery, A J

2017-01-01

An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Acute Inocybe mushroom toxicosis in dogs: 5 cases (2010-2014).

PubMed

Seljetun, Kristin Opdal; von Krogh, Anita

2017-03-01

To describe the clinical course, treatment, and outcome of 5 dogs following ingestion of mushrooms belonging to the Inocybe genus. Five dogs with witnessed Inocybe ingestions were presented with clinical signs compatible with poisoning. Vomiting, ptyalism, diarrhea, depression, and tachycardia were common clinical findings in the dogs in this case series. The prognosis with Inocybe toxicosis appears to be excellent as all dogs fully recovered following supportive care. This is the first reported case series of Inocybe mushroom ingestions in dogs where identification of the mushrooms were confirmed by an expert mycologist. © Veterinary Emergency and Critical Care Society 2017.

A revision of the Chinese Gasteruptiidae (Hymenoptera, Evanioidea)

PubMed Central

Zhao, Ke-xin; van Achterberg, Cornelis; Xu, Zai-fu

2012-01-01

Abstract The Chinese fauna of the family Gasteruptiidae is revised, keyed and fully illustrated for the first time. Only one genus of this family, Gasteruption Latreille, 1796, is recorded from China. In total 28 valid species of the genus Gasteruption are recognized. Six species are new to science (Gasteruption angulatum sp. n., Gasteruption assectoides sp. n., Gasteruption coloratum sp. n., Gasteruption latitibia sp. n., Gasteruption sinepunctatum sp. n. and Gasteruption strigosum sp. n.) and eight species are reported new for China (Gasteruption bimaculatum Pasteels, 1958, Gasteruption birmanense Pasteels, 1958, Gasteruption dimidiatum Semenov, 1892, Gasteruption formilis Alekseev, 1995, Gasteruption subhamatum Pasteels, 1958, Gasteruption tonkinense Pasteels, 1958, Gasteruption tournieri Schletterer, 1885, Gasteruption transversiceps Pasteels, 1958). Three new synonyms are proposed: Gasteruption curiosum Pasteels, 1958, of Gasteruption amoyense Pasteels, 1958; Gasteruption sinense var. minus Kieffer, 1924, with Gasteruption japonicum Cameron, 1888,and Gasteruption sinense Kieffer, 1924, of Gasteruption sinarum Kieffer, 1911. Lectotypes are designated for Gasteruption corniculigerum Enderlein, 1913, Gasteruption sinense Kieffer, 1924, and Gasteruption transversiceps Pasteels, 1958. Gasteruption bihamatum Kieffer, 1911, previously reported from South China, is a South American species. PMID:23226703

Lectotype designation for Murex nebula Montagu 1803 (Mangeliidae) and its implications for Bela Leach in Gray 1847.

PubMed

Daniele, Scarponi; Landau, Bernard; Janssen, Ronald; Morgenroth, Holly; Bella, Giano Della

2014-11-12

Bela Leach in Gray is a misapplied and broadly defined genus within the family Mangeliidae Fischer, 1883. Examination of material from the Montagu collection at the Royal Albert Memorial Museum & Art Gallery (RAMM) in Exeter (UK) led to the discovery of six specimens of Murex nebula Montagu 1803 (the type species of Bela). This material is considered to belong to the original lot used by Montagu to define his species. We selected the best-preserved specimen as a lectotype. The lectotype and paralectotypes deposited at the RAMM are fully described and illustrated. Furthermore, diagnostic characters for recognizing B. nebula specimens are presented: protoconch shows weak ornamentation; teleoconch is fusiform with slightly convex whorls characterized by broad, suture-to-suture ribs and dense but weak spiral elements; outer lip is thin; anal sinus is shallow, placed on the shoulder ramp. These key features are of basic importance for: i) restricting the usage of the genus Bela and promoting its stability and consistent usage in literature and ii) separating two allied (and sometimes interchanged) genera: Bela and Mangelia Risso 1826.

Entrapped by the uneven central and Middle Eastern terrains: Genetic status of populations of Hirudo orientalis (Annelida, Clitellata, Hirudinida) with a phylogenetic review of the genus Hirudo.

PubMed

Darabi-Darestani, Kaveh; Sari, Alireza; Sarafrazi, Alimorad; Utevsky, Serge

2018-04-01

Phylogenetic relationships between species of the genus Hirudo plus genetic variation in the entire distribution range of Hirudo orientalis were investigated based on mitochondrial (COI and 12S rDNA) and nuclear (ITS1+5.8S+ITS2) genome regions. The sister relationship of Hirudo orientalis and H. medicinalis was revealed with a high posterior probability. A broad and patchy distribution with minor genetic differences was observed in populations of H. orientalis along the central and Middle Eastern parts of Asia. The known distribution range occurred in topographically heterogeneous landscapes around the Caspian Sea. The demographic analysis suggests the selection of the COI locus under unfavourable respiratory conditions, but population size expansion cannot be fully rejected. The genetic variation trend indicated northward dispersal. Higher haplotype diversity in the South Caspian region potentially suggests the area as a historical refugium for the species. The vast dispersal is assumed to occur after the Pleistocene glaciations via vertebrate hosts. Copyright © 2017 Elsevier Inc. All rights reserved.

On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species

PubMed Central

Parapar, Julio; Moreira, Juan

2016-01-01

The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsae spec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented. PMID:27602280

On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species.

PubMed

Parapar, Julio; Moreira, Juan; Martin, Daniel

2016-01-01

The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsae spec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented.

Two new species of Xanthagaricus and some notes on Heinemannomyces from Asia

PubMed Central

Hosen, Md. Iqbal; Song, Zong-ping; Gates, Genevieve; Samantha C. Karunarathna; Chowdhury, M. Salahuddin M.; Li, Tai-Hui

2017-01-01

Abstract Xanthagaricus flavosquamosus and X. necopinatus, two new species of Agaricaceae, are described and illustrated from Asia. Macroscopically, both species are closely related to each other, but there are obvious micromorphological and molecular differences between them. Morphological and phylogenetic data showed that the two new species are distinct from other known species of the genus Xanthagaricus. Xanthagaricus flavosquamosus from China is characterized by its small, yellow basidiomata, short clavate cheilocystidia, epithelial pileipellis, and verrucose basidiospores measuring 5–5.5 × 3–3.5 μm. Xanthagaricus necopinatus from Bangladesh is characterized by having small, yellow basidiomata, a fugacious annulus, clavate to narrowly clavate cheilocystidia, epithelial pileipellis, and rugulose-rough basidiospores measuring 4–5 × 2.7–3.2 μm. In addition to the new species, a Heinemannomyces collection from China is reported. Morphological data and molecular phylogenetic analyses fully support the Chinese collection being Heinemannomyces splendidissimus, a species of Agaricaceae, originally described from Southeast Asia. Detailed descriptions, color photos and illustrations of the three species are presented. A key to the genus Xanthagaricus occurring in Bangladesh and China is provided. PMID:29559820

Unraveling the benzocaine-receptor interaction at molecular level using mass-resolved spectroscopy.

PubMed

Aguado, Edurne; León, Iker; Millán, Judith; Cocinero, Emilio J; Jaeqx, Sander; Rijs, Anouk M; Lesarri, Alberto; Fernández, José A

2013-10-31

The benzocaine-toluene cluster has been used as a model system to mimic the interaction between the local anesthetic benzocaine and the phenylalanine residue in Na(+) channels. The cluster was generated in a supersonic expansion of benzocaine and toluene in helium. Using a combination of mass-resolved laser-based experimental techniques and computational methods, the complex was fully characterized, finding four conformational isomers in which the molecules are bound through N-H···π and π···π weak hydrogen bonds. The structures of the detected isomers closely resemble those predicted for benzocaine in the inner pore of the ion channels, giving experimental support to previously reported molecular chemistry models.

Time-Domain Filtering for Spatial Large-Eddy Simulation

NASA Technical Reports Server (NTRS)

Pruett, C. David

1997-01-01

An approach to large-eddy simulation (LES) is developed whose subgrid-scale model incorporates filtering in the time domain, in contrast to conventional approaches, which exploit spatial filtering. The method is demonstrated in the simulation of a heated, compressible, axisymmetric jet, and results are compared with those obtained from fully resolved direct numerical simulation. The present approach was, in fact, motivated by the jet-flow problem and the desire to manipulate the flow by localized (point) sources for the purposes of noise suppression. Time-domain filtering appears to be more consistent with the modeling of point sources; moreover, time-domain filtering may resolve some fundamental inconsistencies associated with conventional space-filtered LES approaches.

Assessment of the Partially Resolved Numerical Simulation (PRNS) Approach in the National Combustion Code (NCC) for Turbulent Nonreacting and Reacting Flows

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, Nan-Suey

2008-01-01

This paper describes an approach which aims at bridging the gap between the traditional Reynolds-averaged Navier-Stokes (RANS) approach and the traditional large eddy simulation (LES) approach. It has the characteristics of the very large eddy simulation (VLES) and we call this approach the partially-resolved numerical simulation (PRNS). Systematic simulations using the National Combustion Code (NCC) have been carried out for fully developed turbulent pipe flows at different Reynolds numbers to evaluate the PRNS approach. Also presented are the sample results of two demonstration cases: nonreacting flow in a single injector flame tube and reacting flow in a Lean Direct Injection (LDI) hydrogen combustor.

A revision of the New World species of Gymnoclasiopa Hendel (Diptera, Ephydridae)

PubMed Central

Mathis, Wayne N.; Zatwarnicki, Tadeusz

2012-01-01

Abstract Species of the shore-fly genus Gymnoclasiopa Hendel from the New World are revised, including Gymnoclasiopa grecorum sp. n. (Alaska. Juneau: Gastineau Channel, Thane Road (S Juneau; 58°16.9'N, 134°22.4'W)) and Gymnoclasiopa matanuska sp. n. (Alaska. Matanuska-Susitna: Palmer (Matanuska River; 61°36.5'N, 149°04.1'W)). We also clarify the status of previously described species, including those now discovered to have Holarctic distributions and/or for which sexual dimorphism was not appreciated and the species was described twice, including Gymnoclasiopa montana (Cresson) as a syn. n. of Gymnoclasiopa bohemanni (Becker). Two species, Gymnoclasiopa bella (Mathis), comb. n., and Gymnoclasiopa chiapas (Mathis), comb. n., are transferred from Ditrichophora to Gymnoclasiopa, and Gymnoclasiopa cana Cresson stat. rev. and Ditrichophora canifrons Cresson, stat. rev. are returned to Ditrichophora, the genus in which Cresson originally described them. A neotype is designated for Gymnoclasiopa tacoma to stabilize the nomenclature of this species. The two excluded species, Ditrichophora cana and Ditrichophora canifrons, are diagnosed and distributional data are also provided. For all known New World species of Gymnoclasiopa, structures of the male terminalia are described for the first time and are fully illustrated. Detailed locality data and distribution maps are also included. To provide context and also to facilitate identification, diagnoses are included for the tribe Discocerinini and genus in addition to a key to the genera and species occurring in the New World. PMID:23275757

Short communication: Traits unique to genus Homo within primates at the cervical spine (C2-C7).

PubMed

Rios, Luis; Muñoz, Alexandra; Cardoso, Hugo; Pastor, Francisco

2014-05-01

From a comparative study of 222 human and 261 nonhuman primates complete cervical spines, two bony variants associated to the course of the vertebral artery are proposed as unique to genus Homo within primates. First, the opening of the foramen transversarium at C2, a trait present at low frequency in humans (3 to 5.6%). Second, the presence of a bipartite foramen transversarium in the cervical segment C3-C6, a trait that can be observed fully formed in human fetal skeletons, with a clear frequency pattern along the cervical spine (C3>C4>C5>C6

Art as a Singular Rule

ERIC Educational Resources Information Center

Avital, Doron

2007-01-01

This paper will examine an unresolved tension inherent in the question of art and argue for the idea of a singular rule as a natural resolution. In so doing, the structure of a singular rule will be fully outlined and its paradoxical constitution will be resolved. The tension I mention above unfolds both as a matter of history and as a product of…

Water You Engineering? An Activity to Develop Water-Quality Awareness

ERIC Educational Resources Information Center

Riskowski, Jody; Todd, Carrie Davis

2009-01-01

Water is one of our most precious resources. However, for many in the United States, having fresh, safe drinking water is taken for granted, and due to this perceived lack of relevance, students may not fully appreciate the luxury of having safe running water--in the home. One approach to resolving water-quality issues in the United States may…

The Role of Nurse Educators in the Development of Reflective Practitioners: A Selective Case Study of the Australian and UK Experience.

ERIC Educational Resources Information Center

Mallik, Maggie

1998-01-01

A study tour of two British and eight Australian nursing schools found reflective practice fully endorsed in Australia, but the movement is threatened by concern with cost effectiveness. Issues to be resolved include ethical use of student journals and process and outcome evaluation of the effectiveness of reflection. (SK)

49 CFR 1109.4 - Mandatory mediation in rate cases to be considered under the stand-alone cost methodology.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) The mediator will work with the parties to try to reach a settlement of all or some of their dispute or to narrow the issues in dispute, and reach stipulations that may be incorporated into any adjudication before the Board if mediation does not fully resolve the dispute. If the parties reach a...

Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci.

Treesearch

John Syring; Ann Willyard; Richard Cronn; Aaron Liston

2005-01-01

Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low-copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses and in...

Disjunctitermes insularis, a new soldierless termite genus and species (Isoptera, Termitidae, Apicotermitinae) from Guadeloupe and Peru

PubMed Central

Scheffrahn, Rudolf H.; Carrijo, Tiago F.; Postle, Anthony C.; Tonini, Francesco

2017-01-01

Abstract Disjunctitermes insularis gen. n. & sp. n. is described from workers collected on Guadeloupe and in Peru and is the first soldierless termite found on a deep-water island. As with many soldierless and soil-feeding termite species, the enteric valve morphology is an essential diagnostic character of D. insularis. The D. insularis sequence cluster, derived from a barcode analysis with twelve other described genera of New World Apicotermitinae, is well resolved. Results of a stochastic dynamic spread model suggest that the occurrence of D. insularis on Guadeloupe may be the result of a pre-Colombian overwater dispersal event from mainland South America. PMID:28769627

Weil’s disease in a 36 years old female: a case report

NASA Astrophysics Data System (ADS)

Rozalena, S.; Handayani, L.; Arman, A.; Permata, M.; Hudari, H.

2018-03-01

Leptospirosis is an acute zoonotic infection, itis caused by spirochetes of the genus Leptospira, has extensive vasculitis characterizes, can usually be transmitted indirectly, per contaminated water, rarely directly, and through contact with infected animals. Leptospira bacteria commonly enter the body through the damaged skin or mucous membranes. The clinical syndromes may vary from a subclinical infection and mild febrile condition to severe clinical symptoms with jaundice and renal failure. It is the case report from a woman 36 years old with leptospirosis (Weil’s disease) whose clinical manifestations included: icterus, renal failure, hemorrhagic syndrome and disturbances of consciousness. After the use of antibiotics, symptomatic and substitution therapy, all symptoms resolved completely.

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

PubMed

Marcussen, Thomas; Heier, Lise; Brysting, Anne K; Oxelman, Bengt; Jakobsen, Kjetill S

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the "correct" network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ("ghost subgenome lineages") significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage-between 67% and 88%-of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Fully Resolved Simulations of 3D Printing

NASA Astrophysics Data System (ADS)

Tryggvason, Gretar; Xia, Huanxiong; Lu, Jiacai

2017-11-01

Numerical simulations of Fused Deposition Modeling (FDM) (or Fused Filament Fabrication) where a filament of hot, viscous polymer is deposited to ``print'' a three-dimensional object, layer by layer, are presented. A finite volume/front tracking method is used to follow the injection, cooling, solidification and shrinking of the filament. The injection of the hot melt is modeled using a volume source, combined with a nozzle, modeled as an immersed boundary, that follows a prescribed trajectory. The viscosity of the melt depends on the temperature and the shear rate and the polymer becomes immobile as its viscosity increases. As the polymer solidifies, the stress is found by assuming a hyperelastic constitutive equation. The method is described and its accuracy and convergence properties are tested by grid refinement studies for a simple setup involving two short filaments, one on top of the other. The effect of the various injection parameters, such as nozzle velocity and injection velocity are briefly examined and the applicability of the approach to simulate the construction of simple multilayer objects is shown. The role of fully resolved simulations for additive manufacturing and their use for novel processes and as the ``ground truth'' for reduced order models is discussed.

A fully resolved fluid-structure-muscle-activation model for esophageal transport

NASA Astrophysics Data System (ADS)

Kou, Wenjun; Bhalla, Amneet P. S.; Griffith, Boyce E.; Johnson, Mark; Patankar, Neelesh A.

2013-11-01

Esophageal transport is a mechanical and physiological process that transfers the ingested food bolus from the pharynx to the stomach through a multi-layered esophageal tube. The process involves interactions between the bolus, esophageal wall composed of mucosal, circular muscle (CM) and longitudinal muscle (LM) layers, and neurally coordinated muscle activation including CM contraction and LM shortening. In this work, we present a 3D fully-resolved model of esophageal transport based on the immersed boundary method. The model describes the bolus as a Newtonian fluid, the esophageal wall as a multi-layered elastic tube represented by springs and beams, and the muscle activation as a traveling wave of sequential actuation/relaxation of muscle fibers, represented by springs with dynamic rest lengths. Results on intraluminal pressure profile and bolus shape will be shown, which are qualitatively consistent with experimental observations. Effects of activating CM contraction only, LM shortening only or both, for the bolus transport, are studied. A comparison among them can help to identify the role of each type of muscle activation. The support of grant R01 DK56033 and R01 DK079902 from NIH is gratefully acknowledged.

3D critical layers in fully-developed turbulent flows

NASA Astrophysics Data System (ADS)

Saxton-Fox, Theresa; McKeon, Beverley

2016-11-01

Recent work has shown that 3D critical layers drive self-sustaining behavior of exact coherent solutions of the Navier-Stokes equations (Wang et al. 2007; Hall and Sherwin 2010; Park and Graham 2015). This study investigates the role of 3D critical layers in fully-developed turbulent flows. 3D critical layer effects are identified in instantaneous snapshots of turbulent boundary layers in both experimental and DNS data (Wu et al. 2014). Additionally, a 3D critical layer effect is demonstrated to appear using only a few resolvent response modes from the resolvent analysis of McKeon and Sharma 2010, with phase relationships appropriately chosen. Connections are sought to the thin shear layers observed in turbulent boundary layers (Klewicki and Hirschi 2004; Eisma et al. 2015) and to amplitude modulation observations (Mathis et al. 2009; Duvvuri and McKeon 2014). This research is made possible by the Department of Defense through the National Defense & Engineering Graduate Fellowship (NDSEG) Program and by the Air Force Office of Scientific Research Grant # FA9550-12-1-0060. The support of the Center for Turbulence Research (CTR) summer program at Stanford is gratefully acknowledged.

Spin-resolved band structure of a densely packed Pb monolayer on Si(111)

NASA Astrophysics Data System (ADS)

Brand, C.; Muff, S.; Fanciulli, M.; Pfnür, H.; Tringides, M. C.; Dil, J. H.; Tegenkamp, C.

2017-07-01

Monolayer structures of Pb on Si(111) attracted recently considerable interest as superconductivity was found in these truly two-dimensional (2D) structures. In this study, we analyzed the electronic surface band structure of the so-called striped incommensurate Pb phase with 4/3 ML coverage by means of spin-resolved photoemission spectroscopy. Our results fully agree with density functional theory calculations done by Ren et al. [Phys. Rev. B 94, 075436 (2016), 10.1103/PhysRevB.94.075436]. We observe a local Zeeman-type splitting of a fully occupied and spin-polarized surface band at the K¯√{3} points. The growth of this densely packed Pb structure results in the formation of imbalanced rotational domains, which triggered the detection of C3 v symmetry forbidden spin components for surface states around the Fermi energy. Moreover, the Fermi surface of the metallic surface state of this phase is Rashba spin split and revealed a pronounced warping. However, the 2D nesting vectors are incommensurate with the atomic structure, thus keeping this system rather immune against charge density wave formation and possibly enabling a superconducting behavior.

Goos-Hänchen-like shift in biased silicene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Bang-Shan; Wang, Yu, E-mail: ywang@semi.ac.cn; Lou, Yi-Yi

2016-04-28

We have theoretically studied the Goos-Hänchen-like shift of spinor-unpolarized beams tunneling through various gate-biased silicene nanostructures. Following the stationary-phase method, lateral displacement in single-, dual-, and multiple-gated silicene systems has been systematically demonstrated. It is shown for simple single-gated silicene that lateral displacement can be generally enhanced by Fabry-Perot interference, and near the transition point turning on the evanescent mode a very large lateral shift could be observed. For the dual-gated structure, we have also shown the crucial role of localized modes like quantum well states in enhancing the beam lateral displacement, while for the multiple gate-biased systems the resultingmore » superlattice subbands are also favorable for lateral displacement enhancement. Importantly, including the degeneracy-broken mechanisms such as gate-field and magnetic modulations, a fully spinor-resolved beam can be distinguished from the rest counterparts by aligning the incident beam with a proper spinor-resolved transition point, localized state, and subband, all of which can be flexibly modulated via electric means, offering the very desirable strategies to achieve the fully spinor-polarized beam for functional electronic applications.« less

Investigation of unsteadiness in Shock-particle cloud interaction: Fully resolved two-dimensional simulation and one-dimensional modeling

NASA Astrophysics Data System (ADS)

Hosseinzadeh-Nik, Zahra; Regele, Jonathan D.

2015-11-01

Dense compressible particle-laden flow, which has a complex nature, exists in various engineering applications. Shock waves impacting a particle cloud is a canonical problem to investigate this type of flow. It has been demonstrated that large flow unsteadiness is generated inside the particle cloud from the flow induced by the shock passage. It is desirable to develop models for the Reynolds stress to capture the energy contained in vortical structures so that volume-averaged models with point particles can be simulated accurately. However, the previous work used Euler equations, which makes the prediction of vorticity generation and propagation innacurate. In this work, a fully resolved two dimensional (2D) simulation using the compressible Navier-Stokes equations with a volume penalization method to model the particles has been performed with the parallel adaptive wavelet-collocation method. The results still show large unsteadiness inside and downstream of the particle cloud. A 1D model is created for the unclosed terms based upon these 2D results. The 1D model uses a two-phase simple low dissipation AUSM scheme (TSLAU) developed by coupled with the compressible two phase kinetic energy equation.

Ethiopian highlands as a cradle of the African fossorial root-rats (genus Tachyoryctes), the genetic evidence.

PubMed

Šumbera, Radim; Krásová, Jarmila; Lavrenchenko, Leonid A; Mengistu, Sewnet; Bekele, Afework; Mikula, Ondřej; Bryja, Josef

2018-09-01

Root-rats of the genus Tachyoryctes (Spalacidae) are subterranean herbivores occupying open humid habitats in the highlands of Eastern Africa. There is strong disagreement about species diversity of the genus, because some authors accept two species, while others more than ten. Species with relatively high surface activity, the giant root-rat Tachyoryctes macrocephalus, which is by far largest member of the genus, and the more fossorial African root-rat Tachyoryctes splendens, which eventually has been divided up to 12-13 species, represent two major morphological forms within the genus. In our study, we carried out a multilocus analysis of root-rats' genetic diversity based on samples from 41 localities representing most of Tachyoryctes geographic distribution. Using two mitochondrial and three nuclear genes, we found six main genetic clades possibly representing separate species. These clades were organised into three basal groups whose branching is not well resolved, probably due to fast radiation in the late Pliocene and early Pleistocene. Climatic changes in that time, i.e. fast and repeated changes between extremely dry and humid conditions, which both limited root-rat dispersal, probably stimulated their initial genetic diversification. Contrary to expectation based on the largest root-rat diversity in Kenya (up to eight species by some authors), we found the highest diversity in the Ethiopian highlands, because all but one putative species occur there. All individuals outside of Ethiopia belong to a single recently diverged and expanded clade. This species should bear the name T. annectens (Thomas, 1891), and all other names of taxa described from outside of Ethiopia should be considered its junior synonyms. However, to solve taxonomic issues, future detailed morphological analyses should be conducted on all main clades together with genetic analysis of material from areas of their supposed contact. One of the most interesting findings of the study is the internal position of T. macrocephalus in T. splendens sensu lato. This demonstrates the intriguing phenomenon of accelerated morphological evolution of rodents occupying the Afroalpine zone in Ethiopia. Finally, we discuss how the distribution of Tachyoryctes is influenced by competition with another group of subterranean herbivores on the continent, the African mole-rats. We assume that both groups do not compete directly as previously expected, but specialisation to different subterranean niches is the main factor responsible for their spatial segregation. Copyright © 2018 Elsevier Inc. All rights reserved.

Revision of the Neotropical bark mantis genus Liturgusa Saussure, 1869 (Insecta, Mantodea, Liturgusini)

PubMed Central

Svenson, Gavin J.

2014-01-01

Abstract The praying mantis genus Liturgusa Saussure, 1869 occurs only in Central and South America and represents the most diverse genus of Neotropical Liturgusini (Ehrmann 2002). The genus includes bark dwelling species, which live entirely on the trunks and branches of trees and run extremely fast. All species included within the genus Liturgusa are comprehensively revised with a distribution stretching from central Mexico, the island of Dominica to the southeastern regions of Brazil and southern Bolivia. All known species are redescribed to meet the standards of the new treatment of the genus (11 species). Three new genera are described including Fuga gen. n., Velox gen. n., and Corticomantis gen. n. for species previously included in Liturgusa as well as Hagiomantis. Liturgusa mesopoda Westwood, 1889 is moved to within the previously described genus Hagiomantis Audinet Serville, 1838. A total of 19 species are newly described within Liturgusa, Fuga, and Velox including L. algorei sp. n., L. bororum sp. n., L. cameroni sp. n., L. cura sp. n., L. dominica sp. n., L. fossetti sp. n., L. kirtlandi sp. n., L. krattorum sp. n., L. manausensis sp. n., L. maroni sp. n., L. milleri sp. n., L. neblina sp. n., L. purus sp. n., L. stiewei sp. n., L. tessae sp. n., L. trinidadensis sp. n., L. zoae sp. n., F. grimaldii sp. n., and V. wielandi sp. n. Four species names are synonymized: Liturgusa peruviana Giglio-Tos, 1914, syn. n. = Liturgusa nubeculosa Gerstaecker, 1889 and Hagiomantis parva Piza, 1966, syn. n., Liturgusa sinvalnetoi Piza, 1982, syn. n., and Liturgusa parva Giglio-Tos, 1914, syn. n. = Mantis annulipes Audinet Serville, 1838. Lectotypes are designated for the following two species: Liturgusa maya Saussure & Zehntner, 1894 and Fuga annulipes (Audinet Serville, 1838). A male neotype is designated for Liturgusa guyanensis La Greca, 1939. Males for eight species are described for the first time including Liturgusa cayennensis Saussure, 1869, Liturgusa lichenalis Gerstaecker, 1889, Liturgusa guyanensis La Greca, 1939, Liturgusa maya Saussure & Zehntner, 1894, Liturgusa nubeculosa Gerstaecker, 1889, Fuga annulipes (Audinet Serville, 1838), Corticomantis atricoxata (Beier, 1931), and Hagiomantis mesopoda (Westwood, 1889). The female of Fuga fluminensis (Piza, 1965) is described for the first time. Complete bibliographic histories are provided for previously described species. The spelling confusion surrounding Liturgusa/Liturgousa is resolved. Full habitus images for males and females are provided for nearly all species. Habitus and label images of type specimens are provided when possible. Diagnostic illustrations of the head and pronotum for males and females are provided for all species when possible. Illustrations of male genital structures are provided for all species for which males are known. Measurement data, including ranges and averages, are provided for males and females of all species. Combined male and female genus and species level dichotomous keys are provided with a Spanish translation. A complete table of all examined specimens lists label data, museum codes, repositories, and other specimen specific information. A KML file with all georeferenced locality records is downloadable from mantodearesearch.com for viewing in Google Earth. Natural history information is provided for species observed by the author. PMID:24715776

Revision of the Neotropical bark mantis genus Liturgusa Saussure, 1869 (Insecta, Mantodea, Liturgusini).

PubMed

Svenson, Gavin J

2014-01-01

The praying mantis genus Liturgusa Saussure, 1869 occurs only in Central and South America and represents the most diverse genus of Neotropical Liturgusini (Ehrmann 2002). The genus includes bark dwelling species, which live entirely on the trunks and branches of trees and run extremely fast. All species included within the genus Liturgusa are comprehensively revised with a distribution stretching from central Mexico, the island of Dominica to the southeastern regions of Brazil and southern Bolivia. All known species are redescribed to meet the standards of the new treatment of the genus (11 species). Three new genera are described including Fuga gen. n., Velox gen. n., and Corticomantis gen. n. for species previously included in Liturgusa as well as Hagiomantis. Liturgusa mesopoda Westwood, 1889 is moved to within the previously described genus Hagiomantis Audinet Serville, 1838. A total of 19 species are newly described within Liturgusa, Fuga, and Velox including L. algorei sp. n., L. bororum sp. n., L. cameroni sp. n., L. cura sp. n., L. dominica sp. n., L. fossetti sp. n., L. kirtlandi sp. n., L. krattorum sp. n., L. manausensis sp. n., L. maroni sp. n., L. milleri sp. n., L. neblina sp. n., L. purus sp. n., L. stiewei sp. n., L. tessae sp. n., L. trinidadensis sp. n., L. zoae sp. n., F. grimaldii sp. n., and V. wielandi sp. n. Four species names are synonymized: Liturgusa peruviana Giglio-Tos, 1914, syn. n. = Liturgusa nubeculosa Gerstaecker, 1889 and Hagiomantis parva Piza, 1966, syn. n., Liturgusa sinvalnetoi Piza, 1982, syn. n., and Liturgusa parva Giglio-Tos, 1914, syn. n. = Mantis annulipes Audinet Serville, 1838. Lectotypes are designated for the following two species: Liturgusa maya Saussure & Zehntner, 1894 and Fuga annulipes (Audinet Serville, 1838). A male neotype is designated for Liturgusa guyanensis La Greca, 1939. Males for eight species are described for the first time including Liturgusa cayennensis Saussure, 1869, Liturgusa lichenalis Gerstaecker, 1889, Liturgusa guyanensis La Greca, 1939, Liturgusa maya Saussure & Zehntner, 1894, Liturgusa nubeculosa Gerstaecker, 1889, Fuga annulipes (Audinet Serville, 1838), Corticomantis atricoxata (Beier, 1931), and Hagiomantis mesopoda (Westwood, 1889). The female of Fuga fluminensis (Piza, 1965) is described for the first time. Complete bibliographic histories are provided for previously described species. The spelling confusion surrounding Liturgusa/Liturgousa is resolved. Full habitus images for males and females are provided for nearly all species. Habitus and label images of type specimens are provided when possible. Diagnostic illustrations of the head and pronotum for males and females are provided for all species when possible. Illustrations of male genital structures are provided for all species for which males are known. Measurement data, including ranges and averages, are provided for males and females of all species. Combined male and female genus and species level dichotomous keys are provided with a Spanish translation. A complete table of all examined specimens lists label data, museum codes, repositories, and other specimen specific information. A KML file with all georeferenced locality records is downloadable from mantodearesearch.com for viewing in Google Earth. Natural history information is provided for species observed by the author.

A fully-integrated aptamer-based affinity assay platform for monitoring astronaut health in space.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xianbin; Durland, Ross H.; Hecht, Ariel H.

2010-07-01

Here we demonstrate the suitability of robust nucleic acid affinity reagents in an integrated point-of-care diagnostic platform for monitoring proteomic biomarkers indicative of astronaut health in spaceflight applications. A model thioaptamer targeting nuclear factor-kappa B (NF-{kappa}B) is evaluated in an on-chip electrophoretic gel-shift assay for human serum. Key steps of (i) mixing sample with the aptamer, (ii) buffer exchange, and (iii) preconcentration of sample were successfully integrated upstream of fluorescence-based detection. Challenges due to (i) nonspecific interactions with serum, and (ii) preconcentration at a nanoporous membrane are discussed and successfully resolved to yield a robust, rapid, and fully-integrated diagnostic system.

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

PubMed Central

Meerow, Alan W.; Noblick, Larry; Borrone, James W.; Couvreur, Thomas L. P.; Mauro-Herrera, Margarita; Hahn, William J.; Kuhn, David N.; Nakamura, Kyoko; Oleas, Nora H.; Schnell, Raymond J.

2009-01-01

Background The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. Methodology/Principal Findings We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. Conclusions/Significance This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family. PMID:19806212

Host and Phenology Shifts in the Evolution of the Social Moth Genus Thaumetopoea

PubMed Central

Simonato, Mauro; Battisti, Andrea; Kerdelhué, Carole; Burban, Christian; Lopez-Vaamonde, Carlos; Pivotto, Isabelle; Salvato, Paola; Negrisolo, Enrico

2013-01-01

The genus Thaumetopoea contains the processionary moths, a group of lepidopteran associated with forest trees, well known for the social behaviour of the larvae and for carrying urticating setae. The taxonomy of the genus is partly unresolved and a phylogenetic approach is lacking. The goal of this work is to produce a phylogeny for Thaumetopoea and to identify the main traits driving the evolution of this group. Eighteen mitochondrial and three nuclear genes were fully/partly sequenced. Markers were aligned and analysed singularly or in various combinations. Phylogenetic analyses were performed according to maximum likelihood and Bayesian inference methods. Trees obtained from largest data sets provided identical topologies that received strong statistical support. Three main clades were identified within Thaumetopoea and were further supported by several signatures located in the mitochondrial tRNAs and intergenic spacers. The reference topology was used to investigate the evolution of life history traits related to biogeography, host plant, ecology, and morphology. A multigenic approach allowed to produce a robust phylogenetic analysis of the genus Thaumetopoea, with the identification of three major clades linked to different ecological and life history traits. The first clade is associated with Angiosperm host plants and has a fast spring development of larvae on young foliage. The other clades have originated by one event of host plant shift to Gymnosperm Pinaceae, which implied a longer larval developmental time due to the lower nutritional quality of leaves. These clades showed different adaptations to such a constraint, the first with a switch of larval feeding to cold season (winter pine processionary moths), and the second with a retraction to high altitude and latitude and a development cycle extended over two years (summer pine processionary moths). Recent global warming is affecting all species and seems able to further shape the evolution of the group. PMID:23460830

In-pile Thermal Conductivity Characterization with Time Resolved Raman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xinwei; Hurley, David H.

The project is designed to achieve three objectives: (1) Develop a novel time resolved Raman technology for direct measurement of fuel and cladding thermal conductivity. (2) Validate and improve the technology development by measuring ceramic materials germane to the nuclear industry. (3) Conduct instrumentation development to integrate optical fiber into our sensing system for eventual in-pile measurement. We have developed three new techniques: time-domain differential Raman (TD-Raman), frequency-resolved Raman (FR-Raman), and energy transport state-resolved Raman (ET-Raman). The TD-Raman varies the laser heating time and does simultaneous Raman thermal probing, the FR-Raman probes the material’s thermal response under periodical laser heatingmore » of different frequencies, and the ET-Raman probes the thermal response under steady and pulsed laser heating. The measurement capacity of these techniques have been fully assessed and verified by measuring micro/nanoscale materials. All these techniques do not need the data of laser absorption and absolute material temperature rise, yet still be able to measure the thermal conductivity and thermal diffusivity with unprecedented accuracy. It is expected they will have broad applications for in-pile thermal characterization of nuclear materials based on pure optical heating and sensing.« less

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity

PubMed Central

Dendrou, Calliope A.; Cortes, Adrian; Shipman, Lydia; Evans, Hayley G.; Attfield, Kathrine E.; Jostins, Luke; Barber, Thomas; Kaur, Gurman; Kuttikkatte, Subita Balaram; Leach, Oliver A.; Desel, Christiane; Faergeman, Soren L.; Cheeseman, Jane; Neville, Matt J.; Sawcer, Stephen; Compston, Alastair; Johnson, Adam R.; Everett, Christine; Bell, John I.; Karpe, Fredrik; Ultsch, Mark; Eigenbrot, Charles; McVean, Gil; Fugger, Lars

2017-01-01

Thousands of genetic variants have been identified that contribute to the development of complex diseases, but determining how to fully elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders, subsequent molecular, cellular, in vivo and structural functional follow-up and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for multiple autoimmune disorders. PMID:27807284

A dielectric model of self-assembled monolayer interfaces by capacitive spectroscopy.

PubMed

Góes, Márcio S; Rahman, Habibur; Ryall, Joshua; Davis, Jason J; Bueno, Paulo R

2012-06-26

The presence of self-assembled monolayers at an electrode introduces capacitance and resistance contributions that can profoundly affect subsequently observed electronic characteristics. Despite the impact of this on any voltammetry, these contributions are not directly resolvable with any clarity by standard electrochemical means. A capacitive analysis of such interfaces (by capacitance spectroscopy), introduced here, enables a clean mapping of these features and additionally presents a means of studying layer polarizability and Cole-Cole relaxation effects. The resolved resistive term contributes directly to an intrinsic monolayer uncompensated resistance that has a linear dependence on the layer thickness. The dielectric model proposed is fully aligned with the classic Helmholtz plate capacitor model and additionally explains the inherently associated resistive features of molecular films.

Examining diseased states in a scaled-up vocal fold model using simultaneous temporally resolved DPIV and pressure measurements

NASA Astrophysics Data System (ADS)

Rogers, Dylan; Wei, Nathaniel; Ringenber, Hunter; Krane, Michael; Wei, Timothy

2017-11-01

This study builds on the parallel presentation of Ringenberg, et al. (APS-DFD 2017) involving simultaneous, temporally and spatially resolved flow and pressure measurements in a scaled-up vocal fold model. In this talk, data from experiments replicating characteristics of diseased vocal folds are presented. This begins with vocal folds that do not fully close and continues with asymmetric oscillations. Data are compared to symmetric, i.e. `healthy', oscillatory motions presented in the companion talk. Having pressure and flow data for individual as well as phase averaged oscillations for these diseased cases highlights the potential for aeroacoustic analysis in this complex system. Supported by NIH Grant No. 2R01 DC005642-11.

Resolved, That the Federal Government Should Fully Finance a Defensible Minimum Education for All Children in the Public Schools. An Affirmative Position.

ERIC Educational Resources Information Center

Hack, Walter G.

This report discusses several kinds of Federal aid to education and decides that a Federal foundation program is the best type. Arguments in favor of such a program are that (1) contemporary societal problems require a national policy (including a federally financed education program), (2) equity of financial responsibility for the educational…

Muslim Insurgency in Mindanao, Philippines

DTIC Science & Technology

2002-05-31

city of Marawi.5 When General Fidel V. Ramos assumed the presidency, the painstaking negotiation process with the MNLF was continued. Eventually both...witnessed this meaningful occasion. It was also during President Ramos ’ incumbency that the exploratory talks with the MILF began. The incumbent...policies of the Ramos administration and the compromise between his administration and the Moro National Liberation Front may have fully resolved the

Development of high-resolution (250 m) historical daily gridded air temperature data using reanalysis and distributed sensor networks for the US northern Rocky Mountains

Treesearch

Zachary A. Holden; Alan Swanson; Anna E. Klene; John T. Abatzoglou; Solomon Z. Dobrowski; Samuel A. Cushman; John Squires; Gretchen G. Moisen; Jared W. Oyler

2016-01-01

Gridded temperature data sets are typically produced at spatial resolutions that cannot fully resolve fine-scale variation in surface air temperature in regions of complex topography. These data limitations have become increasingly important as scientists and managers attempt to understand and plan for potential climate change impacts. Here, we describe the...

Mechanisms of base-cation depletion by acid deposition in forest soils of the northeastern U.S.

Treesearch

Gregory B. Lawrence; Mark B. David; Walter C. Shortle; Scott W. Bailey; Gary M. Lovett

1999-01-01

Several studies have indicated a long-term decrease in exchangeable Ca in forest soils within the northeastern Unrted States, but the regional extent of these decreases and the importance of acid deposition as a cause has not been fully resolved. Results, from two recently completed studies have provided the opportunity to further investigate the role of acid...

Zonal PANS: evaluation of different treatments of the RANS-LES interface

NASA Astrophysics Data System (ADS)

Davidson, L.

2016-03-01

The partially Reynolds-averaged Navier-Stokes (PANS) model can be used to simulate turbulent flows either as RANS, large eddy simulation (LES) or DNS. Its main parameter is fk whose physical meaning is the ratio of the modelled to the total turbulent kinetic energy. In RANS fk = 1, in DNS fk = 0 and in LES fk takes values between 0 and 1. Three different ways of prescribing fk are evaluated for decaying grid turbulence and fully developed channel flow: fk = 0.4, fk = k3/2tot/ɛ and, from its definition, fk = k/ktot where ktot is the sum of the modelled, k, and resolved, kres, turbulent kinetic energy. It is found that the fk = 0.4 gives the best results. In Girimaji and Wallin, a method was proposed to include the effect of the gradient of fk. This approach is used at RANS- LES interface in the present study. Four different interface models are evaluated in fully developed channel flow and embedded LES of channel flow: in both cases, PANS is used as a zonal model with fk = 1 in the unsteady RANS (URANS) region and fk = 0.4 in the LES region. In fully developed channel flow, the RANS- LES interface is parallel to the wall (horizontal) and in embedded LES, it is parallel to the inlet (vertical). The importance of the location of the horizontal interface in fully developed channel flow is also investigated. It is found that the location - and the choice of the treatment at the interface - may be critical at low Reynolds number or if the interface is placed too close to the wall. The reason is that the modelled turbulent shear stress at the interface is large and hence the relative strength of the resolved turbulence is small. In RANS, the turbulent viscosity - and consequently also the modelled Reynolds shear stress - is only weakly dependent on Reynolds number. It is found in the present work that it also applies in the URANS region.

Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes

PubMed Central

Lin, Xiaolong; Stur, Elisabeth; Ekrem, Torbjørn

2015-01-01

DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120–242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4–5% threshold is appropriate to delineate species of Tanytarsus non-biting midges. PMID:26406595

The evolution of trypanosomatid taxonomy.

PubMed

Kaufer, Alexa; Ellis, John; Stark, Damien; Barratt, Joel

2017-06-08

Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge that informs the present taxonomy of these important parasites.

Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.

PubMed

Yu, Xiang-Qin; Drew, Bryan T; Yang, Jun-Bo; Gao, Lian-Ming; Li, De-Zhu

2017-01-01

Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

Albicetus oxymycterus, a New Generic Name and Redescription of a Basal Physeteroid (Mammalia, Cetacea) from the Miocene of California, and the Evolution of Body Size in Sperm Whales.

PubMed

Boersma, Alexandra T; Pyenson, Nicholas D

2015-01-01

Living sperm whales are represented by only three species (Physeter macrocephalus, Kogia breviceps and Kogia sima), but their fossil record provides evidence of an ecologically diverse array of different forms, including morphologies and body sizes without analog among living physeteroids. Here we provide a redescription of Ontocetus oxymycterus, a large but incomplete fossil sperm whale specimen from the middle Miocene Monterey Formation of California, described by Remington Kellogg in 1925. The type specimen consists of a partial rostrum, both mandibles, an isolated upper rostrum fragment, and incomplete tooth fragments. Although incomplete, these remains exhibit characteristics that, when combined, set it apart morphologically from all other known physeteroids (e.g., a closed mesorostral groove, and the retention of enameled tooth crowns). Kellogg originally placed this species in the genus Ontocetus, a enigmatic tooth taxon reported from the 19th century, based on similarities between the type specimen Ontocetus emmonsi and the conspicuously large lower dentition of Ontocetus oxymycterus. However, the type of the genus Ontocetus is now known to represent a walrus tusk (belonging to fossil Odobenidae) instead of a cetacean tooth. Thus, we assign this species to the new genus Albicetus, creating the new combination of Albicetus oxymycterus, gen. nov. We provide new morphological observations of the type specimen, including a 3D model. We also calculate a total length of approximately 6 m in life, using cranial proxies of body size for physeteroids. Lastly, a phylogenetic analysis of Albicetus oxymycterus with other fossil and living Physeteroidea resolves its position as a stem physeteroid, implying that large body size and robust dentition in physeteroids evolved multiple times and in distantly related lineages.

Albicetus oxymycterus, a New Generic Name and Redescription of a Basal Physeteroid (Mammalia, Cetacea) from the Miocene of California, and the Evolution of Body Size in Sperm Whales

PubMed Central

2015-01-01

Living sperm whales are represented by only three species (Physeter macrocephalus, Kogia breviceps and Kogia sima), but their fossil record provides evidence of an ecologically diverse array of different forms, including morphologies and body sizes without analog among living physeteroids. Here we provide a redescription of Ontocetus oxymycterus, a large but incomplete fossil sperm whale specimen from the middle Miocene Monterey Formation of California, described by Remington Kellogg in 1925. The type specimen consists of a partial rostrum, both mandibles, an isolated upper rostrum fragment, and incomplete tooth fragments. Although incomplete, these remains exhibit characteristics that, when combined, set it apart morphologically from all other known physeteroids (e.g., a closed mesorostral groove, and the retention of enameled tooth crowns). Kellogg originally placed this species in the genus Ontocetus, a enigmatic tooth taxon reported from the 19th century, based on similarities between the type specimen Ontocetus emmonsi and the conspicuously large lower dentition of Ontocetus oxymycterus. However, the type of the genus Ontocetus is now known to represent a walrus tusk (belonging to fossil Odobenidae) instead of a cetacean tooth. Thus, we assign this species to the new genus Albicetus, creating the new combination of Albicetus oxymycterus, gen. nov. We provide new morphological observations of the type specimen, including a 3D model. We also calculate a total length of approximately 6 m in life, using cranial proxies of body size for physeteroids. Lastly, a phylogenetic analysis of Albicetus oxymycterus with other fossil and living Physeteroidea resolves its position as a stem physeteroid, implying that large body size and robust dentition in physeteroids evolved multiple times and in distantly related lineages. PMID:26651027

A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity.

PubMed

Milla, Liz; van Nieukerken, Erik J; Vijverberg, Ruben; Doorenweerd, Camiel; Wilcox, Stephen A; Halsey, Mike; Young, David A; Jones, Therésa M; Kallies, Axel; Hilton, Douglas J

2018-03-01

Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences

PubMed Central

Lauber, Chris; Gorbalenya, Alexander E.

2012-01-01

We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. PMID:23170166

Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.

PubMed

Lauber, Chris; Gorbalenya, Alexander E

2012-09-01

We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification.

Gut microbiota trajectory in patients with severe burn: A time series study.

PubMed

Wang, Xinying; Yang, Jianbo; Tian, Feng; Zhang, Li; Lei, Qiucheng; Jiang, Tingting; Zhou, Jihong; Yuan, Siming; Wang, Jun; Feng, Zhijian; Li, Jieshou

2017-12-01

This time series experiments aimed to investigate the dynamic change of gut microbiomes after severe burn and its association with enteral nutrition (EN). Seven severely burned patients who suffered from a severe metal dust explosion injury were recruited in this study. The dynamic changes of gut microbiome of fecal samples at six time points (1-3days, 2, 3, 4, 5 and 6weeks after severe burn) were detected using 16S ribosomal RNA pyrosequencing technology. Following the post-burn temporal order, gut microbiota dysbiosis was detected in the gut microbiome after severe burn, then it was gradually resolved. The bio-diversity of gut bacteria was initially decreased, and then returned to normal level. In addition, at the early stage (from 2 to 4weeks), the majority of those patients' gut microbiome were opportunistic pathogen genus, Enterococcus and Escherichia; while at the end of this study, the majority was a beneficial genus, Bacteroides. EN can promote the recovery of gut microbiota, especially in EN well-tolerated patients. Severe burn injury can cause a dramatic dysbiosis of gut microbiota. A trend of enriched beneficial bacteria and diminished opportunistic pathogen bacteria may serve as prognosis microbiome biomarkers of severe burn patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Diversity of Phylogenetic Information According to the Locus and the Taxonomic Level: An Example from a Parasitic Mesostigmatid Mite Genus

PubMed Central

Roy, Lise; Dowling, Ashley P.G.; Chauve, Claude Marie; Buronfosse, Thierry

2010-01-01

Molecular markers for cladistic analyses may perform differently according to the taxonomic group considered and the historical level under investigation. Here we evaluate the phylogenetic potential of five different markers for resolving evolutionary relationships within the ectoparasitic genus Dermanyssus at the species level, and their ability to address questions about the evolution of specialization. COI provided 9–18% divergence between species (up to 9% within species), 16S rRNA 10–16% (up to 4% within species), ITS1 and 2 2–9% (up to 1% within species) and Tropomyosin intron n 8–20% (up to 6% within species). EF-1α revealed different non-orthologous copies within individuals of Dermanyssus and Ornithonyssus. Tropomyosin intron n was shown containing consistent phylogenetic signal at the specific level within Dermanyssus and represents a promising marker for future prospects in phylogenetics of Acari. Phylogenetic analyses revealed that the generalist condition is apomorphic and D. gallinae might represent a complex of hybridized lineages. The split into hirsutus-group and gallinae-group in Dermanyssus does not seem to be appropriate based upon these results and D. longipes appears to be composed of two different entities. PMID:20480038

The first occurrence of the enigmatic archosauriform Crosbysaurus Heckert 2004 from the Chinle Formation of southern Utah.

PubMed

Gay, Robert J; Aude, Isabella St

2015-01-01

Originally identified as an ornithischian dinosaur, Crosbysaurus harrisae has been found in New Mexico, Arizona, and its type locality in Texas, as well as in North Carolina. The genus has been reassessed by other workers in light of reinterpretations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurs and ornithischian dinosaur dental morphologies. We report here on a new specimen of Crosbysaurus (MNA V10666) from the Chinle Formation at Comb Ridge in southeastern Utah. This new specimen is assigned to Crosbysaurus sp. on the basis of the unique compound posterior denticles, labiolingual width, and curvature. While MNA V10666 does not help resolve the affinities of Crosbysaurus, it does represent the extension of the geographic range of this taxon for approximately 250 kilometers. This is the first record of the genus Crosbysaurus in Utah and as such it represents the northernmost known record of this taxon. This indicates that Crosbysaurus was not limited to the southern area of the Chinle/Dockum deposition but instead was widespread across the Late Triassic paleoriver systems of western Pangea. The reported specimen was found in close association with a typical Late Triassic Chinle fauna, including phytosaurs, metoposaurs, and dinosauromorphs.

Haemoproteus iwa in Great Frigatebirds (Fregata minor) in the Islands of the Western Indian Ocean

PubMed Central

Bastien, Matthieu; Jaeger, Audrey; Le Corre, Matthieu; Tortosa, Pablo; Lebarbenchon, Camille

2014-01-01

Blood parasites of the sub-genus Haemoproteus have been reported in seabirds, in particular in species in the Suliformes order. These parasites are transmitted by hippoboscid flies of the genus Olfersia; strong specificity has been suggested between the vector and its vertebrate host. We investigated the prevalence of Haemoproteus infection in Suliformes and hippoboscid flies in two oceanic islands of the Western Indian Ocean: Europa and Tromelin. In total, 209 blood samples were collected from great frigatebirds (Fregata minor), masked boobies (Sula dactylatra) and red-footed boobies (Sula sula). Forty-one hippoboscid flies were also collected from birds. Seventeen frigatebirds and one fly collected on Europa tested positive for the presence of Haemoproteus parasites by polymerase chain reaction. Phylogenetic analyses based on partial sequences of the Cytochrome b gene showed that parasites were closely related to Haemoproteus iwa reported from frigatebirds in the Pacific Ocean and in the Caribbean. Plasmodium was also detected in a frigatebird on Europa; however, its placement on the phylogenetic tree could not be resolved. We provide strong support for transmission of blood parasites in seabirds in the Western Indian Ocean and suggest that migrations between the Pacific and the Indian oceans could favor the large-scale distribution of Haemoproteus iwa in frigatebird populations. PMID:24810172

Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers.

PubMed

Winterton, Shaun L; Wiegmann, Brian M; Schlinger, Evert I

2007-06-01

The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.

Vigna (Leguminosae) sensu lato: the names and identities of the American segregate genera.

PubMed

Delgado-Salinas, Alfonso; Thulin, Mats; Pasquet, Rémy; Weeden, Norm; Lavin, Matt

2011-10-01

The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

Reinvestigating an enigmatic Late Cretaceous monocot: morphology, taxonomy, and biogeography of Viracarpon

PubMed Central

Manchester, Steven R.; Ramteke, Deepak; Villarraga-Gómez, Herminso

2018-01-01

Angiosperm-dominated floras of the Late Cretaceous are essential for understanding the evolutionary, ecological, and geographic radiation of flowering plants. The Late Cretaceous–early Paleogene Deccan Intertrappean Beds of India contain angiosperm-dominated plant fossil assemblages known from multiple localities in central India. Numerous monocots have been documented from these assemblages, providing a window into an important but poorly understood time in their diversification. One component of the Deccan monocot diversity is the genus Viracarpon, known from anatomically preserved infructescences. Viracarpon was first collected over a century ago and has been the subject of numerous studies. However, resolution of its three-dimensional (3D) morphology and anatomy, as well as its taxonomic affinities, has remained elusive. In this study we investigated the morphology and taxonomy of genus Viracarpon, combining traditional paleobotanical techniques and X-ray micro-computed tomography (μCT). Re-examination of type and figured specimens, 3D reconstructions of fruits, and characterization of structures in multiple planes of section using μCT data allowed us to resolve conflicting interpretations of fruit morphology and identify additional characters useful in refining potential taxonomic affinities. Among the four Viracarpon species previously recognized, we consider two to be valid (Viracarpon hexaspermum and Viracarpon elongatum), and the other two to be synonyms of these. Furthermore, we found that permineralized infructescences of Coahuilocarpon phytolaccoides from the late Campanian of Mexico correspond closely in morphology to V. hexaspermum. We argue that Viracarpon and Coahuilocarpon are congeneric and provide the new combination, Viracarpon phytolaccoides (Cevallos-Ferriz, Estrada-Ruiz & Perez-Hernandez) Matsunaga, S.Y. Smith, & Manchester comb. nov. The significant geographic disjunction between these two occurrences indicates that the genus Viracarpon was widespread and may be present in other Late Cretaceous assemblages. Viracarpon exhibits character combinations not present in any extant taxa and its affinities remain unresolved, possibly representing an extinct member of Alismatales. The character mosaic observed in Viracarpon and the broad distribution of the genus provide new data relevant to understanding early monocot evolution and suggest that the (thus far) largely invisible Late Cretaceous monocot diversification was characterized by enigmatic and/or stem taxa. PMID:29637023

Fully implicit moving mesh adaptive algorithm

NASA Astrophysics Data System (ADS)

Chacon, Luis

2005-10-01

In many problems of interest, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. The former is best dealt with with fully implicit methods, which are able to step over fast frequencies to resolve the dynamical time scale of interest. The latter requires grid adaptivity for efficiency. Moving-mesh grid adaptive methods are attractive because they can be designed to minimize the numerical error for a given resolution. However, the required grid governing equations are typically very nonlinear and stiff, and of considerably difficult numerical treatment. Not surprisingly, fully coupled, implicit approaches where the grid and the physics equations are solved simultaneously are rare in the literature, and circumscribed to 1D geometries. In this study, we present a fully implicit algorithm for moving mesh methods that is feasible for multidimensional geometries. A crucial element is the development of an effective multilevel treatment of the grid equation.ootnotetextL. Chac'on, G. Lapenta, A fully implicit, nonlinear adaptive grid strategy, J. Comput. Phys., accepted (2005) We will show that such an approach is competitive vs. uniform grids both from the accuracy (due to adaptivity) and the efficiency standpoints. Results for a variety of models 1D and 2D geometries, including nonlinear diffusion, radiation-diffusion, Burgers equation, and gas dynamics will be presented.

Resilient Nodeless d -Wave Superconductivity in Monolayer FeSe

NASA Astrophysics Data System (ADS)

Agterberg, D. F.; Shishidou, T.; O'Halloran, J.; Brydon, P. M. R.; Weinert, M.

2017-12-01

Monolayer FeSe exhibits the highest transition temperature among the iron based superconductors and appears to be fully gapped, seemingly consistent with s -wave superconductivity. Here, we develop a theory for the superconductivity based on coupling to fluctuations of checkerboard magnetic order (which has the same translation symmetry as the lattice). The electronic states are described by a symmetry based k .p -like theory and naturally account for the states observed by angle resolved photoemission spectroscopy. We show that a prediction of this theory is that the resultant superconducting state is a fully gapped, nodeless, d -wave state. This state, which would usually have nodes, stays nodeless because, as seen experimentally, the relevant spin-orbit coupling has an energy scale smaller than the superconducting gap.

Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer.

PubMed

Tischer, Karolin; Kleinsteuber, Sabine; Schleinitz, Kathleen M; Fetzer, Ingo; Spott, Oliver; Stange, Florian; Lohse, Ute; Franz, Janett; Neumann, Franziska; Gerling, Sarah; Schmidt, Christian; Hasselwander, Eyk; Harms, Hauke; Wendeberg, Annelie

2013-09-01

Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Comparison of Large eddy dynamo simulation using dynamic sub-grid scale (SGS) model with a fully resolved direct simulation in a rotating spherical shell

NASA Astrophysics Data System (ADS)

Matsui, H.; Buffett, B. A.

2017-12-01

The flow in the Earth's outer core is expected to have vast length scale from the geometry of the outer core to the thickness of the boundary layer. Because of the limitation of the spatial resolution in the numerical simulations, sub-grid scale (SGS) modeling is required to model the effects of the unresolved field on the large-scale fields. We model the effects of sub-grid scale flow and magnetic field using a dynamic scale similarity model. Four terms are introduced for the momentum flux, heat flux, Lorentz force and magnetic induction. The model was previously used in the convection-driven dynamo in a rotating plane layer and spherical shell using the Finite Element Methods. In the present study, we perform large eddy simulations (LES) using the dynamic scale similarity model. The scale similarity model is implement in Calypso, which is a numerical dynamo model using spherical harmonics expansion. To obtain the SGS terms, the spatial filtering in the horizontal directions is done by taking the convolution of a Gaussian filter expressed in terms of a spherical harmonic expansion, following Jekeli (1981). A Gaussian field is also applied in the radial direction. To verify the present model, we perform a fully resolved direct numerical simulation (DNS) with the truncation of the spherical harmonics L = 255 as a reference. And, we perform unresolved DNS and LES with SGS model on coarser resolution (L= 127, 84, and 63) using the same control parameter as the resolved DNS. We will discuss the verification results by comparison among these simulations and role of small scale fields to large scale fields through the role of the SGS terms in LES.

Unmanned Aerial Systems: Air Force and Army Should Improve Strategic Human Capital Planning for Pilot Workforces

DTIC Science & Technology

2017-01-01

UNMANNED AERIAL SYSTEMS Air Force and Army Should Improve Strategic Human Capital Planning for Pilot Workforces...Should Improve Strategic Human Capital Planning for Pilot Workforces What GAO Found The Air Force and the Army have not fully applied four of the five...key principles for effective strategic human capital planning for managing pilots of unmanned aerial systems (UAS) that are important for resolving

Discovery of natural gain amplification in the 10-micrometer carbon dioxide laser bands on Mars - A natural laser

NASA Technical Reports Server (NTRS)

Mumma, M. J.; Buhl, D.; Chin, G.; Deming, D.; Espenak, F.; Kostiuk, T.; Zipoy, D.

1981-01-01

Fully resolved intensity profiles of various lines in the carbon dioxide band at 10.4 micrometers have been measured on Mars with an infrared heterodyne spectrometer. Analysis of the line shapes shows that the Mars atmosphere exhibits positive gain in these lines. The detection of natural optical gain amplification enables identification of these lines as a definite natural laser.

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

Spectral characteristics of time resolved magnonic spin Seebeck effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Etesami, S. R.; Chotorlishvili, L.; Berakdar, J.

2015-09-28

Spin Seebeck effect (SSE) holds promise for new spintronic devices with low-energy consumption. The underlying physics, essential for a further progress, is yet to be fully clarified. This study of the time resolved longitudinal SSE in the magnetic insulator yttrium iron garnet concludes that a substantial contribution to the spin current stems from small wave-vector subthermal exchange magnons. Our finding is in line with the recent experiment by S. R. Boona and J. P. Heremans [Phys. Rev. B 90, 064421 (2014)]. Technically, the spin-current dynamics is treated based on the Landau-Lifshitz-Gilbert equation also including magnons back-action on thermal bath, whilemore » the formation of the time dependent thermal gradient is described self-consistently via the heat equation coupled to the magnetization dynamics.« less

Polarized reflectance and transmittance properties of windblown sea surfaces.

PubMed

Mobley, Curtis D

2015-05-20

Generation of random sea surfaces using wave variance spectra and Fourier transforms is formulated in a way that guarantees conservation of wave energy and fully resolves wave height and slope variances. Monte Carlo polarized ray tracing, which accounts for multiple scattering between light rays and wave facets, is used to compute effective Mueller matrices for reflection and transmission of air- or water-incident polarized radiance. Irradiance reflectances computed using a Rayleigh sky radiance distribution, sea surfaces generated with Cox-Munk statistics, and unpolarized ray tracing differ by 10%-18% compared with values computed using elevation- and slope-resolving surfaces and polarized ray tracing. Radiance reflectance factors, as used to estimate water-leaving radiance from measured upwelling and sky radiances, are shown to depend on sky polarization, and improved values are given.

Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form.

PubMed Central

Morrison, C L; Harvey, A W; Lavery, S; Tieu, K; Huang, Y; Cunningham, C W

2002-01-01

The repeated appearance of strikingly similar crab-like forms in independent decapod crustacean lineages represents a remarkable case of parallel evolution. Uncertainty surrounding the phylogenetic relationships among crab-like lineages has hampered evolutionary studies. As is often the case, aligned DNA sequences by themselves were unable to fully resolve these relationships. Four nested mitochondrial gene rearrangements--including one of the few reported movements of an arthropod protein-coding gene--are congruent with the DNA phylogeny and help to resolve a crucial node. A phylogenetic analysis of DNA sequences, and gene rearrangements, supported five independent origins of the crab-like form, and suggests that the evolution of the crab-like form may be irreversible. This result supports the utility of mitochondrial gene rearrangements in phylogenetic reconstruction. PMID:11886621

Infrared detection of (H 2O) 20 isomers of exceptional stability: A drop-like and a face-sharing pentagonal prism cluster

DOE PAGES

Pradzynski, Christoph C.; Dierking, Christoph W.; Zurheide, Florian; ...

2014-09-01

Water clusters containing fully coordinated water molecules are model systems that mimic the local environment of the condensed phase. Present knowledge about the water cluster size regime in which the transition from the allsurface to the fully solvated water molecules occurs is mainly based on theoretical predictions in lieu of the absence of precisely size resolved experimental measurements. Here, we report size and isomer selective infrared (IR) spectra of (H 2O) 20 clusters tagged with a sodium atom by employing IR excitation modulated photoionization spectroscopy. The observed absorption patterns in the OH stretching ”fingerprint” region are consistent with the theoreticallymore » predicted spectra of two structurally distinct isomers: A drop-like cluster with a fully coordinated (interior) water and an edge-sharing pentagonal prism cluster in which all atoms are on the surface. The observed isomers show exceptional stability and are predicted to be nearly isoenergetic.« less

Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint.

PubMed

Toulmin, Anita; Baltierra-Jasso, Laura E; Morten, Michael J; Sabir, Tara; McGlynn, Peter; Schröder, Gunnar F; Smith, Brian O; Magennis, Steven W

2017-09-19

DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19 F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.

A near-wall turbulence model and its application to fully developed turbulent channel and pipe flows

NASA Technical Reports Server (NTRS)

Kim, S.-W.

1988-01-01

A near wall turbulence model and its incorporation into a multiple-time-scale turbulence model are presented. In the method, the conservation of mass, momentum, and the turbulent kinetic energy equations are integrated up to the wall; and the energy transfer rate and the dissipation rate inside the near wall layer are obtained from algebraic equations. The algebraic equations for the energy transfer rate and the dissipation rate inside the near wall layer were obtained from a k-equation turbulence model and the near wall analysis. A fully developed turbulent channel flow and fully developed turbulent pipe flows were solved using a finite element method to test the predictive capability of the turbulence model. The computational results compared favorably with experimental data. It is also shown that the present turbulence model could resolve the over shoot phenomena of the turbulent kinetic energy and the dissipation rate in the region very close to the wall.

An Eulerian two-phase flow model for sediment transport under realistic surface waves

NASA Astrophysics Data System (ADS)

Hsu, T. J.; Kim, Y.; Cheng, Z.; Chauchat, J.

2017-12-01

Wave-driven sediment transport is of major importance in driving beach morphology. However, the complex mechanisms associated with unsteadiness, free-surface effects, and wave-breaking turbulence have not been fully understood. Particularly, most existing models for sediment transport adopt bottom boundary layer approximation that mimics the flow condition in oscillating water tunnel (U-tube). However, it is well-known that there are key differences in sediment transport when comparing to large wave flume datasets, although the number of wave flume experiments are relatively limited regardless of its importance. Thus, a numerical model which can resolve the entire water column from the bottom boundary layer to the free surface can be a powerful tool. This study reports an on-going effort to better understand and quantify sediment transport under shoaling and breaking surface waves through the creation of open-source numerical models in the OpenFOAM framework. An Eulerian two-phase flow model, SedFoam (Cheng et al., 2017, Coastal Eng.) is fully coupled with a volume-of-fluid solver, interFoam/waves2Foam (Jacobsen et al., 2011, Int. J. Num. Fluid). The fully coupled model, named SedWaveFoam, regards the air and water phases as two immiscible fluids with the interfaces evolution resolved, and the sediment particles as dispersed phase. We carried out model-data comparisons with the large wave flume sheet flow data for nonbreaking waves reported by Dohmen-Janssen and Hanes (2002, J. Geophysical Res.) and good agreements were obtained for sediment concentration and net transport rate. By further simulating a case without free-surface (mimic U-tube condition), the effects of free-surface, most notably the boundary layer streaming effect on total transport, can be quantified.

Characterization of Rare Reverse Flow Events in Adverse Pressure Gradient Turbulent Boundary Layers

NASA Astrophysics Data System (ADS)

Kaehler, Christian J.; Bross, Matthew; Fuchs, Thomas

2017-11-01

Time-resolved tomographic flow fields measured in the viscous sublayer region of a turbulent boundary layer subjected to an adverse pressure gradient (APG) are examined with the aim to resolve and characterize reverse flow events at Reτ = 5000. The fields were measured using a novel high resolution tomographic particle tracking technique. It is shown that this technique is able to fully resolve mean and time dependent features of the complex three-dimensional flow with high accuracy down to very near-wall distances ( 10 μm). From time resolved Lagrangian particle trajectories, statistical information as well as instantaneous topological features of near-wall flow events are deduced. Similar to the zero pressure gradient case (ZPG), it was found that individual events with reverse flow components still occur relatively rarely under the action of the pressure gradient investigated here. However, reverse flow events comprised of many individual events, are shown to appear in relatively organized groupings in both spanwise and streamise directions. Furthermore, instantaneous measurements of reverse flow events show that these events are associated with the motion of low-momentum streaks in the near-wall region. This work is supported by the Priority Programme SPP 1881 Turbulent Superstructures and the individual project Grant KA1808/8-2 of the Deutsche Forschungsgemeinschaft.

Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics

NASA Astrophysics Data System (ADS)

Großerueschkamp, Frederik; Bracht, Thilo; Diehl, Hanna C.; Kuepper, Claus; Ahrens, Maike; Kallenbach-Thieltges, Angela; Mosig, Axel; Eisenacher, Martin; Marcus, Katrin; Behrens, Thomas; Brüning, Thomas; Theegarten, Dirk; Sitek, Barbara; Gerwert, Klaus

2017-03-01

Diffuse malignant mesothelioma (DMM) is a heterogeneous malignant neoplasia manifesting with three subtypes: epithelioid, sarcomatoid and biphasic. DMM exhibit a high degree of spatial heterogeneity that complicates a thorough understanding of the underlying different molecular processes in each subtype. We present a novel approach to spatially resolve the heterogeneity of a tumour in a label-free manner by integrating FTIR imaging and laser capture microdissection (LCM). Subsequent proteome analysis of the dissected homogenous samples provides in addition molecular resolution. FTIR imaging resolves tumour subtypes within tissue thin-sections in an automated and label-free manner with accuracy of about 85% for DMM subtypes. Even in highly heterogeneous tissue structures, our label-free approach can identify small regions of interest, which can be dissected as homogeneous samples using LCM. Subsequent proteome analysis provides a location specific molecular characterization. Applied to DMM subtypes, we identify 142 differentially expressed proteins, including five protein biomarkers commonly used in DMM immunohistochemistry panels. Thus, FTIR imaging resolves not only morphological alteration within tissue but it resolves even alterations at the level of single proteins in tumour subtypes. Our fully automated workflow FTIR-guided LCM opens new avenues collecting homogeneous samples for precise and predictive biomarkers from omics studies.

Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics.

PubMed

Großerueschkamp, Frederik; Bracht, Thilo; Diehl, Hanna C; Kuepper, Claus; Ahrens, Maike; Kallenbach-Thieltges, Angela; Mosig, Axel; Eisenacher, Martin; Marcus, Katrin; Behrens, Thomas; Brüning, Thomas; Theegarten, Dirk; Sitek, Barbara; Gerwert, Klaus

2017-03-30

Diffuse malignant mesothelioma (DMM) is a heterogeneous malignant neoplasia manifesting with three subtypes: epithelioid, sarcomatoid and biphasic. DMM exhibit a high degree of spatial heterogeneity that complicates a thorough understanding of the underlying different molecular processes in each subtype. We present a novel approach to spatially resolve the heterogeneity of a tumour in a label-free manner by integrating FTIR imaging and laser capture microdissection (LCM). Subsequent proteome analysis of the dissected homogenous samples provides in addition molecular resolution. FTIR imaging resolves tumour subtypes within tissue thin-sections in an automated and label-free manner with accuracy of about 85% for DMM subtypes. Even in highly heterogeneous tissue structures, our label-free approach can identify small regions of interest, which can be dissected as homogeneous samples using LCM. Subsequent proteome analysis provides a location specific molecular characterization. Applied to DMM subtypes, we identify 142 differentially expressed proteins, including five protein biomarkers commonly used in DMM immunohistochemistry panels. Thus, FTIR imaging resolves not only morphological alteration within tissue but it resolves even alterations at the level of single proteins in tumour subtypes. Our fully automated workflow FTIR-guided LCM opens new avenues collecting homogeneous samples for precise and predictive biomarkers from omics studies.

The Army Did Not Fully Document Procedures for Processing Wholesale Equipment in Kuwait

DTIC Science & Technology

2016-02-24

accountability , integrity, and efficiency; advises the Secretary of Defense and Congress; and informs the public. Vision Our vision is to be a model oversight...property accountability in support of Operation Inherent Resolve. Findings Army Field Support Battalion (AFSBn)–Kuwait generally had effective...established and equipment moving into and out of Camp Arifjan is properly accounted for and maintained. During the audit, we also observed a lack of physical

VizieR Online Data Catalog: FTS reference UV wavelengths of CrIII (Smillie+, 2008)

NASA Astrophysics Data System (ADS)

Smillie, D. G.; Pickering, J. C.; Smith, P. L.

2009-03-01

The Cr III spectrum was acquired in the wavenumber range 31596 to 63192cm-1, using the Imperial College (IC) VUV FTS, and a PDL as light source. The spectral resolution used, 0.12cm-1, was sufficient to fully resolve the Doppler broadened transition line profiles, for which the average unblended full-width at half maximum (FWHM) was just under 0.3cm-1. (1 data file).

Development of Commercially Useable Codes to Simulate Aluminized Propellant Combustion and Related Issues

DTIC Science & Technology

2009-11-03

functions and the second derivative of Green’s function. We exploit the geometrical characteristics of our integrand, i.e., we use spherical coordinates...statistically equivalent medium. Both the fully resolved probability spectrum and the geometrically exact particle shapes are considered in this...18 Buckmaster Research A1-18 FA9550-07-C-0123 References [1] B.D. Lubachevsky and F.H. Stillinger. “ Geometric properties of random disk packings”, J

Submesoscale Flows and Mixing in the Oceanic Surface Layer Using the Regional Oceanic Modeling System (ROMS)

DTIC Science & Technology

2014-09-30

continuation of the evolution of the Regional Oceanic Modeling System (ROMS) as a multi-scale, multi-process model and its utilization for...hydrostatic component of ROMS (Kanarska et al., 2007) is required to increase its efficiency and generality. The non-hydrostatic ROMS involves the solution...instability and wind-driven mixing. For the computational regime where those processes can be partially, but not yet fully resolved, it will

Thermal and Denaturation Studies of the Time-Resolved Fluorescence Decay of Human Superoxide Dismutase

NASA Astrophysics Data System (ADS)

Silva, Norberto De Jesus

Previous studies have shown that time-resolved fluorescence decay of various single tryptophan proteins is best described by a distribution of fluorescence lifetimes rather than one or two lifetimes. The thermal dependence of the lifetime distributions is consistent with the hypothesis that proteins fluctuate between a hierarchy of many conformational substates. With this scenario as a theoretical framework, the correlations between protein dynamic and structure are investigated by studying the time-resolved fluorescence and anisotropy decay of the single tryptophan (Trp) residue of human superoxide dismutase (HSOD) over a wide range of temperatures and at different denaturant concentrations. First, it is demonstrated that the center of the lifetime distribution can characterize the average deactivation environment of the excited Trp-protein system. A qualitative model is introduced to explain the time-resolved fluorescence decay of HSOD in 80% glycerol over a wide range of temperatures. The dynamical model features isoenergetic conformational substates separated by a hierarchy of energy barriers. The HSOD system is also investigated as a function of denaturant concentration in aqueous solution. As a function of guanidine hydrochloride (GdHCl), the width of the fluorescence lifetime distribution of HSOD displays a maximum which is not coincident with the fully denatured form of HSOD at 6.5M GdHCl. Furthermore, the width for the fully denatured form of HSOD is greater than that of the native form. This is consistent with the scenario that more conformational substates are being created upon denaturation of HSOD. HSOD is a dimeric protein and it was observed that the width of the lifetime distribution of HSOD at intermediate GdHCl concentrations increased with decreasing protein concentration. In addition, the secondary structure of HSOD at intermediate GdHCl concentration does not change with protein concentration. These results suggest that HSOD display structural microheterogeneity which is consistent with the hypothesis of conformational substates. Further analysis show that, during denaturation, the monomeric form of HSOD is an intermediate which displays native-like secondary structure and fluctuating tertiary structure; i.e., the monomeric form of HSOD is a molten globule.

Bodotria jejuensis sp. nov. (Crustacea, Cumacea, Bodotriidae), a new Korean cumacean.

PubMed

Lee, Chang-Mok; Kim, Sung-Hyun; Kim, Young-Hyo

2016-09-06

A new species of Cumacea belonging to the genus Bodotria Goodsir, 1843 was collected from the Jeju-do Island, Korea. The new speices, Bodotria jejuensis sp. nov. is similar to B. similis Calman, 1907, B. rugosa Gamô, 1963, B. carinata Gamô, 1964, and B. biplicata Gamô, 1964 in having a pitted carapace, prominent dorso-lateral carina, and unarticulated endopod of uropod. However, longish elliptical shape of carapace, well-developed dorso-lateral carina and distinct lateral ridge are the major characteristics which serve to distinguish the new species from its congeners. The new species is fully illustrated and extensively compared with related species. A key to the Korean Bodotria species is also provided.

A multilocus phylogeny of Malagasy scincid lizards elucidates the relationships of the fossorial genera Androngo and Cryptoscincus.

PubMed

Crottini, Angelica; Dordel, Janina; Köhler, Jörn; Glaw, Frank; Schmitz, Andreas; Vences, Miguel

2009-10-01

A phylogeny for 29 species of scincine lizards from Madagascar, based on 3693 bp of six mitochondrial and five nuclear genes, revealed multiple parallel evolution of adaptations for a burrowing life, and unexpected relationships of the monotypic genera Androngo and Cryptoscincus. Androngo trivittatus was sister to Pygomeles braconnieri, and Cryptoscincus minimus was deeply nested within the genus Paracontias, all of these being fossorial taxa of elongated bodies and partly or fully reduced limbs. To account for these results, we place Cryptoscincus as a junior synonym of Paracontias, and discuss possible taxonomic consequences that may affect the status of Androngo, once additional data become available.

Methyl tert-butyl ether biodegradation by microbial consortia obtained from soil samples of gasoline-polluted sites in Mexico.

PubMed

Morales, Marcia; Velázquez, Elia; Jan, Janet; Revah, Sergio; González, Uriel; Razo-Flores, Elías

2004-02-01

Microbial consortia obtained from soil samples of gasoline-polluted sites were individually enriched with pentane, hexane, isooctane and toluene. Cometabolism with methyl tert-butyl ether, (MTBE), gave maximum degradation rates of 49, 12, 32 and 0 mg g(-1)protein h(-1), respectively. MTBE was fully degraded even when pentane was completely depleted with a cometabolic coefficient of 1 mgMTBE mg(-1)pentane. The analysis of 16S rDNA from isolated microorganisms in the pentane-adapted consortia showed that microorganisms could be assigned to Pseudomonas. This is the first work reporting the cometabolic mineralization of MTBE by consortium of this genus.

Taxonomic revision of Paraustrosimulium Wygodzinsky & Coscarón: reassignment of Austrosimulium colboi and description of P. obcidens n. sp. from Western Australia.

PubMed

Craig, Douglas A; Moulton, John K; Currie, Douglas C

2017-10-20

The hitherto monotypic South American genus Paraustrosimulium Wygodzinsky & Coscarón is revised to accommodate two Australian species: Austrosimulium colboi Davies & Györkös and Paraustrosimulium obcidens n. sp. The generic diagnosis is updated and the eastern Australian species Paraustrosimulium colboi (Davies & Györkös) n. stat. is re-described, including the male for the first time. The Western, Australian sister species of P. colbo, namely P. obcidens Craig, Moulton Currie n. sp. is also fully described. The relationship of Paraustrosimulium to other simuliid genera is discussed, as are aspects of historical biogeography.

Time resolved PIV and flow visualization of 3D sheet cavitation

NASA Astrophysics Data System (ADS)

Foeth, E. J.; van Doorne, C. W. H.; van Terwisga, T.; Wieneke, B.

2006-04-01

Time-resolved PIV was applied to study fully developed sheet cavitation on a hydrofoil with a spanwise varying angle of attack. The hydrofoil was designed to have a three-dimensional cavitation pattern closely related to propeller cavitation, studied for its adverse effects as vibration, noise, and erosion production. For the PIV measurements, fluorescent tracer particles were applied in combination with an optical filter, in order to remove the reflections of the laser lightsheet by the cavitation. An adaptive mask was developed to find the interface between the vapor and liquid phase. The velocity at the interface of the cavity was found to be very close to the velocity predicted by a simple streamline model. For a visualization of the global flow dynamics, the laser beam was expanded and used to illuminate the entire hydrofoil and cavitation structure. The time-resolved recordings reveal the growth of the attached cavity and the cloud shedding. Our investigation proves the viability of accurate PIV measurements around developed sheet cavitation. The presented results will further be made available as a benchmark for the validation of numerical simulations of this complicated flow.

Noncontact blood species identification method based on spatially resolved near-infrared transmission spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Linna; Sun, Meixiu; Wang, Zhennan; Li, Hongxiao; Li, Yingxin; Li, Gang; Lin, Ling

2017-09-01

The inspection and identification of whole blood are crucially significant for import-export ports and inspection and quarantine departments. In our previous research, we proved Near-Infrared diffuse transmitted spectroscopy method was potential for noninvasively identifying three blood species, including macaque, human and mouse, with samples measured in the cuvettes. However, in open sampling cases, inspectors may be endangered by virulence factors in blood samples. In this paper, we explored the noncontact measurement for classification, with blood samples measured in the vacuum blood vessels. Spatially resolved near-infrared spectroscopy was used to improve the prediction accuracy. Results showed that the prediction accuracy of the model built with nine detection points was more than 90% in identification between all five species, including chicken, goat, macaque, pig and rat, far better than the performance of the model built with single-point spectra. The results fully supported the idea that spatially resolved near-infrared spectroscopy method can improve the prediction ability, and demonstrated the feasibility of this method for noncontact blood species identification in practical applications.

Quasilinear models through the lens of resolvent analysis

NASA Astrophysics Data System (ADS)

McKeon, Beverley; Chini, Greg

2017-11-01

Quasilinear (QL) and generalized quasilinear (GQL) analyses, e.g. Marston et al., also variously described as statistical state dynamics models, e.g., Farrell et al., restricted nonlinear models, e.g. Thomas et al., or 2D/3C models, e.g. Gayme et al., have achieved considerable success in recovering the mean velocity profile for a range of turbulent flows. In QL approaches, the portion of the velocity field that can be represented as streamwise constant, i.e. with streamwise wavenumber kx = 0 , is fully resolved, while the streamwise-varying dynamics are linearized about the streamwise-constant field; that is, only those nonlinear interactions that drive the streamwise-constant field are retained, and the non-streamwise constant ``fluctuation-fluctuation'' interactions are ignored. Here, we show how these QL approaches can be reformulated in terms of the closed-loop resolvent analysis of McKeon & Sharma (2010), which enables us to identify reasons for their evident success as well as algorithms for their efficient computation. The support of ONR through Grant No. N00014-17-2307 is gratefully acknowledged.

Rectal prolapse in a free-ranging mountain gorilla (Gorilla beringei beringei): clinical presentation and surgical management.

PubMed

Kalema-Zikusoka, G; Lowenstine, L

2001-12-01

A juvenile female mountain gorilla (Gorilla beringei beringei) of the Mubare tourist group in Bwindi Impenetrable National Park, Uganda, developed a severe, complete rectal prolapse that did not spontaneously resolve. Eight months prior, a juvenile female mountain gorilla of the Mubare group developed a mild, complete rectal prolapse that resolved spontaneously within 24 hr. Field guides reported that spontaneously resolving prolapses had been seen previously in two other juveniles, one of which was from the Mubare group. The tissue became increasingly necrotic and maggot infested over the course of 1 wk. Surgical intervention involved amputation of the affected rectal tissues and suturing the viable portion to the anal sphincter muscle with simple interrupted absorbable sutures. The surgery was performed in the field in accordance with Uganda Wildlife Authority policies. Antibiotics and anthelmintics were administered systemically, and the gorilla returned to the group. The gorilla appeared to recover fully after 3 wk. Histology of the resected rectal tissue confirmed intense inflammation and necrosis with myiasis but did not reveal an underlying etiology.

Prospective time-resolved LCA of fully electric supercap vehicles in Germany.

PubMed

Zimmermann, Benedikt M; Dura, Hanna; Baumann, Manuel J; Weil, Marcel R

2015-07-01

The ongoing transition of the German electricity supply toward a higher share of renewable and sustainable energy sources, called Energiewende in German, has led to dynamic changes in the environmental impact of electricity over the last few years. Prominent scenario studies predict that comparable dynamics will continue in the coming decades, which will further improve the environmental performance of Germany's electricity supply. Life cycle assessment (LCA) is the methodology commonly used to evaluate environmental performance. Previous LCA studies on electric vehicles have shown that the electricity supply for the vehicles' operation is responsible for the major part of their environmental impact. The core question of this study is how the prospective dynamic development of the German electricity mix will affect the impact of electric vehicles operated in Germany and how LCA can be adapted to analyze this impact in a more robust manner. The previously suggested approach of time-resolved LCA, which is located between static and dynamic LCA, is used in this study and compared with several static approaches. Furthermore, the uncertainty issue associated with scenario studies is addressed in general and in relation to time-resolved LCA. Two scenario studies relevant to policy making have been selected, but a moderate number of modifications have been necessary to adapt the data to the requirements of a life cycle inventory. A potential, fully electric vehicle powered by a supercapacitor energy storage system is used as a generic example. The results show that substantial improvements in the environmental repercussions of the electricity supply and, consequentially, of electric vehicles will be achieved between 2020 and 2031 on the basis of the energy mixes predicted in both studies. This study concludes that although scenarios might not be able to predict the future, they should nonetheless be used as data sources in prospective LCA studies, because in many cases historic data appears to be unsuitable for providing realistic information on the future. The time-resolved LCA approach improves the assessment's robustness substantially, especially when nonlinear developments are foreseen in the future scenarios. This allows for a reduction of bias in LCA-based decision making. However, a deeper integration of time-resolved data in the life cycle inventory and the implementation of a more suitable software framework are desirable. The study describes how life cycle assessment's (LCA) robustness can be improved by respecting prospective fluctuations, like the transition of the German electricity mix, in the modeling of the life cycle inventory. It presents a feasible and rather simple process to add time-resolved data to LCA. The study selects 2 different future scenarios from important German studies and processes their data systematically to make them compatible with the requirements of a life cycle inventory. The use of external scenarios as basis for future-oriented LCA is reflected critically. A case study on electric mobility is presented and used to compare historic, prospective static, and prospective time-resolved electricity mix modeling approaches. The case study emphasizes the benefits of time-resolved LCA in direct comparison with the currently used approaches. © 2015 SETAC.

Near-wall turbulence model and its application to fully developed turbulent channel and pipe flows

NASA Technical Reports Server (NTRS)

Kim, S.-W.

1990-01-01

A near-wall turbulence model and its incorporation into a multiple-timescale turbulence model are presented. The near-wall turbulence model is obtained from a k-equation turbulence model and a near-wall analysis. In the method, the equations for the conservation of mass, momentum, and turbulent kinetic energy are integrated up to the wall, and the energy transfer and the dissipation rates inside the near-wall layer are obtained from algebraic equations. Fully developed turbulent channel and pipe flows are solved using a finite element method. The computational results compare favorably with experimental data. It is also shown that the turbulence model can resolve the overshoot phenomena of the turbulent kinetic energy and the dissipation rate in the region very close to the wall.

Integrated Fossil and Molecular Data Reveal the Biogeographic Diversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.)

PubMed Central

Zhang, Jing-Bo; Li, Rui-Qi; Xiang, Xiao-Guo; Manchester, Steven R.; Lin, Li; Wang, Wei; Wen, Jun; Chen, Zhi-Duan

2013-01-01

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy. PMID:23875028

Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.).

PubMed

Zhang, Jing-Bo; Li, Rui-Qi; Xiang, Xiao-Guo; Manchester, Steven R; Lin, Li; Wang, Wei; Wen, Jun; Chen, Zhi-Duan

2013-01-01

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.

A phylogeographic investigation of the kelp genus Laminaria (Laminariales, Phaeophyceae), with emphasis on the South Atlantic Ocean.

PubMed

Rothman, Mark D; Mattio, Lydiane; Anderson, Robert J; Bolton, John J

2017-08-01

The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time-calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time-calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively. © 2017 Phycological Society of America.

Cytoplasmic effects on DNA methylation between male sterile lines and the maintainer in wheat (Triticum aestivum L.).

PubMed

Ba, Qingsong; Zhang, Gaisheng; Niu, Na; Ma, Shoucai; Wang, Junwei

2014-10-01

Male sterile cytoplasm plays an important role in hybrid wheat, and three-line system including male sterile (A line), its maintainer (B line) and restoring (R line) has played a major role in wheat hybrid production. It is well known that DNA methylation plays an important role in gene expression regulation during biological development in wheat. However, no reports are available on DNA methylation affected by different male sterile cytoplasms in hybrid wheat. We employed a methylation-sensitive amplified polymorphism technique to characterize nuclear DNA methylation in three male sterile cytoplasms. A and B lines share the same nucleus, but have different cytoplasms which is male sterile for the A and fertile for the B. The results revealed a relationship of DNA methylation at these sites specifically with male sterile cytoplasms, as well as male sterility, since the only difference between the A lines and B line was the cytoplasm. The DNA methylation was markedly affected by male sterile cytoplasms. K-type cytoplasm affected the methylation to a much greater degree than T-type and S-type cytoplasms, as indicated by the ratio of methylated sites, ratio of fully methylated sites, and polymorphism between A lines and B line for these cytoplasms. The genetic distance between the cytoplasm and nucleus for the K-type is much greater than for the T- and S-types because the former is between Aegilops genus and Triticum genus and the latter is within Triticum genus between Triticum spelta and Triticum timopheevii species. Thus, this difference in genetic distance may be responsible for the variation in methylation that we observed. Copyright © 2014. Published by Elsevier B.V.

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status.

PubMed

Richards, Vincent P; Alvarez, Andres J; Luce, Amy R; Bedenbaugh, Molly; Mitchell, Mary Lyn; Burne, Robert A; Nascimento, Marcelle M

2017-08-01

The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMI NGS ) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMI NGS , and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different ( P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis , which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans , Scardovia wiggsiae , Parascardovia denticolens , and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. Copyright © 2017 American Society for Microbiology.

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status

PubMed Central

Alvarez, Andres J.; Luce, Amy R.; Bedenbaugh, Molly; Mitchell, Mary Lyn

2017-01-01

ABSTRACT The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMINGS) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMINGS, and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different (P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis, which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans, Scardovia wiggsiae, Parascardovia denticolens, and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. PMID:28507066

A phylogeny of Astyanax (Characiformes: Characidae) in Central and North America.

PubMed

Schmitter-Soto, Juan J

2016-05-06

A phylogeny is presented for 34 species of Astyanax, 27 of them once included within A. aeneus or A. fasciatus in Central America and Mexico, based on 52 morphological characters (mostly osteological, but also pigmentation and meristics), with three outgroups. Monophyly is not supported for A. aeneus s. lat., as Brazilian species such as A. fasciatus s. str. and others occur also within that clade. There were only five resolved clades, three of them including both Brazilian and Central American species, one purely Nicaraguan, and one for central-northern Mexico and Texas. Coincidence with previous cladistic hypotheses is only partial. The genus Bramocharax Gill is not recovered, and thus confirmed as a synonym of Astyanax Baird & Girard. The findings point at a more complex biogeographic history of the region than usually recognized.

Symbiotic Dinoflagellate Functional Diversity Mediates Coral Survival under Ecological Crisis.

PubMed

Suggett, David J; Warner, Mark E; Leggat, William

2017-10-01

Coral reefs have entered an era of 'ecological crisis' as climate change drives catastrophic reef loss worldwide. Coral growth and stress susceptibility are regulated by their endosymbiotic dinoflagellates (genus Symbiodinium). The phylogenetic diversity of Symbiodinium frequently corresponds to patterns of coral health and survival, but knowledge of functional diversity is ultimately necessary to reconcile broader ecological success over space and time. We explore here functional traits underpinning the complex biology of Symbiodinium that spans free-living algae to coral endosymbionts. In doing so we propose a mechanistic framework integrating the primary traits of resource acquisition and utilisation as a means to explain Symbiodinium functional diversity and to resolve the role of Symbiodinium in driving the stability of coral reefs under an uncertain future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Externally Calibrated Parallel Imaging for 3D Multispectral Imaging Near Metallic Implants Using Broadband Ultrashort Echo Time Imaging

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Reeder, Scott B.

2017-01-01

Purpose To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. Theory and Methods A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Results Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. Conclusion A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. PMID:27403613

Analysis of Highly-Resolved Simulations of 2-D Humps Toward Improvement of Second-Moment Closures

NASA Technical Reports Server (NTRS)

Jeyapaul, Elbert; Rumsey Christopher

2013-01-01

Fully resolved simulation data of flow separation over 2-D humps has been used to analyze the modeling terms in second-moment closures of the Reynolds-averaged Navier- Stokes equations. Existing models for the pressure-strain and dissipation terms have been analyzed using a priori calculations. All pressure-strain models are incorrect in the high-strain region near separation, although a better match is observed downstream, well into the separated-flow region. Near-wall inhomogeneity causes pressure-strain models to predict incorrect signs for the normal components close to the wall. In a posteriori computations, full Reynolds stress and explicit algebraic Reynolds stress models predict the separation point with varying degrees of success. However, as with one- and two-equation models, the separation bubble size is invariably over-predicted.

A numerical resolution study of high order essentially non-oscillatory schemes applied to incompressible flow

NASA Technical Reports Server (NTRS)

Weinan, E.; Shu, Chi-Wang

1994-01-01

High order essentially non-oscillatory (ENO) schemes, originally designed for compressible flow and in general for hyperbolic conservation laws, are applied to incompressible Euler and Navier-Stokes equations with periodic boundary conditions. The projection to divergence-free velocity fields is achieved by fourth-order central differences through fast Fourier transforms (FFT) and a mild high-order filtering. The objective of this work is to assess the resolution of ENO schemes for large scale features of the flow when a coarse grid is used and small scale features of the flow, such as shears and roll-ups, are not fully resolved. It is found that high-order ENO schemes remain stable under such situations and quantities related to large scale features, such as the total circulation around the roll-up region, are adequately resolved.

A numerical resolution study of high order essentially non-oscillatory schemes applied to incompressible flow

NASA Technical Reports Server (NTRS)

Weinan, E.; Shu, Chi-Wang

1992-01-01

High order essentially non-oscillatory (ENO) schemes, originally designed for compressible flow and in general for hyperbolic conservation laws, are applied to incompressible Euler and Navier-Stokes equations with periodic boundary conditions. The projection to divergence-free velocity fields is achieved by fourth order central differences through Fast Fourier Transforms (FFT) and a mild high-order filtering. The objective of this work is to assess the resolution of ENO schemes for large scale features of the flow when a coarse grid is used and small scale features of the flow, such as shears and roll-ups, are not fully resolved. It is found that high-order ENO schemes remain stable under such situations and quantities related to large-scale features, such as the total circulation around the roll-up region, are adequately resolved.

Quantum Theory of Three-Dimensional Superresolution Using Rotating-PSF Imagery

NASA Astrophysics Data System (ADS)

Prasad, S.; Yu, Z.

The inverse of the quantum Fisher information (QFI) matrix (and extensions thereof) provides the ultimate lower bound on the variance of any unbiased estimation of a parameter from statistical data, whether of intrinsically quantum mechanical or classical character. We calculate the QFI for Poisson-shot-noise-limited imagery using the rotating PSF that can localize and resolve point sources fully in all three dimensions. We also propose an experimental approach based on the use of computer generated hologram and projective measurements to realize the QFI-limited variance for the problem of super-resolving a closely spaced pair of point sources at a highly reduced photon cost. The paper presents a preliminary analysis of quantum-limited three-dimensional (3D) pair optical super-resolution (OSR) problem with potential applications to astronomical imaging and 3D space-debris localization.

High Cryptic Diversity across the Global Range of the Migratory Planktonic Copepods Pleuromamma piseki and P. gracilis

PubMed Central

Halbert, Kristin M. K.; Goetze, Erica; Carlon, David B.

2013-01-01

Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide. PMID:24167556

Hydroides Gunnerus, 1768 (Annelida, Serpulidae) is feminine: a nomenclatural checklist of updated names

PubMed Central

Read, Geoffrey B.; ten Hove, Harry A.; Sun, Yanan; Kupriyanova, Elena K.

2017-01-01

Abstract As a service to taxonomists and ecologists using names in the well-known and species-rich ship-fouling serpulid genus Hydroides we present an update of all 107 non-synonymised scientific names, with additional information on Hydroides nomenclature, original names, etymologies, and type localities derived from original literature, and in accord with the World Register of Marine Species (WoRMS) database. An update is needed because the gender of genus Hydroides has from 1 January 2000 reverted to the original feminine, due to a change in the wording of International Code of Zoological Nomenclature which was overlooked at that time, and is contrary to the usage in practice of Hydroides as masculine which had started about 1992, although Code-required from the 1960s. We match 31 further original names of current WoRMS subjective junior synonyms to each non-synonymised name, and also report on the world distribution of the genus as illustrated by type localities of the valid names. We include notes on seven species inquirenda. The correct rendering is given of six names that have been altered for gender agreement for the first time herein. Hydroides gottfriedi nom. n. replaces junior homonym Hydroides rostrata Pillai, 1971. Currently there are 41 non-synonymised species-group names in Hydroides which should be gender invariant, and 23 names which would only change if moved to a neuter genus; the remaining 43 names are fully gender variable. Place-names (23), and personal names (16) make up more than a third (36%) of the species names, with most of the remainder (68) being descriptive of species character states, usually of operculum morphology (54). All species, except Hydroides norvegica (63°N), have type localities in shallow-water coastal locations in temperate to tropical waters below latitude 44°, with the highest number of new species (54) from the adjoining Western Pacific and Indian Ocean areas. The other concentration of new species (31) are those first found on the Pacific and Atlantic coasts of North America and in the Caribbean. PMID:28138297

Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.

PubMed

Rodríguez, Ariel; Burgon, James D; Lyra, Mariana; Irisarri, Iker; Baurain, Denis; Blaustein, Leon; Göçmen, Bayram; Künzel, Sven; Mable, Barbara K; Nolte, Arne W; Veith, Michael; Steinfartz, Sebastian; Elmer, Kathryn R; Philippe, Hervé; Vences, Miguel

2017-10-01

The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduces a risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra, a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity. For all six species of the genus Salamandra, and two outgroup species from its sister genus Lyciasalamandra, we used RNA sequencing (RNAseq) and restriction site associated DNA sequencing (RADseq) to obtain data for: (1) 3070 nuclear protein-coding genes from RNAseq; (2) 7440 loci obtained by RADseq; and (3) full mitochondrial genomes. The RNAseq and RADseq data sets retrieved fully congruent topologies when each of them was analyzed in a concatenation approach, with high support for: (1) S. infraimmaculata being sister group to all other Salamandra species; (2) S. algira being sister to S. salamandra; (3) these two species being the sister group to a clade containing S. atra, S. corsica and S. lanzai; and (4) the alpine species S. atra and S. lanzai being sister taxa. The phylogeny inferred from the mitochondrial genome sequences differed from these results, most notably by strongly supporting a clade containing S. atra and S. corsica as sister taxa. A different placement of S. corsica was also retrieved when analysing the RNAseq and RADseq data under species tree approaches. Closer examination of gene trees derived from RNAseq revealed that only a low number of them supported each of the alternative placements of S. atra. Furthermore, gene jackknife support for the S. atra - S. lanzai node stabilized only with very large concatenated data sets. The phylogeny of true salamanders thus provides a compelling example of how classical node support metrics such as bootstrap and Bayesian posterior probability can provide high confidence values in a phylogenomic topology even if the phylogenetic signal for some nodes is spurious, highlighting the importance of complementary approaches such as gene jackknifing. Yet, the general congruence among the topologies recovered from the RNAseq and RADseq data sets increases our confidence in the results, and validates the use of phylotranscriptomic approaches for reconstructing shallow relationships among closely related taxa. We hypothesize that the evolution of Salamandra has been characterized by episodes of introgressive hybridization, which would explain the difficulties of fully reconstructing their evolutionary relationships. Copyright © 2017. Published by Elsevier Inc.

Resolution Improvements in in Vivo1H NMR Spectra with Increased Magnetic Field Strength

NASA Astrophysics Data System (ADS)

Gruetter, Rolf; Weisdorf, Sally A.; Rajanayagan, Vasantham; Terpstra, Melissa; Merkle, Hellmut; Truwit, Charles L.; Garwood, Michael; Nyberg, Scott L.; Ugurbil, Kâmil

1998-11-01

The measurement of cerebral metabolites using highly homologous localization techniques and similar shimming methods was performed in the human brain at 1.5 and 4 T as well as in the dog and rat brain at 9.4 T. In rat brain, improved resolution was achieved by shimming all first- and second-order shim coils using a fully adiabatic FASTMAP sequence. The spectra showed a clear improvement in spectral resolution for all metabolite resonances with increased field strength. Changes in cerebral glutamine content were clearly observed at 4 T compared to 1.5 T in patients with hepatic encephalopathy. At 9.4 T, glutamine H4 at 2.46 ppm was fully resolved from glutamate H4 at 2.37 ppm, as was the potential resonance from γ-amino-butyric acid at 2.30 ppm and N-acetyl-aspartyl-glutamate at 2.05 ppm. Singlet linewidths were found to be as low as 6 Hz (0.015 ppm) at 9.4 T, indicating a substantial decrease in ppm linewidth with field strength. Furthermore, the methylene peak of creatine was partially resolved from phosphocreatine, indicating a close to 1:1 relationship in gray matter. We conclude that increasing the magnetic field strength increases spectral resolution also for1H NMR, which can lead to more than linear sensitivity gains.

Origins and Domestication of Cultivated Banana Inferred from Chloroplast and Nuclear Genes

PubMed Central

Zhang, Cui; Wang, Xin-Feng; Shi, Feng-Xue; Chen, Wen-Na; Ge, Xue-Jun

2013-01-01

Background Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved. Methodology/Principal Findings We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas. Conclusions/Significance Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas. PMID:24260405

The genus Clathria from the Gulf of Mexico and Mexican Caribbean, with redescription and resurrection of Clathria carteri (Poecilosclerida: Microcionidae).

PubMed

Gómez, Patricia

2014-04-16

The present study deals with the morphologic variability of eight Clathria species from the southern Gulf of Mexico and Mexican Caribbean. Clathria (Clathria) foliacea, C. (C.) carteri, C. (Microciona) calla, C. (M.) echinata, C. (M.) spinosa, C. (Thalysias.) venosa, and C. (T.) virgultosa were collected by scuba diving and dredging from the southern Gulf of Mexico (Veracruz, Campeche Bank, Yucatan) to the Caribbean coast (Quintana Roo) from shoreline to 120 m depth. The population of Clathria seems to be neither abundant nor diverse in the studied area. However, the seven species considered here are presumed to have a slight morphologic variability, and the interspecific relationships had not been fully resolved. The present study focuses on their differentiation through comparison of external morphology, skeletal architecture, spiculation and measurements of characters as well as scanning electronic microscopy.    Comparisons were made among intra- and interspecific material and with the available type material. In particular, C. carteri Topsent (1889), previously synonymized with C. foliacea, is resurrected by establishing a neotype from material from the type locality, Campeche Bank; this has not been studied since its original description and is here redescribed for the first time. Another neotype is assigned for C. foliacea from Campeche also, since the original material is no longer available, and this species is redescribed also. Significant differences in spiculation between C. foliacea and C. carteri were found by one-way ANOVA. Although C. (T.) venosa resembles C. (T.) raraechelae in spiculation, these two species differ in measurements and skeletal organization. C. (T.) virgultosa is typified by a peculiar acanthostyle that is markedly spined on distal parts of the shaft, and by two types of tiny microscleres. This study has extended the known geographic distribution of each of these Clathria spp. within the lower Gulf of Mexico.

Phylogeny and classification of Prunus sensu lato (Rosaceae).

PubMed

Shi, Shuo; Li, Jinlu; Sun, Jiahui; Yu, Jing; Zhou, Shiliang

2013-11-01

The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü & L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed. © 2013 Institute of Botany, Chinese Academy of Sciences.

The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.

PubMed

Banker, Sarah E; Wade, Elizabeth J; Simon, Chris

2017-11-01

Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution. Copyright © 2017 Elsevier Inc. All rights reserved.

Phylogeographic analysis of the true lemurs (genus Eulemur) underlines the role of river catchments for the evolution of micro-endemism in Madagascar.

PubMed

Markolf, Matthias; Kappeler, Peter M

2013-11-14

Due to its remarkable species diversity and micro-endemism, Madagascar has recently been suggested to serve as a biogeographic model region. However, hypothesis-based tests of various diversification mechanisms that have been proposed for the evolution of the island's micro-endemic lineages are still limited. Here, we test the fit of several diversification hypotheses with new data on the broadly distributed genus Eulemur using coalescent-based phylogeographic analyses. Time-calibrated species tree analyses and population genetic clustering resolved the previously polytomic species relationships among eulemurs. The most recent common ancestor of eulemurs was estimated to have lived about 4.45 million years ago (mya). Divergence date estimates furthermore suggested a very recent diversification among the members of the "brown lemur complex", i.e. former subspecies of E. fulvus, during the Pleistocene (0.33-1.43 mya). Phylogeographic model comparisons of past migration rates showed significant levels of gene flow between lineages of neighboring river catchments as well as between eastern and western populations of the redfronted lemur (E. rufifrons). Together, our results are concordant with the centers of endemism hypothesis (Wilmé et al. 2006, Science 312:1063-1065), highlight the importance of river catchments for the evolution of Madagascar's micro-endemic biota, and they underline the usefulness of testing diversification mechanisms using coalescent-based phylogeographic methods.

The internal transcribed spacer of ribosomal RNA genes in plant trypanosomes (Phytomonas spp.) resolves 10 groups.

PubMed

Dollet, Michel; Sturm, Nancy R; Campbell, David A

2012-03-01

The distinction between plant trypanosomatids and opportunistic monoxenous insect trypanosomatids has not been demarcated clearly due to the mass placement of all trypanosomatids isolated from plants into the arbitrary genus Phytomonas spp. The advent of molecular markers has been useful in distinguishing plant trypanosomatids from the rest of the Trypanosomatidae family. Here we have examined the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) locus for classification purposes. This region contains two distinct ITSs flanked by the small subunit and large subunit of ribosomal RNA genes and separated by the 5.8S ribosomal RNA gene. Sequences within the 5.8S ribosomal RNA gene and in the ITS sequences can serve as specific markers for several of the Phytomonas groups. Microsatellite sequences were identified in Phytomonas spp. in both ITS regions. Several classes of microsatellites were seen, with inter-isolate variation that has potential for future use. Maximum Likelihood analysis of the ITS sequences of 20 Phytomonas isolates representing the eight defined groups and a few unclassified isolates revealed a total of 10 distinct subgroups within our collection, of which two are new. The ITS region, which includes the 5.8S sequence, is a robust marker for the subdivisions within the genus Phytomonas spp. Copyright © 2011 Elsevier B.V. All rights reserved.

Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains.

PubMed

Morgan, Jess A T; Godwin, Rosamond M

2017-08-30

Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X, -Y and -Z. The resulting phylogeny provides a comprehensive view of species relatedness highlighting where the OTUs align with respect to others members of the genus. All three OTUs fall within the Eimeria clade that contains only chicken-infecting species with close affinities to E. maxima, E. brunetti and E. mitis. Mitochondrial genetic diversity was low among Australian isolates likely reflecting their recent introduction to the country post-European settlement. The lack of observed genetic diversity is a promising outcome as it suggests that the currently used live vaccines should continue to offer widespread protection against Eimeria outbreaks in all states and territories. Flocks were frequently found to host multiple strains of the same species, a factor that should be considered when studying disease epidemiology in the field. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Robust Phylogeny of Tetrastigma (Vitaceae) Based on Ten Plastid DNA Regions: Implications for Infrageneric Classification and Seed Character Evolution

PubMed Central

Habib, Sadaf; Dang, Viet-Cuong; Ickert-Bond, Stefanie M.; Zhang, Jin-Long; Lu, Li-Min; Wen, Jun; Chen, Zhi-Duan

2017-01-01

Tetrastigma (Miq.) Planch. is one of the most species-rich genera of the economically and agronomically important grape family Vitaceae. It includes ca. 95 species widely distributed in the tropics and subtropics of Asia and Australia. Species of Tetrastigma exhibit great diversity in both vegetative and reproductive characters. Here we inferred a well-supported phylogeny of Tetrastigma based on ten chloroplast DNA regions with an expanded taxon sampling of 72 species and two varieties. Our molecular results support six major clades within Tetrastigma and the relationships among these clades were well-resolved. We also documented seed morphology of 44 species covering the six major clades of the genus. Ancestral states of eight characters (seed shape, seed surface rumination pattern, chalaza length/width ratio, chalaza position, ventral infold position, ventral infold divergence, ventral infold depth in cross section, and endosperm shape) were reconstructed in Mesquite and R with four models. Character optimizations suggest that all character states have evolved multiple times except that the irregular-shaped surface rumination has derived only once in Tetrastigma. We evaluated the taxonomic importance of seed morphology and identified potential morphological evidence to support each major clade. Our comprehensive analyses of Tetrastigma shed insights into the infrageneric classification of this morphologically diverse and ecologically important genus in tropical and subtropical Asia. PMID:28491066

Clinical Evaluation of a Loop-Mediated Amplification Kit for Diagnosis of Imported Malaria

PubMed Central

Polley, Spencer D.; González, Iveth J.; Mohamed, Deqa; Daly, Rosemarie; Bowers, Kathy; Watson, Julie; Mewse, Emma; Armstrong, Margaret; Gray, Christen; Perkins, Mark D.; Bell, David; Kanda, Hidetoshi; Tomita, Norihiro; Kubota, Yutaka; Mori, Yasuyoshi; Chiodini, Peter L.; Sutherland, Colin J.

2013-01-01

Background. Diagnosis of malaria relies on parasite detection by microscopy or antigen detection; both fail to detect low-density infections. New tests providing rapid, sensitive diagnosis with minimal need for training would enhance both malaria diagnosis and malaria control activities. We determined the diagnostic accuracy of a new loop-mediated amplification (LAMP) kit in febrile returned travelers. Methods. The kit was evaluated in sequential blood samples from returned travelers sent for pathogen testing to a specialist parasitology laboratory. Microscopy was performed, and then malaria LAMP was performed using Plasmodium genus and Plasmodium falciparum–specific tests in parallel. Nested polymerase chain reaction (PCR) was performed on all samples as the reference standard. Primary outcome measures for diagnostic accuracy were sensitivity and specificity of LAMP results, compared with those of nested PCR. Results. A total of 705 samples were tested in the primary analysis. Sensitivity and specificity were 98.4% and 98.1%, respectively, for the LAMP P. falciparum primers and 97.0% and 99.2%, respectively, for the Plasmodium genus primers. Post hoc repeat PCR analysis of all 15 tests with discrepant results resolved 4 results in favor of LAMP, suggesting that the primary analysis had underestimated diagnostic accuracy. Conclusions. Malaria LAMP had a diagnostic accuracy similar to that of nested PCR, with a greatly reduced time to result, and was superior to expert microscopy. PMID:23633403

Phylogeny and character evolution of the fern genus Tectaria (Tectariaceae) in the Old World inferred from chloroplast DNA sequences.

PubMed

Ding, Hui-Hui; Chao, Yi-Shan; Callado, John Rey; Dong, Shi-Yong

2014-11-01

In this study we provide a phylogeny for the pantropical fern genus Tectaria, with emphasis on the Old World species, based on sequences of five plastid regions (atpB, ndhF plus ndhF-trnL, rbcL, rps16-matK plus matK, and trnL-F). Maximum parsimony, maximum likelihood, and Bayesian inference are used to analyze 115 individuals, representing ca. 56 species of Tectaria s.l. and 36 species of ten related genera. The results strongly support the monophyly of Tectaria in a broad sense, in which Ctenitopsis, Hemigramma, Heterogonium, Psomiocarpa, Quercifilix, Stenosemia, and Tectaridium should be submerged. Such broadly circumscribed Tectaria is supported by the arising pattern of veinlets and the base chromosome number (x=40). Four primary clades are well resolved within Tectaria, one from the Neotropic (T. trifoliata clade) and three from the Old World (T. subtriphylla clade, Ctenitopsis clade, and T. crenata clade). Tectaria crenata clade is the largest one including six subclades. Of the genera previously recognized as tectarioid ferns, Ctenitis, Lastreopsis, and Pleocnemia, are confirmed to be members in Dryopteridaceae; while Pteridrys and Triplophyllum are supported in Tectariaceae. To infer morphological evolution, 13 commonly used characters are optimized on the resulting phylogenetic trees and in result, are all homoplastic in Tectaria. Copyright © 2014 Elsevier Inc. All rights reserved.

Anti-angiogenesis effect of the novel anti-inflammatory and pro-resolving lipid mediators.

PubMed

Jin, Yiping; Arita, Makoto; Zhang, Qiang; Saban, Daniel R; Chauhan, Sunil K; Chiang, Nan; Serhan, Charles N; Dana, Reza

2009-10-01

Resolvins and lipoxins are lipid mediators generated from essential polyunsaturated fatty acids that are the first dual anti-inflammatory and pro-resolving signals identified in the resolution phase of inflammation. Here the authors investigated the potential of aspirin-triggered lipoxin (LX) A4 analog (ATLa), resolving (Rv) D1, and RvE1, in regulating angiogenesis in a murine model. ATLa and RvE1 receptor expression was tested in different corneal cell populations by RT-PCR. Corneal neovascularization (CNV) was induced by suture or micropellet (IL-1 beta, VEGF-A) placement. Mice were then treated with ATLa, RvD1, RvE1, or vehicle, subconjunctivally at 48-hour intervals. Infiltration of neutrophils and macrophages was quantified after immunofluorescence staining. The mRNA expression levels of inflammatory cytokines, VEGFs, and VEGFRs were analyzed by real-time PCR. CNV was evaluated intravitally and morphometrically. The receptors for LXA4, ALX/Fpr-rs-2 and for RvE1, ChemR23 were each expressed by epithelium, stromal keratocytes, and infiltrated CD11b(+) cells in corneas. Compared to the vehicle-treated eye, ATLa-, RvD1-, and RvE1-treated eyes had reduced numbers of infiltrating neutrophils and macrophages and reduced mRNA expression levels of TNF-alpha, IL-1 alpha, IL-1 beta, VEGF-A, VEGF-C, and VEGFR2. Animals treated with these mediators had significantly suppressed suture-induced or IL-1 beta-induced hemangiogenesis (HA) but not lymphangiogenesis. Interestingly, only the application of ATLa significantly suppressed VEGF-A-induced HA. ATLa, RvE1, and RvD1 all reduce inflammatory corneal HA by early regulation of resolution mechanisms in innate immune responses. In addition, ATLa directly inhibits VEGF-A-mediated angiogenesis and is the most potent inhibitor of NV among this new genus of dual anti-inflammatory and pro-resolving lipid mediators.

Towards European-scale convection-resolving climate simulations with GPUs: a study with COSMO 4.19

NASA Astrophysics Data System (ADS)

Leutwyler, David; Fuhrer, Oliver; Lapillonne, Xavier; Lüthi, Daniel; Schär, Christoph

2016-09-01

The representation of moist convection in climate models represents a major challenge, due to the small scales involved. Using horizontal grid spacings of O(1km), convection-resolving weather and climate models allows one to explicitly resolve deep convection. However, due to their extremely demanding computational requirements, they have so far been limited to short simulations and/or small computational domains. Innovations in supercomputing have led to new hybrid node designs, mixing conventional multi-core hardware and accelerators such as graphics processing units (GPUs). One of the first atmospheric models that has been fully ported to these architectures is the COSMO (Consortium for Small-scale Modeling) model.Here we present the convection-resolving COSMO model on continental scales using a version of the model capable of using GPU accelerators. The verification of a week-long simulation containing winter storm Kyrill shows that, for this case, convection-parameterizing simulations and convection-resolving simulations agree well. Furthermore, we demonstrate the applicability of the approach to longer simulations by conducting a 3-month-long simulation of the summer season 2006. Its results corroborate the findings found on smaller domains such as more credible representation of the diurnal cycle of precipitation in convection-resolving models and a tendency to produce more intensive hourly precipitation events. Both simulations also show how the approach allows for the representation of interactions between synoptic-scale and meso-scale atmospheric circulations at scales ranging from 1000 to 10 km. This includes the formation of sharp cold frontal structures, convection embedded in fronts and small eddies, or the formation and organization of propagating cold pools. Finally, we assess the performance gain from using heterogeneous hardware equipped with GPUs relative to multi-core hardware. With the COSMO model, we now use a weather and climate model that has all the necessary modules required for real-case convection-resolving regional climate simulations on GPUs.

Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

PubMed Central

Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

2015-01-01

DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. PMID:25837628

Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.

PubMed

Lui, Lauren M; Uzilov, Andrew V; Bernick, David L; Corredor, Andrea; Lowe, Todd M; Dennis, Patrick P

2018-05-16

Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

Secondary Metabolites, Glandular Trichomes and Biological Activity of Sideritis montana L. subsp. montana from Central Italy.

PubMed

Venditti, Alessandro; Bianco, Armandodoriano; Frezza, Claudio; Serafini, Mauro; Giacomello, Ginevra; Giuliani, Claudia; Bramucci, Massimo; Quassinti, Luana; Lupidi, Giulio; Lucarini, Domenico; Papa, Fabrizio; Maggi, Filippo

2016-10-01

Sideritis montana subsp. montana is a small annual herb occurring in countries bordering the Mediterranean and Balkan regions. The secondary metabolism of this plant has not been fully explored so far. The aim of the present study was to understand the complex mixture of secondary metabolites and the type of secretory structures. The polar constituents were isolated by column chromatography from the ethanolic extract, and their structure was elucidated by NMR and MS. The essential oil was isolated by hydrodistillation and analysed by GC/MS. The plant indumentum was studied by light and scanning electron microscopy. To complete the work, the essential oil antioxidant activity and cytotoxicity on tumor cells were evaluated by DPPH, ABTS, FRAP, and MTT methods. Four different classes of secondary metabolites were isolated, namely flavonoids, caffeoylquinic derivatives, glycosidic hydroquinones and iridoids. The essential oil was mainly characterized by sesquiterpenene hydrocarbons. Peltate and long-capitate hairs were the main sites where terpenes and polar constituents are produced. The secondary metabolites found in S. montana subsp. montana are of chemotaxonomic interest, some of them being typical of the genus Sideritis. The trichomes types observed partially differ from those described in other members of the genus Sideritis. The essential oil showed noteworthy inhibition on tumor cells. © 2016 Wiley-VHCA AG, Zürich.

Chayote mosaic virus, a New Tymovirus Infecting Cucurbitaceae.

PubMed

Bernal, J J; Jiménez, I; Moreno, M; Hord, M; Rivera, C; Koenig, R; Rodríguez-Cerezo, E

2000-10-01

ABSTRACT Chayote mosaic virus (ChMV) is a putative tymovirus isolated from chayote crops in Costa Rica. ChMV was characterized at the host range, serological, and molecular levels. ChMV was transmitted mechanically and induced disease symptoms mainly in Cucurbitaceae hosts. Asymptomatic infections were detected in other host families. Serologically, ChMV is related to the Andean potato latent virus (APLV) and the Eggplant mosaic virus (EMV), both members of the genus Tymovirus infecting solanaceous hosts in the Caribbean Basin and South America. The sequence of the genomic RNA of ChMV was determined and its genetic organization was typical of tymoviruses. Comparisons with other tymoviral sequences showed that ChMV was a new member of the genus Tymovirus. The phylogenetic analyses of the coat protein gene were consistent with serological comparisons and positioned ChMV within a cluster of tymoviruses infecting mainly cucurbit or solanaceous hosts, including APLV and EMV. Phylogenetic analyses of the replicase protein gene confirmed the close relationship of ChMV and EMV. Our results suggest that ChMV is related to two tymoviruses (APLV and EMV) of proximal geographical provenance but with different natural host ranges. ChMV is the first cucurbit-infecting tymovirus to be fully characterized at the genomic level.

How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews.

PubMed

Göker, Markus; Voglmayr, Hermann; Riethmüller, Alexandra; Oberwinkler, Franz

2007-02-01

Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.

A Decade-Long European-Scale Convection-Resolving Climate Simulation on GPUs

NASA Astrophysics Data System (ADS)

Leutwyler, D.; Fuhrer, O.; Ban, N.; Lapillonne, X.; Lüthi, D.; Schar, C.

2016-12-01

Convection-resolving models have proven to be very useful tools in numerical weather prediction and in climate research. However, due to their extremely demanding computational requirements, they have so far been limited to short simulations and/or small computational domains. Innovations in the supercomputing domain have led to new supercomputer designs that involve conventional multi-core CPUs and accelerators such as graphics processing units (GPUs). One of the first atmospheric models that has been fully ported to GPUs is the Consortium for Small-Scale Modeling weather and climate model COSMO. This new version allows us to expand the size of the simulation domain to areas spanning continents and the time period up to one decade. We present results from a decade-long, convection-resolving climate simulation over Europe using the GPU-enabled COSMO version on a computational domain with 1536x1536x60 gridpoints. The simulation is driven by the ERA-interim reanalysis. The results illustrate how the approach allows for the representation of interactions between synoptic-scale and meso-scale atmospheric circulations at scales ranging from 1000 to 10 km. We discuss some of the advantages and prospects from using GPUs, and focus on the performance of the convection-resolving modeling approach on the European scale. Specifically we investigate the organization of convective clouds and on validate hourly rainfall distributions with various high-resolution data sets.

A Decade-long Continental-Scale Convection-Resolving Climate Simulation on GPUs

NASA Astrophysics Data System (ADS)

Leutwyler, David; Fuhrer, Oliver; Lapillonne, Xavier; Lüthi, Daniel; Schär, Christoph

2016-04-01

The representation of moist convection in climate models represents a major challenge, due to the small scales involved. Convection-resolving models have proven to be very useful tools in numerical weather prediction and in climate research. Using horizontal grid spacings of O(1km), they allow to explicitly resolve deep convection leading to an improved representation of the water cycle. However, due to their extremely demanding computational requirements, they have so far been limited to short simulations and/or small computational domains. Innovations in the supercomputing domain have led to new supercomputer-designs that involve conventional multicore CPUs and accelerators such as graphics processing units (GPUs). One of the first atmospheric models that has been fully ported to GPUs is the Consortium for Small-Scale Modeling weather and climate model COSMO. This new version allows us to expand the size of the simulation domain to areas spanning continents and the time period up to one decade. We present results from a decade-long, convection-resolving climate simulation using the GPU-enabled COSMO version. The simulation is driven by the ERA-interim reanalysis. The results illustrate how the approach allows for the representation of interactions between synoptic-scale and meso-scale atmospheric circulations at scales ranging from 1000 to 10 km. We discuss the performance of the convection-resolving modeling approach on the European scale. Specifically we focus on the annual cycle of convection in Europe, on the organization of convective clouds and on the verification of hourly rainfall with various high resolution datasets.

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

PubMed

Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

2012-02-01

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches.

PubMed

Rodrigues, P; Santos, C; Venâncio, A; Lima, N

2011-10-01

Section Flavi is one of the most significant sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF ICMS) and to evaluate the discriminatory power of the various approaches in species identification.   Aspergillus section Flavi isolates obtained from Portuguese almonds were characterized in terms of macro- and micromorphology, mycotoxin pattern, calmodulin gene sequence and MALDI-TOF protein fingerprint spectra. For each approach, dendrograms were created and results were compared. All data sets divided the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus and Aspergillus tamarii. In the A. flavus clade, molecular and spectral analyses were not able to resolve between aflatoxigenic and nonaflatoxigenic isolates. In the A. parasiticus cluster, two well-resolved clades corresponded to unidentified taxa, corresponding to those isolates with mycotoxin profile different from that expected for A. parasiticus. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Small acid soluble proteins for rapid spore identification.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branda, Steven S.; Lane, Todd W.; VanderNoot, Victoria A.

2006-12-01

This one year LDRD addressed the problem of rapid characterization of bacterial spores such as those from the genus Bacillus, the group that contains pathogenic spores such as B. anthracis. In this effort we addressed the feasibility of using a proteomics based approach to spore characterization using a subset of conserved spore proteins known as the small acid soluble proteins or SASPs. We proposed developing techniques that built on our previous expertise in microseparations to rapidly characterize or identify spores. An alternative SASP extraction method was developed that was amenable to both the subsequent fluorescent labeling required for laser-induced fluorescencemore » detection and the low ionic strength requirements for isoelectric focusing. For the microseparations, both capillary isoelectric focusing and chip gel electrophoresis were employed. A variety of methods were evaluated to improve the molecular weight resolution for the SASPs, which are in a molecular weight range that is not well resolved by the current methods. Isoelectric focusing was optimized and employed to resolve the SASPs using UV absorbance detection. Proteomic signatures of native wild type Bacillus spores and clones genetically engineered to produce altered SASP patterns were assessed by slab gel electrophoresis, capillary isoelectric focusing with absorbance detection as well as microchip based gel electrophoresis employing sensitive laser-induced fluorescence detection.« less

Photodissociation of quantum state-selected diatomic molecules yields new insight into ultracold chemistry

NASA Astrophysics Data System (ADS)

McDonald, Mickey; McGuyer, Bart H.; Lee, Chih-Hsi; Apfelbeck, Florian; Zelevinsky, Tanya

2016-05-01

When a molecule is subjected to a sufficiently energetic photon it can break apart into fragments through a process called ``photodissociation''. For over 70 years this simple chemical reaction has served as a vital experimental tool for acquiring information about molecular structure, since the character of the photodissociative transition can be inferred by measuring the 3D photofragment angular distribution (PAD). While theoretical understanding of this process has gradually evolved from classical considerations to a fully quantum approach, experiments to date have not yet revealed the full quantum nature of this process. In my talk I will describe recent experiments involving the photodissociation of ultracold, optical lattice-trapped, and fully quantum state-resolved 88Sr2 molecules. Optical absorption images of the PADs produced in these experiments reveal features which are inherently quantum mechanical in nature, such as matter-wave interference between output channels, and are sensitive to the quantum statistics of the molecular wavefunctions. The results of these experiments cannot be predicted using quasiclassical methods. Instead, we describe our results with a fully quantum mechanical model yielding new intuition about ultracold chemistry.

An NFC-Enabled CMOS IC for a Wireless Fully Implantable Glucose Sensor.

PubMed

DeHennis, Andrew; Getzlaff, Stefan; Grice, David; Mailand, Marko

2016-01-01

This paper presents an integrated circuit (IC) that merges integrated optical and temperature transducers, optical interface circuitry, and a near-field communication (NFC)-enabled digital, wireless readout for a fully passive implantable sensor platform to measure glucose in people with diabetes. A flip-chip mounted LED and monolithically integrated photodiodes serve as the transduction front-end to enable fluorescence readout. A wide-range programmable transimpedance amplifier adapts the sensor signals to the input of an 11-bit analog-to-digital converter digitizing the measurements. Measurement readout is enabled by means of wireless backscatter modulation to a remote NFC reader. The system is able to resolve current levels of less than 10 pA with a single fluorescent measurement energy consumption of less than 1 μJ. The wireless IC is fabricated in a 0.6-μm-CMOS process and utilizes a 13.56-MHz-based ISO15693 for passive wireless readout through a NFC interface. The IC is utilized as the core interface to a fluorescent, glucose transducer to enable a fully implantable sensor-based continuous glucose monitoring system.

Crystal plasticity modeling of β phase deformation in Ti-6Al-4V

NASA Astrophysics Data System (ADS)

Moore, John A.; Barton, Nathan R.; Florando, Jeff; Mulay, Rupalee; Kumar, Mukul

2017-10-01

Ti-6Al-4V is an alloy of titanium that dominates titanium usage in applications ranging from mass-produced consumer goods to high-end aerospace parts. The material’s structure on a microscale is known to affect its mechanical properties but these effects are not fully understood. Specifically, this work will address the effects of low volume fraction intergranular β phase on Ti-6Al-4V’s mechanical response during the transition from elastic to plastic deformation. A crystal plasticity-based finite element model is used to fully resolve the deformation of the β phase for the first time. This high fidelity model captures mechanisms difficult to access via experiments or lower fidelity models. The results are used to assess lower fidelity modeling assumptions and identify phenomena that have ramifications for failure of the material.

A Fully Implemented 12 × 12 Data Vortex Optical Packet Switching Interconnection Network

NASA Astrophysics Data System (ADS)

Shacham, Assaf; Small, Benjamin A.; Liboiron-Ladouceur, Odile; Bergman, Keren

2005-10-01

A fully functional optical packet switching (OPS) interconnection network based on the data vortex architecture is presented. The photonic switching fabric uniquely capitalizes on the enormous bandwidth advantage of wavelength division multiplexing (WDM) wavelength parallelism while delivering minimal packet transit latency. Utilizing semiconductor optical amplifier (SOA)-based switching nodes and conventional fiber-optic technology, the 12-port system exhibits a capacity of nearly 1 Tb/s. Optical packets containing an eight-wavelength WDM payload with 10 Gb/s per wavelength are routed successfully to all 12 ports while maintaining a bit error rate (BER) of 10-12 or better. Median port-to-port latencies of 110 ns are achieved with a distributed deflection routing network that resolves packet contention on-the-fly without the use of optical buffers and maintains the entire payload path in the optical domain.

A fully-automated multiscale kernel graph cuts based particle localization scheme for temporal focusing two-photon microscopy

NASA Astrophysics Data System (ADS)

Huang, Xia; Li, Chunqiang; Xiao, Chuan; Sun, Wenqing; Qian, Wei

2017-03-01

The temporal focusing two-photon microscope (TFM) is developed to perform depth resolved wide field fluorescence imaging by capturing frames sequentially. However, due to strong nonignorable noises and diffraction rings surrounding particles, further researches are extremely formidable without a precise particle localization technique. In this paper, we developed a fully-automated scheme to locate particles positions with high noise tolerance. Our scheme includes the following procedures: noise reduction using a hybrid Kalman filter method, particle segmentation based on a multiscale kernel graph cuts global and local segmentation algorithm, and a kinematic estimation based particle tracking method. Both isolated and partial-overlapped particles can be accurately identified with removal of unrelated pixels. Based on our quantitative analysis, 96.22% isolated particles and 84.19% partial-overlapped particles were successfully detected.

Fully invariant wavelet enhanced minimum average correlation energy filter for object recognition in cluttered and occluded environments

NASA Astrophysics Data System (ADS)

Tehsin, Sara; Rehman, Saad; Riaz, Farhan; Saeed, Omer; Hassan, Ali; Khan, Muazzam; Alam, Muhammad S.

2017-05-01

A fully invariant system helps in resolving difficulties in object detection when camera or object orientation and position are unknown. In this paper, the proposed correlation filter based mechanism provides the capability to suppress noise, clutter and occlusion. Minimum Average Correlation Energy (MACE) filter yields sharp correlation peaks while considering the controlled correlation peak value. Difference of Gaussian (DOG) Wavelet has been added at the preprocessing stage in proposed filter design that facilitates target detection in orientation variant cluttered environment. Logarithmic transformation is combined with a DOG composite minimum average correlation energy filter (WMACE), capable of producing sharp correlation peaks despite any kind of geometric distortion of target object. The proposed filter has shown improved performance over some of the other variant correlation filters which are discussed in the result section.

First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes.

PubMed

Gutiérrez, Verónica; Rego, Natalia; Naya, Hugo; García, Graciela

2015-10-28

Among teleosts, the South American genus Austrolebias (Cyprinodontiformes: Rivulidae) includes 42 taxa of annual fishes divided into five different species groups. It is a monophyletic genus, but morphological and molecular data do not resolve the relationship among intrageneric clades and high rates of substitution have been previously described in some mitochondrial genes. In this work, the complete mitogenome of a species of the genus was determined for the first time. We determined its structure, gene order and evolutionary peculiar features, which will allow us to evaluate the performance of mitochondrial genes in the phylogenetic resolution at different taxonomic levels. Regarding gene content and order, the circular mitogenome of A. charrua (17,271 pb) presents the typical pattern of vertebrate mitogenomes. It contains the full complement of 13 proteins-coding genes, 22 tRNA, 2 rRNA and one non-coding control region. Notably, the tRNA-Cys was only 57 bp in length and lacks the D-loop arm. In three full sibling individuals, heteroplasmatic condition was detected due to a total of 12 variable sites in seven protein-coding genes. Among cyprinodontiforms, the mitogenome of A. charrua exhibits the lowest G+C content (37 %) and GCskew, as well as the highest strand asymmetry with a net difference of T over A at 1st and 3rd codon positions. Considering the 12 coding-genes of the H strand, correspondence analyses of nucleotide composition and codon usage show that A and T at 1st and 3rd codon positions have the highest weight in the first axis, and segregate annual species from the other cyprinodontiforms analyzed. Given the annual life-style, their mitogenomes could be under different selective pressures. All 13 protein-coding genes are under strong purifying selection and we did not find any significant evidence of nucleotide sites showing episodic selection (dN >dS) at annual lineages. When fast evolving third codon positions were removed from alignments, the "supergene" tree recovers our reference species phylogeny as well as the Cytb, ND4L and ND6 genes. Therefore, third codon positions seem to be saturated in the aforementioned coding regions at intergeneric Cyprinodontiformes comparisons. The complete mitogenome obtained in present work, offers relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomic controversial endemic genus of annual fishes.

Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

PubMed

Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

2018-04-23

The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P < 0.001) by PhiPT (Φ PT ) values of 0.433 and 0.344, respectively. Allelic frequency among clusters supported previously developed hypotheses of allopolyploid genome structure. Evidence of cryptic population structure was demonstrated for the k1 O. basilicum cluster suggesting prevalence of gene flow. UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure and genetic relationships among Ocimum spp. germplasm provide the foundation for improved DM resistance breeding strategies and more rapid response to future disease outbreaks.

Evolutionary history of the fish genus Astyanax Baird & Girard (1854) (Actinopterygii, Characidae) in Mesoamerica reveals multiple morphological homoplasies

PubMed Central

2008-01-01

Background Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution. Results Analysis of the entire mitochondrial cytochrome b (Cytb) gene in 208 individuals from 147 localities and of a subset of individuals for three mitochondrial genes (Cytb, 16 S, and COI) and a single nuclear gene (RAG1) yielded similar topologies, recovering six major groups with significant phylogeographic structure. Populations from North America and Upper Central America formed a monophyletic group, while Middle Central America showed evidence of rapid radiation with incompletely resolved relationships. Lower Central America lineages showed a fragmented structure, with geographically restricted taxa showing high levels of molecular divergence. All Bramocharax samples grouped with their sympatric Astyanax lineages (in some cases even with allopatric Astyanax populations), with less than 1% divergence between them. These results suggest a homoplasic nature to the trophic specializations associated with Bramocharax ecomorphs, which seem to have arisen independently in different Astyanax lineages. We observed higher taxonomic diversity compared to previous phylogenetic studies of the Astyanax genus. Colonization of Mesoamerica by Astyanax before the final closure of the Isthmus of Panama (3.3 Mya) explains the deep level of divergence detected in Lower Central America. The colonization of Upper Mesoamerica apparently occurred by two independent routes, with lineage turnover over a large part of the region. Conclusion Our results support multiple, independent origins of morphological traits in Astyanax, whereby the morphotype associated with Bramocharax represents a recurrent trophic adaptation. Molecular clock estimates indicate that Astyanax was present in Mesoamerica during the Miocene (~8 Mya), which implies the existence of an incipient land-bridge connecting South America and Central America before the final closure of the Isthmus of Panama (~3.3 Mya). PMID:19102731

Catalog of the entomologic collections of the Faculty of Public Health of the University of Sao Paulo - (2nd series ii): Triatominae (Hemiptera, Reduviidae)

PubMed Central

Vendrami, Daniel Pagotto; Marrelli, Mauro Toledo; Obara, Marcos Takashi; Barata, José Maria Soares; Ceretti-Junior, Walter

2018-01-01

ABSTRACT This article reports a list with 912 specimens of the subfamily Triatominae deposited in the Entomological Collection of the Faculty of Public Health of the University of Sao Paulo. The collection is composed of 1 holotype, 3 alotypes, 15 paralectotypes, 77 paratypes, distributed in 5 tribes and 12 genera: Tribus Alberprosenini: genus Alberprosenia Martinez & Carcavallo, 1977; Tribus Bolboderini: genus Microtriatoma Prosen & Martinez, 1952; Tribus Cavernicolini: genus Cavernicola Barber, 1937; Tribus Rhodnini: genus Psammolestes Bergroth, 1941; genus Rhodnius Stal, 1859; Tribus Triatomini: genus Dipetalogaster Usinger 1939; genus Eratyrus Stal 1859; genus Hermanlentia Jurberg & Galvão, 1997; genus Linshcosteus Distant, 1904; 1944; genus Panstrongylus Berg 1879; genus Paratriatoma Barber 1938; genus Triatoma Laporte 1833. PMID:29846474

Broad-Range Direct Detection and Identification of Fungi by Use of the PLEX-ID PCR-Electrospray Ionization Mass Spectrometry (ESI-MS) System

PubMed Central

Simner, Patricia J.; Uhl, James R.; Hall, Leslie; Weber, Michelle M.; Walchak, Robert C.; Buckwalter, Seanne

2013-01-01

The PLEX-ID system is a novel technology that couples PCR amplification and electrospray ionization-mass spectrometry to identify pathogens directly in clinical specimens. The analytical performance of the PLEX-ID Broad Fungal assay was compared with that of traditional culture identification by using 91 characterized fungal culture isolates (64 manufacturer-claimed and 27 nonclaimed organisms) and directly by using 395 respiratory specimens. Discordant results were resolved by D2 large-subunit ribosomal DNA fungal sequencing. Environmental studies were performed to monitor for potential contamination. The PLEX-ID Broad Fungal assay correctly identified 95.6% (87/91) and 81.3% (74/91) of the culture isolates to the genus and species levels, respectively. Of the manufacturer-claimed organisms, 100% (64/64) and 92.2% (59/64) were correctly identified to the genus and species levels, respectively. Direct analysis of respiratory specimens resulted in 67.6% (267/395) and 66.6% (263/395) agreement with culture results to the genus and species levels, respectively, with 16.2% (64/395) of the results discordant with culture and 16.2% (64/395) not detected by the system. The majority (>95%) of the isolates not detected directly by the PLEX-ID system ultimately grew in low quantities in culture (≤20 colonies). In 20.3% (35/172) of the respiratory specimens where no growth was observed in culture, the PLEX-ID system identified a fungus, suggesting a potential increase in sensitivity over culture in some instances. The PLEX-ID system provides a rapid method for the detection of a broad array of fungi directly in respiratory specimens and has the potential of impacting turnaround times and patient care by reducing the need to wait for the growth of an organism in culture. PMID:23515540

Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

PubMed Central

Sramkó, Gábor; Paun, Ovidiu

2018-01-01

Abstract Background and Aims Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. Methods At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. Key Results RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. Conclusions The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework. PMID:29325077

Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

PubMed

Liu, Xiu-Qun; Ickert-Bond, Stefanie M; Nie, Ze-Long; Zhou, Zhuo; Chen, Long-Qing; Wen, Jun

2016-02-01

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Copyright © 2015 Elsevier Inc. All rights reserved.

Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

PubMed Central

2008-01-01

Background Little is known about the role ecological shifts play in the evolution of Neotropical radiations that have colonized a variety of environments. We here examine habitat shifts in the evolutionary history of Elaenia flycatchers, a Neotropical bird lineage that lives in a range of forest and open habitats. We evaluate phylogenetic relationships within the genus based on mitochondrial and nuclear DNA sequence data, and then employ parsimony-based and Bayesian methods to reconstruct preferences for a number of habitat types and migratory behaviour throughout the evolutionary history of the genus. Using a molecular clock approach, we date the most important habitat shifts. Results Our analyses resolve phylogenetic relationships among Elaenia species and confirm several species associations predicted by morphology while furnishing support for other taxon placements that are in conflict with traditional classification, such as the elevation of various Elaenia taxa to species level. While savannah specialism is restricted to one basal clade within the genus, montane forest was invaded from open habitat only on a limited number of occasions. Riparian growth may have been favoured early on in the evolution of the main Elaenia clade and subsequently been deserted on several occasions. Austral long-distance migratory behaviour evolved on several occasions. Conclusion Ancestral reconstructions of habitat preferences reveal pronounced differences not only in the timing of the emergence of certain habitat preferences, but also in the frequency of habitat shifts. The early origin of savannah specialism in Elaenia highlights the importance of this habitat in Neotropical Pliocene and late Miocene biogeography. While forest in old mountain ranges such as the Tepuis and the Brazilian Shield was colonized early on, the most important colonization event of montane forest was in conjunction with Pliocene Andean uplift. Riparian habitats may have played an important role in facilitating habitat shifts by birds expanding up the mountains along streams and adapting to newly emerging montane forest habitat. PMID:18601752

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae.

PubMed

Nam, Bo-Hye; Kwak, Woori; Kim, Young-Ok; Kim, Dong-Gyun; Kong, Hee Jeong; Kim, Woo-Jin; Kang, Jeong-Ha; Park, Jung Youn; An, Cheul Min; Moon, Ji-Young; Park, Choul Ji; Yu, Jae Woong; Yoon, Joon; Seo, Minseok; Kim, Kwondo; Kim, Duk Kyung; Lee, SaetByeol; Sung, Samsun; Lee, Chul; Shin, Younhee; Jung, Myunghee; Kang, Byeong-Chul; Shin, Ga-Hee; Ka, Sojeong; Caetano-Anolles, Kelsey; Cho, Seoae; Kim, Heebal

2017-05-01

Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [ 1 ]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H . discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H . discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H . discus hannai , with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution. © The Authors 2017. Published by Oxford University Press.

Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

PubMed Central

Groeneveld, Linn F; Weisrock, David W; Rasoloarison, Rodin M; Yoder, Anne D; Kappeler, Peter M

2009-01-01

Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus) and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2) and three nuclear markers (adora3, fiba and vWF). Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results. PMID:19193227

The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae.

PubMed

Mayer, Werner; Pavlicev, Mihaela

2007-09-01

The family Lacertidae encompasses more than 250 species distributed in the Palearctis, Ethiopis and Orientalis. Lacertids have been subjected in the past to several morphological and molecular studies to establish their phylogeny. However, the problems of convergent adaptation in morphology and of excessively variable molecular markers have hampered the establishment of well supported deeper phylogenetic relationships. Particularly the adaptations to xeric environments have often been used to establish a scenario for the origin and radiation of major lineages within lacertids. Here we present a molecular phylogenetic study based on two nuclear marker genes and representatives of 37 lacertid genera and distinct species groups (as in the case of the collective genus Lacerta). Roughly 1600 bp of the nuclear rag1 and c-mos genes were sequenced and analyzed. While the results provide good support to the hitherto suggested main subfamilies of Gallotiinae (Gallotia and Psammodromus), Eremiainae and Lacertinae [Harris, D.J., Arnold, E.N., Thomas, R.H., 1998. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. R. Soc. Lond. B 265, 1939-1948], they also suggest unexpected relationships. In particular, the oriental genus Takydromus, previously considered the sister-group to the three subfamilies, is nested within Lacertinae. Moreover, the genera within the Eremiainae are further divided into two groups, roughly corresponding to their respective geographical distributions in the Ethiopian and the Saharo-Eurasian ranges. The results support an independent origin of adaptations to xeric conditions in different subfamilies. The relationships within the subfamily Lacertinae could not be resolved with the markers used. The species groups of the collective genus Lacerta show a bush-like topology in the inferred Bayesian tree, suggesting rapid radiation. The composition of the subfamilies Eremiainae and Lacertinae as well as their phylogeography are discussed.

The origins of the giant pill-millipedes from Madagascar (Diplopoda: Sphaerotheriida: Arthrosphaeridae).

PubMed

Wesener, Thomas; Raupach, Michael J; Sierwald, Petra

2010-12-01

Giant pill-millipedes (order Sphaerotheriida) are large-bodied millipedes without poison glands which can roll-up into a complete ball. Their disconnected area of distribution spanning South Africa, Madagascar, India, SE Asia, Australia and New Zealand makes them interesting model organisms for biogeographic studies. The here presented phylogeny is based on a molecular dataset covering all areas of distribution with a special focus on Madagascar, where some species of giant pill-millipedes show island gigantism, reaching the size of a baseball. For our study, two mitochondrial genes (partial 16S rRNA and COI) as well as the complete nuclear 18S rDNA were sequenced. While many recent vertebrate studies hint that the ancestors of the recent Malagasy fauna crossed the >350 km wide Mozambique Channel several times, no such crossing was discovered in the Sphaerotheriida. For the first time in a molecular phylogenetic study of soil arthropods, a Madagascar-India group, the family Arthrosphaeridae, is recovered, hinting to a Gondwanan origin of the Sphaerotheriida. The Malagasy-Indian family Arthrosphaeridae forms a monophyletic, statistically well-supported group in all obtained trees. The giant pill-millipedes from Madagascar are paraphyletic because the Malagasy genus Sphaeromimus is the sister-taxon of the Indian Arthrosphaera. In Sphaeromimus, an ecotone shift occurred only once: the spiny forest species Sphaeromimus musicus forms the sister-clade to the species collected in rainforests and littoral rainforests. The two species of the Malagasy genus Zoosphaerium which express island gigantism form a monophyletic group in some trees, but these trees lack good statistical support. Deeper nodes inside the Sphaerotheriida, like the position of the Australian genera Procyliosoma and Epicyliosoma, the Southeast Asian family Zephroniidae and the South African genus Sphaerotherium could not be resolved. This study is the first genetic study inside the order Sphaerotheriida and provides a proper basis for future molecular biogeographic studies in millipedes and soil organisms from Madagascar. Copyright © 2010 Elsevier Inc. All rights reserved.

Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids.

PubMed

Bateman, Richard M; Sramkó, Gábor; Paun, Ovidiu

2018-01-25

Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company.

Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): Taxonomic implications and evidence of interspecific hybridization.

PubMed

Welker, Cassiano A D; Souza-Chies, Tatiana T; Longhi-Wagner, Hilda M; Peichoto, Myriam Carolina; McKain, Michael R; Kellogg, Elizabeth A

2016-06-01

Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy in many lineages of flowering plants. The first phylogeny of the grass genus Eriochrysis is presented here, focusing on the New World species, in order to examine its relationships to other genera of the subtribe Saccharinae/tribe Andropogoneae and to define the circumscriptions of its taxonomically complicated species. Molecular cloning and sequencing of five regions of four low-copy nuclear genes (apo1, d8, ep2-ex7 and ep2-ex8, kn1) were performed, as well as complete plastome sequencing. Trees were reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference analyses. The present phylogenetic analyses indicate that Eriochrysis is monophyletic and the Old World E. pallida is sister to the New World species. Subtribe Saccharinae is polyphyletic, as is the genus Eulalia. Based on nuclear and plastome sequences plus morphology, we define the circumscriptions of the New World species of Eriochrysis: E. laxa is distinct from E. warmingiana, and E. villosa is distinct from E. cayennensis. Natural hybrids occur between E. laxa and E. villosa. The hybrids are probably tetraploids, based on the number of paralogues in the nuclear gene trees. This is the first record of a polyploid taxon in the genus Eriochrysis. Some incongruities between nuclear genes and plastome analyses were detected and are potentially caused by incomplete lineage sorting and/or ancient hybridization. The set of low-copy nuclear genes used in this study seems to be sufficient to resolve phylogenetic relationships and define the circumscriptions of other species complexes in the grass family and relatives, even in the presence of polyploidy and reticulate evolution. Complete plastome sequencing is also a promising tool for phylogenetic inference. Copyright © 2016 Elsevier Inc. All rights reserved.

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife

PubMed Central

Manen, Jean-François

2004-01-01

Background Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands), I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer) and two nuclear markers, the ribosomal internal transcribed spacer (ITS) and the nuclear encoded plastid glutamine synthetase (nepGS) were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively. Results The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism. Conclusions Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus Ilex. PMID:15550175

Supporting Learners to Succeed: A Thematic Report by Education Scotland on Behalf of the Scottish Funding Council on Provision of Services Delivered by Scotland's Colleges to Support Learners to Succeed in Their Learning. Transforming Lives through Learning

ERIC Educational Resources Information Center

Education Scotland, 2014

2014-01-01

This report focuses on the actions taken by colleges to help learners resolve issues which are affecting their ability to turn up for classes, engage fully in learning and undertake assessments successfully. It explains the range of services and the relationships colleges have with other external bodies to provide support for learning. This report…

Laser heterodyne spectrometer for helioseismology

NASA Technical Reports Server (NTRS)

Glenar, D. A.; Deming, D.; Espenak, F.; Kostiuk, T.; Mumma, M. J.

1986-01-01

The technique of laser heterodyne spectroscopy has been applied to the measurement of solar oscillations. Coherent mixing of solar radiation with the output of a frequency-stabilized CO2 laser permits the measurement of fully resolved profiles of solar absorption lines with high spectral purity and excellent frequency stability. This technique has been used to measure OH pure rotation lines in the infrared solar spectrum. Power spectra of these line frequency measurements show the well-known 5-min oscillations as well as significant velocity power at shorter periods.

Enantiodifferentiation through frequency-selective pure-shift (1)H nuclear magnetic resonance spectroscopy.

PubMed

Castañar, Laura; Pérez-Trujillo, Míriam; Nolis, Pau; Monteagudo, Eva; Virgili, Albert; Parella, Teodor

2014-04-04

A frequency-selective 1D (1) H nuclear magnetic resonance (NMR) experiment for the fast and sensitive determination of chemical-shift differences between overlapped resonances is proposed. The resulting fully homodecoupled (1) H NMR resonances appear as resolved 1D singlets without their typical J(HH) coupling constant multiplet structures. The high signal dispersion that is achieved is then exploited in enantiodiscrimination studies by using chiral solvating agents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The high-resolution infrared spectrum of the ν3 +ν5 combination band of jet-cooled propyne

NASA Astrophysics Data System (ADS)

Doney, K. D.; Zhao, D.; Bouwman, J.; Linnartz, H.

2017-09-01

We present the first detection of the high-resolution ro-vibrational spectrum of the ν3 +ν5 combination band of propyne around 3070 cm-1. The fully resolved spectrum is recorded for supersonically jet-cooled propyne using continuous wave cavity ring-down spectroscopy (cw-CRDS). The assignments are supported with the help of accurate ab initio vibration-rotation interaction constants (αi) and anharmonic frequencies. A detailed analysis of the rotationally cold spectrum is given.

Discovery of natural gain amplification in the 10 muon m CO2 laser bands on Mars: The first definite natural laser

NASA Technical Reports Server (NTRS)

Mumma, M.; Buhl, D.; Chin, G.; Deming, D.; Espenak, F.; Kostiuk, T.; Zipoy, D.

1980-01-01

Fully resolved intensity profiles of various lines in the CO2 bands at 9.4 micrometers and 10.4 micrometers were measured on Mars using an infrared heterodyne spectrometer. Analysis of the line shapes shows that the Mars atmosphere exhibits positive gain on these lines, providing the first definite detection of natural optical gain amplification and enabling identification of these lines as the first definite natural laser ever discovered.

Remote air pollution measurement

NASA Technical Reports Server (NTRS)

Byer, R. L.

1975-01-01

This paper presents a discussion and comparison of the Raman method, the resonance and fluorescence backscatter method, long path absorption methods and the differential absorption method for remote air pollution measurement. A comparison of the above remote detection methods shows that the absorption methods offer the most sensitivity at the least required transmitted energy. Topographical absorption provides the advantage of a single ended measurement, and differential absorption offers the additional advantage of a fully depth resolved absorption measurement. Recent experimental results confirming the range and sensitivity of the methods are presented.

X-rays only when you want them: optimized pump–probe experiments using pseudo-single-bunch operation

PubMed Central

Hertlein, M. P.; Scholl, A.; Cordones, A. A.; Lee, J. H.; Engelhorn, K.; Glover, T. E.; Barbrel, B.; Sun, C.; Steier, C.; Portmann, G.; Robin, D. S.

2015-01-01

Laser pump–X-ray probe experiments require control over the X-ray pulse pattern and timing. Here, the first use of pseudo-single-bunch mode at the Advanced Light Source in picosecond time-resolved X-ray absorption experiments on solutions and solids is reported. In this mode the X-ray repetition rate is fully adjustable from single shot to 500 kHz, allowing it to be matched to typical laser excitation pulse rates. Suppressing undesired X-ray pulses considerably reduces detector noise and improves signal to noise in time-resolved experiments. In addition, dose-induced sample damage is considerably reduced, easing experimental setup and allowing the investigation of less robust samples. Single-shot X-ray exposures of a streak camera detector using a conventional non-gated charge-coupled device (CCD) camera are also demonstrated. PMID:25931090

Lattice-level observation of the elastic-to-plastic relaxation process with subnanosecond resolution in shock-compressed Ta using time-resolved in situ Laue diffraction

DOE PAGES

Wehrenberg, C. E.; Comley, A. J.; Barton, N. R.; ...

2015-09-29

We report direct lattice level measurements of plastic relaxation kinetics through time-resolved, in-situ Laue diffraction of shock-compressed single-crystal [001] Ta at pressures of 27-210 GPa. For a 50 GPa shock, a range of shear strains is observed extending up to the uniaxial limit for early data points (<0.6 ns) and the average shear strain relaxes to a near steady state over ~1 ns. For 80 and 125 GPa shocks, the measured shear strains are fully relaxed already at 200 ps, consistent with rapid relaxation associated with the predicted threshold for homogeneous nucleation of dislocations occurring at shock pressure ~65 GPa.more » The relaxation rate and shear stresses are used to estimate the dislocation density and these quantities are compared to the Livermore Multiscale Strength model as well as various molecular dynamics simulations.« less

Exploring Mbar shock conditions and isochorically heated aluminum at the Matter in Extreme Conditions end station of the Linac Coherent Light Source

DOE PAGES

Doppner, T.; LePape, S.; Ma, T.; ...

2014-08-11

Recent experiments performed at the Matter in Extreme Conditions end station of the Linac Coherent Light Source (LCLS) have demonstrated the first spectrally resolved measurements of plasmons from isochorically heated aluminum. The experiments have been performed using a seeded 8-keV x-ray laser beam as a pump and probe to both volumetrically heat and scatterx-rays from aluminum. Collective x-ray Thomson scattering spectra show a well-resolved plasmon feature that is down-shifted in energy by 19 eV. In addition, Mbar shock pressures from laser-compressed aluminum foils using velocity interferometer system for any reflector have been measured. Furthermore, the combination of experiments fully demonstratesmore » the possibility to perform warm dense matter studies at the LCLS with unprecedented accuracy and precision.« less

Linear estimation of coherent structures in wall-bounded turbulence at Re τ = 2000

NASA Astrophysics Data System (ADS)

Oehler, S.; Garcia–Gutiérrez, A.; Illingworth, S.

2018-04-01

The estimation problem for a fully-developed turbulent channel flow at Re τ = 2000 is considered. Specifically, a Kalman filter is designed using a Navier–Stokes-based linear model. The estimator uses time-resolved velocity measurements at a single wall-normal location (provided by DNS) to estimate the time-resolved velocity field at other wall-normal locations. The estimator is able to reproduce the largest scales with reasonable accuracy for a range of wavenumber pairs, measurement locations and estimation locations. Importantly, the linear model is also able to predict with reasonable accuracy the performance that will be achieved by the estimator when applied to the DNS. A more practical estimation scheme using the shear stress at the wall as measurement is also considered. The estimator is still able to estimate the largest scales with reasonable accuracy, although the estimator’s performance is reduced.

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

PubMed Central

Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Dwayne Miller, R. J.

2015-01-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs. PMID:26798825

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography.

PubMed

Mueller, C; Marx, A; Epp, S W; Zhong, Y; Kuo, A; Balo, A R; Soman, J; Schotte, F; Lemke, H T; Owen, R L; Pai, E F; Pearson, A R; Olson, J S; Anfinrud, P A; Ernst, O P; Dwayne Miller, R J

2015-09-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

X-rays only when you want them: Optimized pump–probe experiments using pseudo-single-bunch operation

DOE PAGES

Hertlein, M. P.; Scholl, A.; Cordones, A. A.; ...

2015-04-02

Laser pump–X-ray probe experiments require control over the X-ray pulse pattern and timing. Here, the first use of pseudo-single-bunch mode at the Advanced Light Source in picosecond time-resolved X-ray absorption experiments on solutions and solids is reported. In this mode the X-ray repetition rate is fully adjustable from single shot to 500 kHz, allowing it to be matched to typical laser excitation pulse rates. Suppressing undesired X-ray pulses considerably reduces detector noise and improves signal to noise in time-resolved experiments. In addition, dose-induced sample damage is considerably reduced, easing experimental setup and allowing the investigation of less robust samples. Single-shotmore » X-ray exposures of a streak camera detector using a conventional non-gated charge-coupled device (CCD) camera are also demonstrated.« less

Two-way coupled SPH and particle level set fluid simulation.

PubMed

Losasso, Frank; Talton, Jerry; Kwatra, Nipun; Fedkiw, Ronald

2008-01-01

Grid-based methods have difficulty resolving features on or below the scale of the underlying grid. Although adaptive methods (e.g. RLE, octrees) can alleviate this to some degree, separate techniques are still required for simulating small-scale phenomena such as spray and foam, especially since these more diffuse materials typically behave quite differently than their denser counterparts. In this paper, we propose a two-way coupled simulation framework that uses the particle level set method to efficiently model dense liquid volumes and a smoothed particle hydrodynamics (SPH) method to simulate diffuse regions such as sprays. Our novel SPH method allows us to simulate both dense and diffuse water volumes, fully incorporates the particles that are automatically generated by the particle level set method in under-resolved regions, and allows for two way mixing between dense SPH volumes and grid-based liquid representations.

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Kocuria kristinae infection associated with acute cholecystitis

PubMed Central

Ma, Edmond SK; Wong, Chris LP; Lai, Kristi TW; Chan, Edmond CH; Yam, WC; Chan, Angus CW

2005-01-01

Background Kocuria, previously classified into the genus of Micrococcus, is commonly found on human skin. Two species, K. rosea and K. kristinae, are etiologically associated with catheter-related bacteremia. Case presentation We describe the first case of K. kristinae infection associated with acute cholecystitis. The microorganism was isolated from the bile of a 56-year old Chinese man who underwent laparoscopic cholecystectomy. He developed post-operative fever that resolved readily after levofloxacin treatment. Conclusion Our report of K. kristinae infection associated with acute cholecystitis expands the clinical spectrum of infections caused by this group of bacteria. With increasing number of recent reports describing the association between Kocuria spp. and infectious diseases, the significance of their isolation from clinical specimens cannot be underestimated. A complete picture of infections related to Kocuria spp. will have to await the documentation of more clinical cases. PMID:16029488

Kocuria kristinae infection associated with acute cholecystitis.

PubMed

Ma, Edmond S K; Wong, Chris L P; Lai, Kristi T W; Chan, Edmond C H; Yam, W C; Chan, Angus C W

2005-07-19

Kocuria, previously classified into the genus of Micrococcus, is commonly found on human skin. Two species, K. rosea and K. kristinae, are etiologically associated with catheter-related bacteremia. We describe the first case of K. kristinae infection associated with acute cholecystitis. The microorganism was isolated from the bile of a 56-year old Chinese man who underwent laparoscopic cholecystectomy. He developed post-operative fever that resolved readily after levofloxacin treatment. Our report of K. kristinae infection associated with acute cholecystitis expands the clinical spectrum of infections caused by this group of bacteria. With increasing number of recent reports describing the association between Kocuria spp. and infectious diseases, the significance of their isolation from clinical specimens cannot be underestimated. A complete picture of infections related to Kocuria spp. will have to await the documentation of more clinical cases.

Phylogenetic and phenotypic characterisation of Sirococcus castaneae comb. nov. (synonym Diplodina castaneae), a fungal endophyte of European chestnut.

PubMed

Meyer, Joana B; Trapiello, Estefanía; Senn-Irlet, Beatrice; Sieber, Thomas N; Cornejo, Carolina; Aghayeva, Dilzara; González, Ana J; Prospero, Simone

2017-08-01

In this paper we resolve the taxonomic status of the fungus Diplodina castaneae (Ascomycetes, Diaporthales, Gnomoniaceae) which occurs on the European chestnut (Castanea sativa) as endophyte and as the causal agent of Javart disease. Specimens from Switzerland, Spain, and Azerbaijan were sequenced at five nuclear loci (β-tubulin, EF-1α, ITS, LSU, and RPB2). Phylogenies were inferred to place D. castaneae in the Gnomoniaceae family. Moreover, growth rates and morphological characteristics on different agar media were assessed and compared to those of Gnomoniopsis castaneae, which can easily be confused with D. castaneae. Based on morphological and phylogenetic characteristics, we propose to reallocate D. castaneae to the genus Sirococcus, as S. castaneae comb. nov. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Keratomycosis due to Tintelnotia destructans refractory to common therapy treated successfully with systemic and local terbinafine in combination with polyhexamethylene biguanide.

PubMed

Behrens-Baumann, Wolfgang J; Hofmüller, Wolfram; Tammer, Ina; Tintelnot, Kathrin

2018-04-28

To report on a wearer of rigid gas-permeable contact lenses with a keratomycosis due to Tintelnotia-a new genus of Phaeosphaeriaceae-treated with terbinafine and polyhexamethylene biguanide. Chart review of a patient with fungal keratitis treated additionally with systemic and topical terbinafine 0.25% after symptoms increased under conventional antimycotic therapy with voriconazole. Antifungal susceptibility had been tested in vitro. After starting an additional treatment with systemic and topical terbinafine, the severe corneal infection was sufficiently resolved. The drug was well tolerated without any neurological, dermatological or gastroenterological problems. Terbinafine revealed a marked in vitro antifungal activity of 0.12 µg/ml. The fungus was identified as Tintelnotia destructans. Terbinafine might be considered as a therapeutic option in severe cases of fungal keratitis refractory to common antifungal therapy.

Smooth Horizonless Geometries Deep Inside the Black-Hole Regime.

PubMed

Bena, Iosif; Giusto, Stefano; Martinec, Emil J; Russo, Rodolfo; Shigemori, Masaki; Turton, David; Warner, Nicholas P

2016-11-11

We construct the first family of horizonless supergravity solutions that have the same mass, charges, and angular momenta as general supersymmetric rotating D1-D5-P black holes in five dimensions. This family includes solutions with arbitrarily small angular momenta, deep within the regime of quantum numbers and couplings for which a large classical black hole exists. These geometries are well approximated by the black-hole solution, and in particular exhibit the same near-horizon throat. Deep in this throat, the black-hole singularity is resolved into a smooth cap. We also identify the holographically dual states in the N=(4,4) D1-D5 orbifold conformal field theory (CFT). Our solutions are among the states counted by the CFT elliptic genus, and provide examples of smooth microstate geometries within the ensemble of supersymmetric black-hole microstates.

Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives.

PubMed

Welch, Andreanna J; Collins, Katherine; Ratan, Aakrosh; Drautz-Moses, Daniela I; Schuster, Stephan C; Lindqvist, Charlotte

2016-06-01

These data are presented in support of a plastid phylogenomic analysis of the recent radiation of the Hawaiian endemic mints (Lamiaceae), and their close relatives in the genus Stachys, "The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)" [1]. Here we describe the chloroplast genome sequences for 12 mint taxa. Data presented include summaries of gene content and length for these taxa, structural comparison of the mint chloroplast genomes with published sequences from other species in the order Lamiales, and comparisons of variability among three Hawaiian taxa vs. three outgroup taxa. Finally, we provide a list of 108 primer pairs targeting the most variable regions within this group and designed specifically for amplification of DNA extracted from degraded herbarium material.

Enhancing SDO/HMI images using deep learning

NASA Astrophysics Data System (ADS)

Baso, C. J. Díaz; Ramos, A. Asensio

2018-06-01

Context. The Helioseismic and Magnetic Imager (HMI) provides continuum images and magnetograms with a cadence better than one per minute. It has been continuously observing the Sun 24 h a day for the past 7 yr. The trade-off between full disk observations and spatial resolution means that HMI is not adequate for analyzing the smallest-scale events in the solar atmosphere. Aims: Our aim is to develop a new method to enhance HMI data, simultaneously deconvolving and super-resolving images and magnetograms. The resulting images will mimic observations with a diffraction-limited telescope twice the diameter of HMI. Methods: Our method, which we call Enhance, is based on two deep, fully convolutional neural networks that input patches of HMI observations and output deconvolved and super-resolved data. The neural networks are trained on synthetic data obtained from simulations of the emergence of solar active regions. Results: We have obtained deconvolved and super-resolved HMI images. To solve this ill-defined problem with infinite solutions we have used a neural network approach to add prior information from the simulations. We test Enhance against Hinode data that has been degraded to a 28 cm diameter telescope showing very good consistency. The code is open source.

Event Centroiding Applied to Energy-Resolved Neutron Imaging at LANSCE

DOE PAGES

Borges, Nicholas; Losko, Adrian; Vogel, Sven

2018-02-13

The energy-dependence of the neutron cross section provides vastly different contrast mechanisms than polychromatic neutron radiography if neutron energies can be selected for imaging applications. In recent years, energy-resolved neutron imaging (ERNI) with epi-thermal neutrons, utilizing neutron absorption resonances for contrast as well as for quantitative density measurements, was pioneered at the Flight Path 5 beam line at LANSCE and continues to be refined. In this work, we present event centroiding, i.e., the determination of the center-of-gravity of a detection event on an imaging detector to allow sub-pixel spatial resolution and apply it to the many frames collected for energy-resolvedmore » neutron imaging at a pulsed neutron source. While event centroiding was demonstrated at thermal neutron sources, it has not been applied to energy-resolved neutron imaging, where the energy resolution requires to be preserved, and we present a quantification of the possible resolution as a function of neutron energy. For the 55 μm pixel size of the detector used for this study, we found a resolution improvement from ~80 μm to ~22 μm using pixel centroiding while fully preserving the energy resolution.« less

Event Centroiding Applied to Energy-Resolved Neutron Imaging at LANSCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borges, Nicholas; Losko, Adrian; Vogel, Sven

The energy-dependence of the neutron cross section provides vastly different contrast mechanisms than polychromatic neutron radiography if neutron energies can be selected for imaging applications. In recent years, energy-resolved neutron imaging (ERNI) with epi-thermal neutrons, utilizing neutron absorption resonances for contrast as well as for quantitative density measurements, was pioneered at the Flight Path 5 beam line at LANSCE and continues to be refined. In this work, we present event centroiding, i.e., the determination of the center-of-gravity of a detection event on an imaging detector to allow sub-pixel spatial resolution and apply it to the many frames collected for energy-resolvedmore » neutron imaging at a pulsed neutron source. While event centroiding was demonstrated at thermal neutron sources, it has not been applied to energy-resolved neutron imaging, where the energy resolution requires to be preserved, and we present a quantification of the possible resolution as a function of neutron energy. For the 55 μm pixel size of the detector used for this study, we found a resolution improvement from ~80 μm to ~22 μm using pixel centroiding while fully preserving the energy resolution.« less

Depth-resolved magnetic and structural analysis of relaxing epitaxial Sr 2 CrReO 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lucy, J. M.; Hauser, A. J.; Liu, Y.

2015-03-01

Structural relaxation in a Sr2CrReO6 epitaxial film, which exhibits strong spin-orbit coupling, leads to depth-dependent magnetism. We combine two depth-resolved synchrotron x-ray techniques, two-dimensional reciprocal space mapping and x-ray magnetic circular dichroism, to quantitatively determine this effect. An 800 nm thick film of Sr2CrReO6, grown with tensile epitaxial strain on SrCr0:5Nb0:5O3(225 nm)/LSAT, relaxes away from the Sr2CrReO6/SrCr0:5Nb0:5O3 interface to its bulk lattice parameters, with much of the film being fully relaxed. Grazing incidence xray diffraction measurements of the film elucidate the in-plane strain relaxation near the film- substrate interface while depth-resolved x-ray magnetic circular dichroism at the Re L edgemore » reveals the magnetic contributions of the Re site. The smooth relaxation of the film near the interface correlates with changes in the magnetic anisotropy. This provides a systematic and powerful way to probe the depth-varying structural and magnetic properties of a complex oxide with synchrotronsource x-ray techniques.« less

State-resolved Photodissociation and Radiative Association Data for the Molecular Hydrogen Ion

NASA Astrophysics Data System (ADS)

Zammit, Mark C.; Savage, Jeremy S.; Colgan, James; Fursa, Dmitry V.; Kilcrease, David P.; Bray, Igor; Fontes, Christopher J.; Hakel, Peter; Timmermans, Eddy

2017-12-01

We present state-resolved (electronic, vibrational, and rotational) cross sections and rate coefficients for the photodissociation (PD) of {{{H}}}2+ and radiative association (RA) of H–H+. We developed a fully quantum mechanical approach within the nonrelativistic Born–Oppenheimer approximation to describe {{{H}}}2+ and calculate the data for transitions between the ground electronic state 1s{σ }g and the 2p{σ }u, 2p{π }u, 3p{σ }u, 3p{π }u, 4p{σ }u, 4f{σ }u, 4f{π }u, and 4p{π }u electronic states (i.e., up to {{{H}}}2+ n = 4). Tables of the dipole-matrix elements and energies needed to calculate state-resolved cross sections and rate coefficients will be made publicly available. These data could be important in astrophysical models when dealing with photon wavelengths (or radiation temperature distributions that are weighted toward such wavelengths) around 100 nm. For example, at these wavelengths and a material temperature of 8400 K, the LTE-averaged PD cross section via the (second electronically excited) 2p{π }u state is over three times larger than the PD cross section via the (first electronically excited) 2p{σ }u state.

Simulations of the impact of localized defects on ICF implosions

NASA Astrophysics Data System (ADS)

Milovich, Jose; Robey, Harry; Weber, Christopher; Sepke, Scott; Clark, Daniel; Koning, Joe; Smalyuk, Vladimir; Martinez, David

2016-10-01

Recent experiments have identified the tent membranes that support the capsule as a source of a large azimuthal perturbation at the point of departure from the surface. Highly-resolved 2D simulations have shown that vorticity generated by the interaction of the ablated capsule material and the tent allows for the penetration of cold ablator material into the burning hot-spot likely cooling the central burning plasma. These observations have motivated the search for alternative supporting methods. One of the techniques being considered uses the existing fill-tube (needed to deliver the cryogenic fuel) supported against gravity by a thin rod (cantilever) spanning the hohlraum diameter. Recent experiments have assessed the perturbation induced on the target as the rod is positioned along the fill-tube at different distances from the capsule surface and found optical-depth modulations oriented along the cantilever direction, possibly caused by laser spot shadowing or hydro-coupling. To fully understand the data we have undertaken an extensive study of highly-resolved 2D integrated simulations abled to resolve the 12 um diameter cantilever. Results of our computations and comparison with the experiments will be presented. Prepared by LLNL under Contract DE-AC52-07NA27344.

Towards Cloud-Resolving European-Scale Climate Simulations using a fully GPU-enabled Prototype of the COSMO Regional Model

NASA Astrophysics Data System (ADS)

Leutwyler, David; Fuhrer, Oliver; Cumming, Benjamin; Lapillonne, Xavier; Gysi, Tobias; Lüthi, Daniel; Osuna, Carlos; Schär, Christoph

2014-05-01

The representation of moist convection is a major shortcoming of current global and regional climate models. State-of-the-art global models usually operate at grid spacings of 10-300 km, and therefore cannot fully resolve the relevant upscale and downscale energy cascades. Therefore parametrization of the relevant sub-grid scale processes is required. Several studies have shown that this approach entails major uncertainties for precipitation processes, which raises concerns about the model's ability to represent precipitation statistics and associated feedback processes, as well as their sensitivities to large-scale conditions. Further refining the model resolution to the kilometer scale allows representing these processes much closer to first principles and thus should yield an improved representation of the water cycle including the drivers of extreme events. Although cloud-resolving simulations are very useful tools for climate simulations and numerical weather prediction, their high horizontal resolution and consequently the small time steps needed, challenge current supercomputers to model large domains and long time scales. The recent innovations in the domain of hybrid supercomputers have led to mixed node designs with a conventional CPU and an accelerator such as a graphics processing unit (GPU). GPUs relax the necessity for cache coherency and complex memory hierarchies, but have a larger system memory-bandwidth. This is highly beneficial for low compute intensity codes such as atmospheric stencil-based models. However, to efficiently exploit these hybrid architectures, climate models need to be ported and/or redesigned. Within the framework of the Swiss High Performance High Productivity Computing initiative (HP2C) a project to port the COSMO model to hybrid architectures has recently come to and end. The product of these efforts is a version of COSMO with an improved performance on traditional x86-based clusters as well as hybrid architectures with GPUs. We present our redesign and porting approach as well as our experience and lessons learned. Furthermore, we discuss relevant performance benchmarks obtained on the new hybrid Cray XC30 system "Piz Daint" installed at the Swiss National Supercomputing Centre (CSCS), both in terms of time-to-solution as well as energy consumption. We will demonstrate a first set of short cloud-resolving climate simulations at the European-scale using the GPU-enabled COSMO prototype and elaborate our future plans on how to exploit this new model capability.

How to model supernovae in simulations of star and galaxy formation

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Wetzel, Andrew; Kereš, Dušan; Faucher-Giguère, Claude-André; Quataert, Eliot; Boylan-Kolchin, Michael; Murray, Norman; Hayward, Christopher C.; El-Badry, Kareem

2018-06-01

We study the implementation of mechanical feedback from supernovae (SNe) and stellar mass loss in galaxy simulations, within the Feedback In Realistic Environments (FIRE) project. We present the FIRE-2 algorithm for coupling mechanical feedback, which can be applied to any hydrodynamics method (e.g. fixed-grid, moving-mesh, and mesh-less methods), and black hole as well as stellar feedback. This algorithm ensures manifest conservation of mass, energy, and momentum, and avoids imprinting `preferred directions' on the ejecta. We show that it is critical to incorporate both momentum and thermal energy of mechanical ejecta in a self-consistent manner, accounting for SNe cooling radii when they are not resolved. Using idealized simulations of single SN explosions, we show that the FIRE-2 algorithm, independent of resolution, reproduces converged solutions in both energy and momentum. In contrast, common `fully thermal' (energy-dump) or `fully kinetic' (particle-kicking) schemes in the literature depend strongly on resolution: when applied at mass resolution ≳100 M⊙, they diverge by orders of magnitude from the converged solution. In galaxy-formation simulations, this divergence leads to orders-of-magnitude differences in galaxy properties, unless those models are adjusted in a resolution-dependent way. We show that all models that individually time-resolve SNe converge to the FIRE-2 solution at sufficiently high resolution (<100 M⊙). However, in both idealized single-SN simulations and cosmological galaxy-formation simulations, the FIRE-2 algorithm converges much faster than other sub-grid models without re-tuning parameters.

Crystal plasticity modeling of β phase deformation in Ti-6Al-4V

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, John A.; Barton, Nathan R.; Florando, Jeff

Ti-6Al-4V is an alloy of titanium that dominates titanium usage in applications ranging from mass-produced consumer goods to high-end aerospace parts. The material's structure on a microscale is known to affect its mechanical properties but these effects are not fully understood. Specifically, this work will address the effects of low volume fraction intergranular β phase on Ti-6Al-4V's mechanical response during the transition from elastic to plastic deformation. A crystal plasticity-based finite element model is used to fully resolve the deformation of the β phase for the first time. This high fidelity model captures mechanisms difficult to access via experiments ormore » lower fidelity models. Lastly, the results are used to assess lower fidelity modeling assumptions and identify phenomena that have ramifications for failure of the material.« less

Fully Controllable Pancharatnam-Berry Metasurface Array with High Conversion Efficiency and Broad Bandwidth

PubMed Central

Liu, Chuanbao; Bai, Yang; Zhao, Qian; Yang, Yihao; Chen, Hongsheng; Zhou, Ji; Qiao, Lijie

2016-01-01

Metasurfaces have powerful abilities to manipulate the properties of electromagnetic waves flexibly, especially the modulation of polarization state for both linearly polarized (LP) and circularly polarized (CP) waves. However, the transmission efficiency of cross-polarization conversion by a single-layer metasurface has a low theoretical upper limit of 25% and the bandwidth is usually narrow, which cannot be resolved by their simple additions. Here, we efficiently manipulate polarization coupling in multilayer metasurface to promote the transmission of cross-polarization by Fabry-Perot resonance, so that a high conversion coefficient of 80–90% of CP wave is achieved within a broad bandwidth in the metasurface with C-shaped scatters by theoretical calculation, numerical simulation and experiments. Further, fully controlling Pancharatnam-Berry phase enables to realize polarized beam splitter, which is demonstrated to produce abnormal transmission with high conversion efficiency and broad bandwidth. PMID:27703254

Crystal plasticity modeling of β phase deformation in Ti-6Al-4V

DOE PAGES

Moore, John A.; Barton, Nathan R.; Florando, Jeff; ...

2017-08-24

Ti-6Al-4V is an alloy of titanium that dominates titanium usage in applications ranging from mass-produced consumer goods to high-end aerospace parts. The material's structure on a microscale is known to affect its mechanical properties but these effects are not fully understood. Specifically, this work will address the effects of low volume fraction intergranular β phase on Ti-6Al-4V's mechanical response during the transition from elastic to plastic deformation. A crystal plasticity-based finite element model is used to fully resolve the deformation of the β phase for the first time. This high fidelity model captures mechanisms difficult to access via experiments ormore » lower fidelity models. Lastly, the results are used to assess lower fidelity modeling assumptions and identify phenomena that have ramifications for failure of the material.« less

Fluid preconditioning for Newton–Krylov-based, fully implicit, electrostatic particle-in-cell simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, G., E-mail: gchen@lanl.gov; Chacón, L.; Leibs, C.A.

2014-02-01

A recent proof-of-principle study proposes an energy- and charge-conserving, nonlinearly implicit electrostatic particle-in-cell (PIC) algorithm in one dimension [9]. The algorithm in the reference employs an unpreconditioned Jacobian-free Newton–Krylov method, which ensures nonlinear convergence at every timestep (resolving the dynamical timescale of interest). Kinetic enslavement, which is one key component of the algorithm, not only enables fully implicit PIC as a practical approach, but also allows preconditioning the kinetic solver with a fluid approximation. This study proposes such a preconditioner, in which the linearized moment equations are closed with moments computed from particles. Effective acceleration of the linear GMRES solvemore » is demonstrated, on both uniform and non-uniform meshes. The algorithm performance is largely insensitive to the electron–ion mass ratio. Numerical experiments are performed on a 1D multi-scale ion acoustic wave test problem.« less

ON THE EVOLUTION OF THE CO SNOW LINE IN PROTOPLANETARY DISKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Rebecca G.; Livio, Mario

2014-03-10

CO is thought to be a vital building block for prebiotic molecules that are necessary for life. Thus, understanding where CO existed in a solid phase within the solar nebula is important for understanding the origin of life. We model the evolution of the CO snow line in a protoplanetary disk. We find that the current observed location of the CO snow line in our solar system, and in the solar system analog TW Hydra, cannot be explained by a fully turbulent disk model. With time-dependent disk models we find that the inclusion of a dead zone (a region ofmore » low turbulence) can resolve this problem. Furthermore, we obtain a fully analytic solution for the CO snow line radius for late disk evolutionary times. This will be useful for future observational attempts to characterize the demographics and predict the composition and habitability of exoplanets.« less

Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation.

PubMed

Iwata, Koichi; Terazima, Masahide; Masuhara, Hiroshi

2018-02-01

Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017. Published by Elsevier B.V.

Investigation of RNA Hairpin Loop Folding with Time-Resolved Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Stancik, Aaron Lee

Ribonucleic acids (RNAs) are a group of functional biopolymers central to the molecular underpinnings of life. To complete the many processes they mediate, RNAs must fold into precise three-dimensional structures. Hairpin loops are the most ubiquitous and basic structural elements present in all folded RNAs, and are the foundation upon which all complex tertiary structures are built. A hairpin loop forms when a single stranded RNA molecule folds back on itself creating a helical stem of paired bases capped by a loop. This work investigates the formation of UNCG hairpin loops with the sequence 5'-GC(UNCG)GC-3' (N = A, U, G, or C) using both equilibrium infrared (IR) and time-resolved IR spectroscopy. Equilibrium IR melting data were used to determine thermodynamic parameters. Melting temperatures ranged from 50 to 60°C, and enthalpies of unfolding were on the order of 100 kJ/mol. In the time-resolved work, temperature jumps of up to 20°C at 2.5°C increments were obtained with transient relaxation kinetics spanning nanoseconds to hundreds of microseconds. The relaxation kinetics for all of the oligomers studied were fit to first or second order exponentials. Multiple vibrational transitions were probed on each oligomer for fully folded and partially denatured structures. In the time-resolved limit, in contrast to equilibrium melting, RNA does not fold according to two-state behavior. These results are some of the first to show that RNA hairpins fold according to a rugged energy landscape, which contradicts their relatively simple nature. In addition, this work has proven that time-resolved IR spectroscopy is a powerful and novel tool for investigating the earliest events of RNA folding, the formation of the hairpin loop.

A portable low-cost long-term live-cell imaging platform for biomedical research and education.

PubMed

Walzik, Maria P; Vollmar, Verena; Lachnit, Theresa; Dietz, Helmut; Haug, Susanne; Bachmann, Holger; Fath, Moritz; Aschenbrenner, Daniel; Abolpour Mofrad, Sepideh; Friedrich, Oliver; Gilbert, Daniel F

2015-02-15

Time-resolved visualization and analysis of slow dynamic processes in living cells has revolutionized many aspects of in vitro cellular studies. However, existing technology applied to time-resolved live-cell microscopy is often immobile, costly and requires a high level of skill to use and maintain. These factors limit its utility to field research and educational purposes. The recent availability of rapid prototyping technology makes it possible to quickly and easily engineer purpose-built alternatives to conventional research infrastructure which are low-cost and user-friendly. In this paper we describe the prototype of a fully automated low-cost, portable live-cell imaging system for time-resolved label-free visualization of dynamic processes in living cells. The device is light-weight (3.6 kg), small (22 × 22 × 22 cm) and extremely low-cost (<€1250). We demonstrate its potential for biomedical use by long-term imaging of recombinant HEK293 cells at varying culture conditions and validate its ability to generate time-resolved data of high quality allowing for analysis of time-dependent processes in living cells. While this work focuses on long-term imaging of mammalian cells, the presented technology could also be adapted for use with other biological specimen and provides a general example of rapidly prototyped low-cost biosensor technology for application in life sciences and education. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Polarization-resolved optical response of plasmonic particle-on-film nanocavities

NASA Astrophysics Data System (ADS)

Zhang, Q.; Li, G.-C.; Lo, T. W.; Lei, D. Y.

2018-02-01

Placing a metal nanoparticle atop a metal film forms a plasmonic particle-on-film nanocavity. Such a nanocavity supports strong plasmonic coupling that results in rich hybridized plasmon modes, rendering the cavity a versatile platform for exploiting a wide range of plasmon-enhanced spectroscopy applications. In this paper, we fully address the polarization-resolved, orientation-dependent far-field optical responses of plasmonic monomer- and dimer-on-film nanocavities by numerical simulations and experiments. With polarization-resolved dark-field spectroscopy, the distinct plasmon resonances of these nanocavities are clearly determined from their scattering spectra. Moreover, the radiation patterns of respective plasmon modes, which are often mixed together in common dark-field imaging, can be unambiguously resolved with our proposed quasi-multispectral imaging method. Explicitly, the radiation pattern of the monomer-on-film nanocavity gradually transitions from a solid spot in the green imaging channel to a doughnut ring in the red channel when tuning the excitation polarization from parallel to perpendicular to the sample surface. This observation holds true for the plasmonic dimer-on-film nanocavity with the dimer axis aligned in the incidence plane; when the dimer axis is normal to the incidence plane, the pattern transitions from a solid spot to a doughnut ring both in the red channel. These studies not only demonstrate a flexible polarization control over the optical responses of plasmonic particle-on-film nanostructures but also enrich the optical tool kit for far-field imaging and spectroscopy characterization of various plasmonic nanostructures.

Efficient non-hydrostatic modelling of 3D wave-induced currents using a subgrid approach

NASA Astrophysics Data System (ADS)

Rijnsdorp, Dirk P.; Smit, Pieter B.; Zijlema, Marcel; Reniers, Ad J. H. M.

2017-08-01

Wave-induced currents are an ubiquitous feature in coastal waters that can spread material over the surf zone and the inner shelf. These currents are typically under resolved in non-hydrostatic wave-flow models due to computational constraints. Specifically, the low vertical resolutions adequate to describe the wave dynamics - and required to feasibly compute at the scales of a field site - are too coarse to account for the relevant details of the three-dimensional (3D) flow field. To describe the relevant dynamics of both wave and currents, while retaining a model framework that can be applied at field scales, we propose a two grid approach to solve the governing equations. With this approach, the vertical accelerations and non-hydrostatic pressures are resolved on a relatively coarse vertical grid (which is sufficient to accurately resolve the wave dynamics), whereas the horizontal velocities and turbulent stresses are resolved on a much finer subgrid (of which the resolution is dictated by the vertical scale of the mean flows). This approach ensures that the discrete pressure Poisson equation - the solution of which dominates the computational effort - is evaluated on the coarse grid scale, thereby greatly improving efficiency, while providing a fine vertical resolution to resolve the vertical variation of the mean flow. This work presents the general methodology, and discusses the numerical implementation in the SWASH wave-flow model. Model predictions are compared with observations of three flume experiments to demonstrate that the subgrid approach captures both the nearshore evolution of the waves, and the wave-induced flows like the undertow profile and longshore current. The accuracy of the subgrid predictions is comparable to fully resolved 3D simulations - but at much reduced computational costs. The findings of this work thereby demonstrate that the subgrid approach has the potential to make 3D non-hydrostatic simulations feasible at the scale of a realistic coastal region.

Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium.

PubMed

Parkinson, John E; Baumgarten, Sebastian; Michell, Craig T; Baums, Iliana B; LaJeunesse, Todd C; Voolstra, Christian R

2016-02-11

Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages ("Clades A-I") and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades-the equivalent of contrasting genera or families in other dinoflagellate groups-making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host-symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

PubMed

Liyanage, K K; Khan, Sehroon; Brooks, Siraprapa; Mortimer, Peter E; Karunarathna, Samantha C; Xu, Jianchu; Hyde, Kevin D

2017-04-01

Powdery mildew is a fungal disease that infects a wide range of plants, including rubber trees, which results in a reduction of latex yields of up to 45%. The causal agent of powdery mildew of rubber was first described as Oidium heveae, but later morpho-molecular research suggested that in the past, O. heveae has been confused with Erysiphe quercicola. However, it is still under debate whether the causal agent should be classified as a species of the genus Erysiphe emend. or Golovinomyces and Podosphaera, respectively. Therefore, the aim of this study was to undertake the morpho-molecular characterization of powdery mildew species associated with rubber trees, thus resolving these taxonomic issues. Morphological observation under light and scanning electron microscopes (SEM) clearly identified two morphotypes of the rubber powdery mildew. With the support of morphological and phylogenetic data, one of the two morphotypes was identified as the asexual morph of E. quercicola, while the second morphotype is still insufficiently known and according to the morphological results obtained we assume that it might belong to the genus Golovinomyces. More collections and additional molecular data are required for final conclusions regarding the exact taxonomic position of the second morphotype of rubber powdery mildew and its relation to the name O. heveae. The haplotype analysis identified eight haplotype groups of E. quercicola indicating the high genetic diversity of the species. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular phylogeny and biogeography of West Indian frogs of the genus Leptodactylus (Anura, Leptodactylidae).

PubMed

Hedges, S Blair; Heinicke, Matthew P

2007-07-01

Three endemic species of the aquatic-breeding frog genus Leptodactylus are recognized from the West Indies: Leptodactylus albilabris (Puerto Rico and the Virgin Islands), Leptodactylus dominicensis (Hispaniola), and Leptodactylus fallax (Lesser Antilles). DNA sequences were obtained from several mitochondrial genes to resolve taxonomic questions involving these species and to provide insights into their origin and distribution in the islands. We found low levels of sequence divergence between L. dominicensis and L. albilabris, supporting morphological evidence that the former species is a junior synonym of the latter species. Phylogenetic analysis supported previous species-group allocations, finding that L. albilabris is a member of the fuscus group and L. fallax is a member of the pentadactylus group. Molecular time estimates for the divergence of L. albilabris from its closest relative in South America (24-58 million years ago, Ma) and for L. fallax from its closest relative in South America (23-34Ma) indicate that they colonized the West Indies independently by over-water dispersal in the mid-Cenozoic. The absence of detectable sequence divergence between the two extant populations of L. fallax (Dominica and Montserrat), a species used for human food and now critically endangered, suggests that one or both arose by human introduction from an island or islands where that species originated. The relatively minor genetic differentiation of populations of L. albilabris can be explained by vicariance and dispersal in the Pleistocene and Holocene, although human introduction of some populations cannot be ruled out.

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar

PubMed Central

Silva, Christian; Besnard, Guillaume; Piot, Anthony; Razanatsoa, Jacqueline; Oliveira, Reyjane P.; Vorontsova, Maria S.

2017-01-01

Background and Aims Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. Methods Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages. Key Results Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory. Conclusions Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups. PMID:28028020

A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes).

PubMed

Bertram, Miranda R; Hamer, Sarah A; Hartup, Barry K; Snowden, Karen F; Medeiros, Matthew C; Outlaw, Diana C; Hamer, Gabriel L

2017-04-01

The unicellular blood parasites in the order Haemosporida are highly diverse, infect many vertebrates, are responsible for a large disease burden among humans and animals, and have reemerged as an important model system to understand the evolutionary and ecological dynamics of host-parasite interactions. The phylogenetics and systematics of Haemosporida are limited by poor sampling of different vertebrate host taxa. We surveyed the Haemosporida of wild whooping cranes (Grus americana) and sandhill cranes (Grus canadensis) (Aves: Gruiformes) using a combination of morphological and molecular approaches. We identified Haemoproteus antigonis in blood smears based on published morphological descriptions. Phylogenetic analysis based on partial cytochrome b (cytb) and cytochrome oxidase (coI) sequences placed H. antigonis parasites in a novel clade, distinct from all avian Haemosporida genera for which cytb and/or coI sequences are available. Molecular clock and divergence estimates suggest this crane clade may represent a new genus. This is the first molecular description of H. antigonis and the first report of H. antigonis in wild whooping cranes, an endangered bird in North America. Further sampling of Haemosporida, especially from hosts of the Gruiformes and other poorly sampled orders, will help to resolve the relationship of the H. antigonis clade to other avian Haemosporida genera. Our study highlights the potential of sampling neglected host species to discover novel lineages of diverse parasite groups. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region.

PubMed

Chaw, Shu-Miaw; Walters, Terrence W; Chang, Chien-Chang; Hu, Shu-Hsuan; Chen, Shin-Hsiao

2005-10-01

Phylogenetic relationships among the three families and 12 living genera of cycads were reconstructed by distance and parsimony criteria using three markers: the chloroplast matK gene, the chloroplast trnK intron and the nuclear ITS/5.8S rDNA sequence. All datasets indicate that Cycadaceae (including only the genus Cycas) is remotely related to other cycads, in which Dioon was resolved as the basal-most clade, followed by Bowenia and a clade containing the remaining nine genera. Encephalartos and Lepidozamia are closer to each other than to Macrozamia. The African genus Stangeria is embedded within the New World subfamily Zamiodeae. Therefore, Bowenia is an unlikely sister to Stangeria, contrary to the view that they form the Stangeriaceae. The generic status of Dyerocycas and Chigua is unsupportable as they are paraphyletic with Cycas and the Zamia, respectively. Nonsense mutations in the matK gene and indels in the other two datasets lend evidence to reinforce the above conclusions. According to the phylogenies, the past geography of the genera of cycads and the evolution of character states are hypothesized and discussed. Within the suborder Zamiieae, Stangeria, and the tribe Zamieae evolved significantly faster than other genera. The matK gene and ITS/5.8S region contain more useful information than the trnK intron in addressing phylogeny. Redelimitations of Zamiaceae, Stangeriaceae, subfamily Encephalartoideae and subtribe Macrozamiineae are necessary.

Spiraling into History: A Molecular Phylogeny and Investigation of Biogeographic Origins and Floral Evolution for the Genus Costus

PubMed Central

Salzman, Shayla; Driscoll, Heather E.; Renner, Tanya; André, Thiago; Shen, Stacy; Specht, Chelsea D.

2015-01-01

Rapid radiations are notoriously difficult to resolve, yet understanding phylogenetic patterns in such lineages can be useful for investigating evolutionary processes associated with bursts of speciation and morphological diversification. Here we present an expansive molecular phylogeny of Costus L. (Costaceae Nakai) with a focus on the Neotropical species within the clade, sampling 47 of the known 51 Neotropical species and including five molecular markers for phylogenetic analysis (ITS, ETS, rps16, trnL-F, and CaM). We use the phylogenetic results to investigate shifts in pollination syndrome, with the intention of addressing potential mechanisms leading to the rapid radiation documented for this clade. Our ancestral reconstruction of pollination syndrome presents the first evidence in this genus of an evolutionary toggle in pollination morphologies, demonstrating both the multiple independent evolutions of ornithophily (bird pollination) as well as reversals to melittophily (bee pollination). We show that the ornithophilous morphology has evolved at least eight times independently with four potential reversals to melittophilous morphology, and confirm prior work showing that neither pollination syndrome defines a monophyletic lineage. Based on the current distribution for the Neotropical and African species, we reconstruct the ancestral distribution of the Neotropical clade as the Pacific Coast of Mexico and Central America. Our results indicate an historic dispersal of a bee-pollinated taxon from Africa to the Pacific Coast of Mexico/Central America, with subsequent diversification leading to the evolution of a bird-pollinated floral morphology in multiple derived lineages. PMID:26146450

Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic – Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences

PubMed Central

Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

2017-01-01

The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered. PMID:28122062

Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic - Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences.

PubMed

Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

2017-01-01

The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered.

Fully implicit moving mesh adaptive algorithm

NASA Astrophysics Data System (ADS)

Serazio, C.; Chacon, L.; Lapenta, G.

2006-10-01

In many problems of interest, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. The former is best dealt with with fully implicit methods, which are able to step over fast frequencies to resolve the dynamical time scale of interest. The latter requires grid adaptivity for efficiency. Moving-mesh grid adaptive methods are attractive because they can be designed to minimize the numerical error for a given resolution. However, the required grid governing equations are typically very nonlinear and stiff, and of considerably difficult numerical treatment. Not surprisingly, fully coupled, implicit approaches where the grid and the physics equations are solved simultaneously are rare in the literature, and circumscribed to 1D geometries. In this study, we present a fully implicit algorithm for moving mesh methods that is feasible for multidimensional geometries. Crucial elements are the development of an effective multilevel treatment of the grid equation, and a robust, rigorous error estimator. For the latter, we explore the effectiveness of a coarse grid correction error estimator, which faithfully reproduces spatial truncation errors for conservative equations. We will show that the moving mesh approach is competitive vs. uniform grids both in accuracy (due to adaptivity) and efficiency. Results for a variety of models 1D and 2D geometries will be presented. L. Chac'on, G. Lapenta, J. Comput. Phys., 212 (2), 703 (2006) G. Lapenta, L. Chac'on, J. Comput. Phys., accepted (2006)

Comparative genomics of Cp8viruses with special reference to Campylobacter phage vB_CjeM_los1, isolated from a slaughterhouse in Ireland.

PubMed

O'Sullivan, Lisa; Lucid, Alan; Neve, Horst; Franz, Charles M A P; Bolton, Declan; McAuliffe, Olivia; Paul Ross, R; Coffey, Aidan

2018-04-23

Campylobacter phage vB_CjeM_Los1 was recently isolated from a slaughterhouse in the Republic of Ireland using the host Campylobacter jejuni subsp. jejuni PT14, and full-genome sequencing and annotation were performed. The genome was found to be 134,073 bp in length and to contain 169 predicted open reading frames. Transmission electron microscopy images of vB_CjeM_Los1 revealed that it belongs to the family Myoviridae, with tail fibres observed in both extended and folded conformations, as seen in T4. The genome size and morphology of vB_CjeM_Los1 suggest that it belongs to the genus Cp8virus, and seven other Campylobacter phages with similar size characteristics have also been fully sequenced. In this work, comparative studies were performed in relation to genomic rearrangements and conservation within each of the eight genomes. None of the eight genomes were found to have undergone internal rearrangements, and their sequences retained more than 98% identity with one another despite the widespread geographical distribution of each phage. Whole-genome phylogenetics were also performed, and clades were shown to be representative of the differing number of tRNAs present in each phage. This may be an indication of lineages within the genus, despite their striking homology.

Redescription of Calyptosuchus (Stagonolepis) wellesi (Archosauria: Pseudosuchia: Aetosauria) from the Late Triassic of the Southwestern United States with a discussion of genera in vertebrate paleontology.

PubMed

Parker, William G

2018-01-01

Calyptosuchus wellesi is a medium-sized desmatosuchian aetosaur common in Adamanian (early to middle Norian) age rocks from the Chinle Formation and Dockum Group of the Western United States. Known chiefly from osteoderms, this taxon has never been fully described and non-osteoderm material assigned to Calyptosuchus has been done so based on questionable criteria. Mapping of aetosaurian elements from the Placerias Quarry allows for the recognition of associated material providing support for referrals of non-osteoderm material. Furthermore, another previously undescribed specimen from the Chinle Formation of Arizona provides more details about this taxon. Presently Calyptosuchus lacks discrete autapomorphies, but can be distinguished from other aetosaurs based on a unique combination of characters supported by a phylogenetic analysis. Calyptosuchus is one of the most common aetosaurians in the Western United States and an index taxon of the early Adamanian biozone. The name Calyptosuchus is retained and encouraged as the applicable genus name for the species wellesi rather than the often used Stagonolepis because assignments of taxa to multi-species genus names are problematic and in this case provides a proposed taxonomic relationship that cannot be unambiguously supported, even by phylogenetic analyses. Because of the inherent limitations of the fossil record, referral of specimens and species to species and genera respectively is an epistemological problem in vertebrate paleontology.

Phylogenetic analyses of the genus Aeromonas based on housekeeping gene sequencing and its influence on systematics.

PubMed

Navarro, Aaron; Martínez-Murcia, Antonio

2018-04-19

The phylogenies derived from housekeeping gene sequence alignments, although mere evolutionary hypotheses, have increased our knowledge about the Aeromonas genetic diversity, providing a robust species delineation framework invaluable for reliable, easy and fast species identification. Previous classifications of Aeromonas, have been fully surpassed by recently developed phylogenetic (natural) classification obtained from the analysis of so-called "molecular chronometers". Despite ribosomal RNAs cannot split all known Aeromonas species, the conserved nature of 16S rRNA offers reliable alignments containing mosaics of sequence signatures which may serve as targets of genus-specific oligonucleotides for subsequent identification/detection tests in samples without culturing. On the contrary, some housekeeping genes coding for proteins show a much better chronometric capacity to discriminate highly related strains. Although both, species and loci, do not all evolve at exactly the same rate, published Aeromonas phylogenies were congruent to each other, indicating that, phylogenetic markers are synchronized and a concatenated multi-gene phylogeny, may be "the mirror" of the entire genomic relationships. Thanks to MLPA approaches, the discovery of new Aeromonas species and strains of rarely isolated species is today more frequent and, consequently, should be extensively promoted for isolate screening and species identification. Although, accumulated data still should be carefully catalogued to inherit a reliable database. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Efficacy of epiphytic bacteria to prevent northern leaf blight caused by Exserohilum turcicum in maize.

PubMed

Sartori, Melina; Nesci, Andrea; García, Julián; Passone, María A; Montemarani, Analía; Etcheverry, Miriam

Eight potential biological control agents (BCAs) were evaluated in planta in order to assess their effectiveness in reducing disease severity of northern leaf blight caused by Exserohilum turcicum. The assay was carried out in greenhouse. Twenty-six-day-old plants, V4 phenological stage, were inoculated with antagonists by foliar spray. Only one biocontrol agent was used per treatment. Ten days after this procedure, all treatments were inoculated with E. turcicum by foliar application. Treatments performed were: C-Et: control of E. turcicum; T1: isolate 1 (Enterococcus genus)+E. turcicum; T2: isolate 2 (Corynebacterium genus)+E. turcicum; T3: isolate 3 (Pantoea genus)+E. turcicum; T4: isolate 4 (Corynebacterium genus)+E. turcicum; T5: isolate 5 (Pantoea genus)+E. turcicum; T6: isolate 6 (Bacillus genus)+E. turcicum; T7: isolate 7 (Bacillus genus)+E. turcicum; T8: isolate 8 (Bacillus genus)+E. turcicum. Monitoring of antagonists on the phyllosphere was performed at different times. Furthermore, the percentage of infected leaves and, plant and leaf incidence were determined. Foliar application of different bacteria significantly reduced the leaf blight between 30-78% and 39-56% at 20 and 39 days respectively. It was observed that in the V10 stage of maize plants, isolate 8 (Bacillus spp.) caused the greatest effect on reducing the severity of northern leaf blight. Moreover, isolate 8 was the potential BCA that showed more stability in the phyllosphere. At 39 days, all potential biocontrol agents had a significant effect on controlling the disease caused by E. turcicum. Copyright © 2016 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Resolving the Tevatron Top Quark Forward-Backward Asymmetry Puzzle: Fully Differential Next-to-Next-to-Leading-Order Calculation.

PubMed

Czakon, Michal; Fiedler, Paul; Mitov, Alexander

2015-07-31

We determine the dominant missing standard model (SM) contribution to the top quark pair forward-backward asymmetry at the Tevatron. Contrary to past expectations, we find a large, around 27%, shift relative to the well-known value of the inclusive asymmetry in next-to-leading order QCD. Combining all known standard model corrections, we find that A(FB)(SM)=0.095±0.007. This value is in agreement with the latest DØ measurement [V. M. Abazov et al. (D0 Collaboration), Phys. Rev. D 90, 072011 (2014)] A(FB)(D∅)=0.106±0.03 and about 1.5σ below that of CDF [T. Aaltonen et al. (CDF Collaboration), Phys. Rev. D 87, 092002 (2013)] A(FB)(CDF)=0.164±0.047. Our result is derived from a fully differential calculation of the next-to-next-to leading order (NNLO) QCD corrections to inclusive top pair production at hadron colliders and includes-without any approximation-all partonic channels contributing to this process. This is the first complete fully differential calculation in NNLO QCD of a two-to-two scattering process with all colored partons.

Resolving the Tevatron Top Quark Forward-Backward Asymmetry Puzzle: Fully Differential Next-to-Next-to-Leading-Order Calculation

NASA Astrophysics Data System (ADS)

Czakon, Michal; Fiedler, Paul; Mitov, Alexander

2015-07-01

We determine the dominant missing standard model (SM) contribution to the top quark pair forward-backward asymmetry at the Tevatron. Contrary to past expectations, we find a large, around 27%, shift relative to the well-known value of the inclusive asymmetry in next-to-leading order QCD. Combining all known standard model corrections, we find that AF BS M = 0.095 ±0.007 . This value is in agreement with the latest DØ measurement [V. M. Abazov et al. (D0 Collaboration), Phys. Rev. D 90, 072011 (2014)] AFBD ∅=0.106 ±0.03 and about 1.5 σ below that of CDF [T. Aaltonen et al. (CDF Collaboration), Phys. Rev. D 87, 092002 (2013)] AFBCDF=0.164 ±0.047 . Our result is derived from a fully differential calculation of the next-to-next-to leading order (NNLO) QCD corrections to inclusive top pair production at hadron colliders and includes—without any approximation—all partonic channels contributing to this process. This is the first complete fully differential calculation in NNLO QCD of a two-to-two scattering process with all colored partons.

Fully Coupled Nonlinear Fluid Flow and Poroelasticity in Arbitrarily Fractured Porous Media: A Hybrid-Dimensional Computational Model

NASA Astrophysics Data System (ADS)

Jin, L.; Zoback, M. D.

2017-10-01

We formulate the problem of fully coupled transient fluid flow and quasi-static poroelasticity in arbitrarily fractured, deformable porous media saturated with a single-phase compressible fluid. The fractures we consider are hydraulically highly conductive, allowing discontinuous fluid flux across them; mechanically, they act as finite-thickness shear deformation zones prior to failure (i.e., nonslipping and nonpropagating), leading to "apparent discontinuity" in strain and stress across them. Local nonlinearity arising from pressure-dependent permeability of fractures is also included. Taking advantage of typically high aspect ratio of a fracture, we do not resolve transversal variations and instead assume uniform flow velocity and simple shear strain within each fracture, rendering the coupled problem numerically more tractable. Fractures are discretized as lower dimensional zero-thickness elements tangentially conforming to unstructured matrix elements. A hybrid-dimensional, equal-low-order, two-field mixed finite element method is developed, which is free from stability issues for a drained coupled system. The fully implicit backward Euler scheme is employed for advancing the fully coupled solution in time, and the Newton-Raphson scheme is implemented for linearization. We show that the fully discretized system retains a canonical form of a fracture-free poromechanical problem; the effect of fractures is translated to the modification of some existing terms as well as the addition of several terms to the capacity, conductivity, and stiffness matrices therefore allowing the development of independent subroutines for treating fractures within a standard computational framework. Our computational model provides more realistic inputs for some fracture-dominated poromechanical problems like fluid-induced seismicity.

Genetic differentiation of the mitochondrial cytochrome oxidase C subunit I gene in genus Paramecium (Protista, Ciliophora).

PubMed

Zhao, Yan; Gentekaki, Eleni; Yi, Zhenzhen; Lin, Xiaofeng

2013-01-01

The mitochondrial cytochrome c oxidase subunit I (COI) gene is being used increasingly for evaluating inter- and intra-specific genetic diversity of ciliated protists. However, very few studies focus on assessing genetic divergence of the COI gene within individuals and how its presence might affect species identification and population structure analyses. We evaluated the genetic variation of the COI gene in five Paramecium species for a total of 147 clones derived from 21 individuals and 7 populations. We identified a total of 90 haplotypes with several individuals carrying more than one haplotype. Parsimony network and phylogenetic tree analyses revealed that intra-individual diversity had no effect in species identification and only a minor effect on population structure. Our results suggest that the COI gene is a suitable marker for resolving inter- and intra-specific relationships of Paramecium spp.

Genetic Differentiation of the Mitochondrial Cytochrome Oxidase c Subunit I Gene in Genus Paramecium (Protista, Ciliophora)

PubMed Central

Zhao, Yan; Gentekaki, Eleni; Yi, Zhenzhen; Lin, Xiaofeng

2013-01-01

Background The mitochondrial cytochrome c oxidase subunit I (COI) gene is being used increasingly for evaluating inter- and intra-specific genetic diversity of ciliated protists. However, very few studies focus on assessing genetic divergence of the COI gene within individuals and how its presence might affect species identification and population structure analyses. Methodology/Principal findings We evaluated the genetic variation of the COI gene in five Paramecium species for a total of 147 clones derived from 21 individuals and 7 populations. We identified a total of 90 haplotypes with several individuals carrying more than one haplotype. Parsimony network and phylogenetic tree analyses revealed that intra-individual diversity had no effect in species identification and only a minor effect on population structure. Conclusions Our results suggest that the COI gene is a suitable marker for resolving inter- and intra-specific relationships of Paramecium spp. PMID:24204730

Delimitation of Umbelopsis (Mucorales, Umbelopsidaceae fam. nov.) based on ITS sequence and RFLP data.

PubMed

Meyer, Wieland; Gams, Walter

2003-03-01

In a continuation of studies started by de Ruiter et al. (1993), all known species of the Mortierella isabellina-group (Micromucor/Umbelopsis clade of O'Donnell et al. 2001) and a few other Mucorales and species of Mortierella were investigated by RFLP (including ITS1, 5.8S, ITS2 and the 5' end of the large subunit rDNA gene) and ITS1 sequence analyses. This monophyletic group is unrelated to Mortierella and is only distantly related to the core group of the Mucoraceae. M. longicollis falls outside the Umbelopsis clade. Molecular data resolved two subclades within the M. isabellina-group; however, they are not correlated with any differences in sporangial wall and shape, spore pigmentation and shape, or sporangiophore branching. Therefore we subsume all taxa in one genus, Umbelopsis. The new family Umbelopsidaceae and the new combinations U. isabellina, U. ramanniana, and U. autotrophica are proposed.

Culicoides and the global epidemiology of bluetongue virus infection.

PubMed

Tabachnick, W J

2004-01-01

The distribution of the bluetongue viruses (BTV) is limited to geographic areas containing competent vector species. All BTV-competent species belong to the genus Culicoides. In the New World, two different BTV epidemiological systems (episystems) occur. Culicoides sonorensis is responsible for transmitting BTV serotypes in North America that differ from South American serotypes transmitted by C. insignis. There are other episystems in the world. The role of different Culicoides vector species and the underlying mechanisms governing their vector capacity for BTV are unknown. It is likely that these vary between Culicoides species and episystems. As a result, our ability to predict and/or mitigate BTV in different episystems will remain problematic. Several complex issues need to be resolved to provide risk assessment and mitigation for BTV. This will require a substantial investment in new research paradigms that investigate details of underlying controlling mechanisms in several species of Culicoides.

Exploring the limits to energy scaling and distant-target delivery of high-intensity midinfrared pulses

NASA Astrophysics Data System (ADS)

Panagiotopoulos, Paris; Kolesik, Miroslav; Moloney, Jerome V.

2016-09-01

We numerically investigate the scaling behavior of midinfrared filaments at extremely high input energies. It is shown that, given sufficient power, kilometer-scale, low-loss atmospheric filamentation is attainable by prechirping the pulse. Fully resolved four-dimensional (x y z t ) simulations show that, while in a spatially imperfect beam the modulation instability can lead to multiple hot-spot formation, the individual filaments are still stabilized by the recently proposed mechanism that relies on the temporal walk-off of short-wavelength radiation.

Ejection mechanisms in the sublayer of a turbulent channel

NASA Technical Reports Server (NTRS)

Jimenez, Javier; Moin, P.; Moser, R.; Keefe, L.

1988-01-01

The structure of the vorticity field in the viscous wall layer of a turbulent channel is studied by examining the results of a fully resolved direct numerical simulation. It is shown that this region is dominated by intense three-dimensional shear layers in which the dominant vorticity component is spanwise. The advection and reproduction processes of these structures are examined and shown to be consistent with the classical generation mechanism for two-dimensional Tollmien-Schlichting waves. This process is fundamentally different from the usually accepted mechanism involving hairpin vortices.

Ultra-small rhenium clusters supported on graphene.

PubMed

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J; Mariscal, Marcelo M; Yacaman, Miguel José

2015-03-28

The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.

Ultra-small rhenium clusters supported on graphene

PubMed Central

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J.; Mariscal, Marcelo M.; Yacaman, Miguel José

2015-01-01

The adsorption of very small rhenium clusters (2 – 13 atoms) supported on graphene was studied with high annular dark field - scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones. PMID:25721176

Revision of New World Species of the Shore-fly Subgenus Allotrichoma Becker of the Genus Allotrichoma with Description of the Subgenus Neotrichoma (Diptera, Ephydridae, Hecamedini)

PubMed Central

Mathis, Wayne N.; Zatwarnicki, Tadeusz

2012-01-01

Abstract The New World species of the subgenera Allotrichoma Becker and Neotrichoma (new subgenus) are revised, including a phylogenetic analysis of the species groups and subgenera within the genus Allotrichoma. For phylogenetic perspective and to document the monophyly of the genus Allotrichoma and its included subgenera and species groups, we also provide a cladistic analysis of genera within the tribe Hecamedini. The ingroup included seven exemplar congeners from within Allotrichoma. Outgroup sampling included exemplars of other genera within Hecamedini and from the putative sister group, Lipochaetini, and to root the analysis, we used an exemplar of the tribe Discocerinini. Analyses with successive weighting and implied weighting recovered a monophyletic Allotrichoma and indicated clades within the genus. Eight new species are described (type locality in parenthesis): Allotrichoma bifurcatum (Utah. Utah: Lake Shore (40°06.9'N, 111°41.8'W; 1370 m)), Allotrichoma dynatum (Oregon. Benton: Finley National Wildlife Refuge (44°24.6'N, 123°19.5'W)), Allotrichoma occidentale (Oregon. Lake: Lakeview (44 km E; Drake Creek; 42°11'N, 119°59.3'W)), Allotrichoma robustum (California. Kern: Kern River (35°16.1'N, 119°18.4'W)), Allotrichoma sabroskyi (New Mexico. Sandoval: La Cueva (Junction of Highways 126 and 4; 35°52'N, 106°38.4'W; 2342 m)), Allotrichoma wallowa (Oregon Baker: Goose Creek (35 km E Baker City; 44°49.2'N, 117°27.79'W; 825 m)), Allotrichoma baliops (Florida. Monroe: Key West (Willie Ward Park; 24°32.9'N, 81°47.9'W)), and Allotrichoma insulare (Dominica. Cabrits Swamp (15°35'N, 61°29'W)). Within Allotrichoma, we recognize three subgenera of which one, Neotrichoma (type species: Allotrichoma atrilabre), is newly described. All known species from the New World are described with an emphasis on structures of the male terminalia, which are fully illustrated. Detailed locality data and distribution maps for the New World species are provided. A lectotype is designated for Discocerina simplex Loew and a neotype is designated for Allotrichoma bezzii Becker. Allotrichoma filiforme Becker, Allotrichoma trispinum Becker, and Allotrichoma dahli Beschovski are reported as new synonyms of Allotrichoma simplex (Loew) and Allotrichoma yosemite Cresson is a new synonym of Allotrichoma atrilabre Cresson. We also clarify the status of previously described species, including those with Holarctic distributions. For perspective and to facilitate genus-group and species-group recognition, the tribe Hecamedini is diagnosed and a key to included genera is provided. PMID:22303122

Phylogenetic relationships and species circumscription in Trentepohlia and Printzina (Trentepohliales, Chlorophyta).

PubMed

Rindi, Fabio; Lam, Daryl W; López-Bautista, Juan M

2009-08-01

Subaerial green microalgae represent a polyphyletic complex of organisms, whose genetic diversity is much higher than their simple morphologies suggest. The order Trentepohliales is the only species-rich group of subaerial algae belonging to the class Ulvophyceae and represents an ideal model taxon to investigate evolutionary patterns of these organisms. We studied phylogenetic relationships in two common genera of Trentepohliales (Trentepohlia and Printzina) by separate and combined analyses of the rbcL and 18S rRNA genes. Trentepohlia and Printzina were not resolved as monophyletic groups. Three main clades were recovered in all analyses, but none corresponded to any trentepohlialean genus as defined based on morphological grounds. The rbcL and 18S rRNA datasets provided congruent phylogenetic signals and similar topologies were recovered in single-gene analyses. Analyses performed on the combined 2-gene dataset inferred generally higher nodal support. The results clarified several taxonomic problems and showed that the evolution of these algae has been characterized by considerable morphological convergence. Trentepohlia abietina and T. flava were shown to be separate species from T. aurea; Printzina lagenifera, T. arborum and T. umbrina were resolved as polyphyletic taxa, whose vegetative morphology appears to have evolved independently in separate lineages. Incongruence between phylogenetic relationships and traditional morphological classification was demonstrated, showing that the morphological characters commonly used in the taxonomy of the Trentepohliales are phylogenetically irrelevant.

Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins.

PubMed

Claramunt, Santiago

2014-09-01

Relationships among genera in the tribe Synallaxini have proved difficult to resolve. In this study, I investigate relationships among Synallaxis, Certhiaxis and Schoeniophylax using DNA sequences from the mitochondrion and three nuclear regions. I implemented novel primers and protocols for amplifying and sequencing autosomal and sex-linked introns in Furnariidae that resolved basal relationships in the Synallaxini with strong support. Synallaxis propinqua is sister to Schoeniophylax phryganophilus, and together they form a clade with Certhiaxis. The results are robust to analytical approaches when all genomic regions are analyzed jointly (parsimony, maximum likelihood, and species-tree analysis) and the same basal relationships are recovered by most genomic regions when analyzed separately. A sister relationship between S. propinqua, an Amazonian river island specialist, and S. phryganophilus, from the Paraná River basin region, reveals a new biogeographic pattern shared by at least other four pairs of taxa with similar distributions and ecologies. Estimates of divergence times for these five pairs span from the late Miocene to the Pleistocene. Identification of the historical events that produced this pattern is difficult and further advances will require additional studies of the taxa involved and a better understanding of the recent environmental history of South America. A new classification is proposed for the Synallaxini, including the description of a new genus for S. propinqua. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular strain typing of Brucella abortus isolates from Italy by two VNTR allele sizing technologies.

PubMed

De Santis, Riccardo; Ancora, Massimo; De Massis, Fabrizio; Ciammaruconi, Andrea; Zilli, Katiuscia; Di Giannatale, Elisabetta; Pittiglio, Valentina; Fillo, Silvia; Lista, Florigio

2013-10-01

Brucellosis, one of the most important re-emerging zoonoses in many countries, is caused by bacteria belonging to the genus Brucella. Furthermore these bacteria represent potential biological warfare agents and the identification of species and biovars of field strains may be crucial for tracing back source of infection, allowing to discriminate naturally occurring outbreaks instead of bioterrorist events. In the last years, multiple-locus variable-number tandem repeat analysis (MLVA) has been proposed as complement of the classical biotyping methods and it has been applied for genotyping large collections of Brucella spp. At present, the MLVA band profiles may be resolved by automated or manual procedures. The Lab on a chip technology represents a valid alternative to standard genotyping techniques (as agarose gel electrophoresis) and it has been previously used for Brucella genotyping. Recently, a new high-throughput genotyping analysis system based on capillary gel electrophoresis, the QIAxcel, has been described. The aim of the study was to evaluate the ability of two DNA sizing equipments, the QIAxcel System and the Lab chip GX, to correctly call alleles at the sixteen loci including one frequently used MLVA assay for Brucella genotyping. The results confirmed that these technologies represent a meaningful advancement in high-throughput Brucella genotyping. Considering the accuracy required to confidently resolve loci discrimination, QIAxcel shows a better ability to measure VNTR allele sizes compared to LabChip GX.

Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

PubMed

Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

2012-06-01

The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

An Immersed Boundary - Adaptive Mesh Refinement solver (IB-AMR) for high fidelity fully resolved wind turbine simulations

NASA Astrophysics Data System (ADS)

Angelidis, Dionysios; Sotiropoulos, Fotis

2015-11-01

The geometrical details of wind turbines determine the structure of the turbulence in the near and far wake and should be taken in account when performing high fidelity calculations. Multi-resolution simulations coupled with an immersed boundary method constitutes a powerful framework for high-fidelity calculations past wind farms located over complex terrains. We develop a 3D Immersed-Boundary Adaptive Mesh Refinement flow solver (IB-AMR) which enables turbine-resolving LES of wind turbines. The idea of using a hybrid staggered/non-staggered grid layout adopted in the Curvilinear Immersed Boundary Method (CURVIB) has been successfully incorporated on unstructured meshes and the fractional step method has been employed. The overall performance and robustness of the second order accurate, parallel, unstructured solver is evaluated by comparing the numerical simulations against conforming grid calculations and experimental measurements of laminar and turbulent flows over complex geometries. We also present turbine-resolving multi-scale LES considering all the details affecting the induced flow field; including the geometry of the tower, the nacelle and especially the rotor blades of a wind tunnel scale turbine. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482 and the Sandia National Laboratories.

Quantification of neutral human milk oligosaccharides by graphitic carbon HPLC with tandem mass spectrometry

PubMed Central

Bao, Yuanwu; Chen, Ceng; Newburg, David S.

2012-01-01

Defining the biologic roles of human milk oligosaccharides (HMOS) requires an efficient, simple, reliable, and robust analytical method for simultaneous quantification of oligosaccharide profiles from multiple samples. The HMOS fraction of milk is a complex mixture of polar, highly branched, isomeric structures that contain no intrinsic facile chromophore, making their resolution and quantification challenging. A liquid chromatography-mass spectrometry (LC-MS) method was devised to resolve and quantify 11 major neutral oligosaccharides of human milk simultaneously. Crude HMOS fractions are reduced, resolved by porous graphitic carbon HPLC with a water/acetonitrile gradient, detected by mass spectrometric specific ion monitoring, and quantified. The HPLC separates isomers of identical molecular weights allowing 11 peaks to be fully resolved and quantified by monitoring mass to charge (m/z) ratios of the deprotonated negative ions. The standard curves for each of the 11 oligosaccharides is linear from 0.078 or 0.156 to 20 μg/mL (R2 > 0.998). Precision (CV) ranges from 1% to 9%. Accuracy is from 86% to 104%. This analytical technique provides sensitive, precise, accurate quantification for each of the 11 milk oligosaccharides and allows measurement of differences in milk oligosaccharide patterns between individuals and at different stages of lactation. PMID:23068043

Towards a Viscous Wall Model for Immersed Boundary Methods

NASA Technical Reports Server (NTRS)

Brehm, Christoph; Barad, Michael F.; Kiris, Cetin C.

2016-01-01

Immersed boundary methods are frequently employed for simulating flows at low Reynolds numbers or for applications where viscous boundary layer effects can be neglected. The primary shortcoming of Cartesian mesh immersed boundary methods is the inability of efficiently resolving thin turbulent boundary layers in high-Reynolds number flow application. The inefficiency of resolving the thin boundary is associated with the use of constant aspect ratio Cartesian grid cells. Conventional CFD approaches can efficiently resolve the large wall normal gradients by utilizing large aspect ratio cells near the wall. This paper presents different approaches for immersed boundary methods to account for the viscous boundary layer interaction with the flow-field away from the walls. Different wall modeling approaches proposed in previous research studies are addressed and compared to a new integral boundary layer based approach. In contrast to common wall-modeling approaches that usually only utilize local flow information, the integral boundary layer based approach keeps the streamwise history of the boundary layer. This allows the method to remain effective at much larger y+ values than local wall modeling approaches. After a theoretical discussion of the different approaches, the method is applied to increasingly more challenging flow fields including fully attached, separated, and shock-induced separated (laminar and turbulent) flows.

Imaging of acute and chronic thromboembolic disease: state of the art.

PubMed

Ruggiero, A; Screaton, N J

2017-05-01

Acute pulmonary embolism (PE) is a life-threatening condition that requires prompt diagnosis and treatment. Recent advances in imaging allow acute and rapid recognition even by the non-specialist radiologist. Most acute emboli resolve on anticoagulation without sequelae; however, some emboli fail to fully resolve becoming endothelialised with the development of chronic thromboembolic disease (CTED). Increased pulmonary vascular resistance arising from CTED may lead to chronic thromboembolic pulmonary hypertension (CTEPH) a debilitating disease affecting up to 5% of survivors of acute PE. Diagnostic evaluation is more complex in CTEPH/CTED than acute PE with subtle imaging features often being overlooked or misinterpreted. Differentiation of acute from chronic PE and from other forms of pulmonary hypertension has profound therapeutic implications. Diverse imaging techniques are available to diagnose and monitor PEs both in the acute and chronic setting. Broadly they include techniques that provide data on lung parenchymal perfusion (ventilation-perfusion [VQ] scintigraphy), angiographic techniques (computed tomography [CT], magnetic resonance imaging [MRI], and invasive angiography) or a combination of both (MR angiography and time-resolved angiography or dual-energy CT angiography). This review aims to describe state of the art imaging highlighting the strength and weaknesses of individual techniques in the diagnosis of acute and chronic PE. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Diffraction in neutron imaging-A review

NASA Astrophysics Data System (ADS)

Woracek, Robin; Santisteban, Javier; Fedrigo, Anna; Strobl, Markus

2018-01-01

Neutron imaging is a highly successful experimental technique ever since adequate neutron sources were available. In general, neutron imaging is performed with a wide wavelength spectrum for best flux conditions in transmission geometry. Neutrons provide outstanding features in the penetration of many structural materials, which often makes them more suited for bulk sample studies than other forms of radiation, often in particular as they are also highly sensitive to some light elements, especially Hydrogen. In contrast to neutron scattering applications, imaging resolves macroscopic structures, nowadays down to, in the best case, below 10 micrometre, directly in real space. However, since more than a decade there is a growing number of techniques and applications in neutron imaging that - supported by powerful neutron sources - are taking advantage of wavelength resolved measurements. In this review we summarize and discuss this outstanding development and how wavelength resolved transmission neutron imaging is successfully exploiting diffraction mechanisms to access crystal structure information in the Angstrom regime, which conventionally is probed in reciprocal space by diffraction techniques. In particular the combination of information gained in real space and on crystallographic length scales makes this neutron imaging technique a valuable tool for a wide range of new applications, while it also qualifies neutron imaging to fully profit from the new generation of powerful pulsed neutron sources.

Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): Another star phylogeny?

PubMed Central

2011-01-01

Background The family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but these studies have included only a fraction of the extant diversity (a maximum of 26 out of the 46 currently recognized genera) and have failed to resolve deep relationships among internal clades. Here we readdress the systematics of pteropodids by applying a strategy to try to resolve ancient relationships within Pteropodidae, while providing further insight into subgroup membership, by 1) increasing the taxonomic sample to 42 genera; 2) increasing the number of characters (to >8,000 bp) and nuclear genomic representation; 3) minimizing missing data; 4) controlling for sequence bias; and 5) using appropriate data partitioning and models of sequence evolution. Results Our analyses recovered six principal clades and one additional independent lineage (consisting of a single genus) within Pteropodidae. Reciprocal monophyly of these groups was highly supported and generally congruent among the different methods and datasets used. Likewise, most relationships within these principal clades were well resolved and statistically supported. Relationships among the 7 principal groups, however, were poorly supported in all analyses. This result could not be explained by any detectable systematic bias in the data or incongruence among loci. The SOWH test confirmed that basal branches' lengths were not different from zero, which points to closely-spaced cladogenesis as the most likely explanation for the poor resolution of the deep pteropodid relationships. Simulations suggest that an increase in the amount of sequence data is likely to solve this problem. Conclusions The phylogenetic hypothesis generated here provides a robust framework for a revised cladistic classification of Pteropodidae into subfamilies and tribes and will greatly contribute to the understanding of character evolution and biogeography of pteropodids. The inability of our data to resolve the deepest relationships of the major pteropodid lineages suggests an explosive diversification soon after origin of the crown pteropodids. Several characteristics of pteropodids are consistent with this conclusion, including high species diversity, great morphological diversity, and presence of key innovations in relation to their sister group. PMID:21961908

Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA.

PubMed

Dutton, P H; Davis, S K; Guerra, T; Owens, D

1996-06-01

Marine turtles are divided into two families, the Dermochelyidae and the Cheloniidae. The majority of species are currently placed within the two tribes of the Cheloniidae, the Chelonini and the Carettini, but debate continues over generic and tribal affinities as well as species boundaries. We used nucleotide sequences (907 bp) from the ND4-LEU tRNA region and the control region (526 bp) of mitochondrial DNA to resolve areas of uncertainty in marine turtle (Chelonioidae) systematics. The ND4-LEU tRNA fragment was more conserved than the fragment from the control region, with sequence divergences ranging from 0.026 to 0.148 and 0.067 to 0.267, respectively. Parsimony analysis based only on the ND4-LEU tRNA data suggests that the hawksbill, Eretmochelys imbricata, lies within the tribe Carettni and is closely related to the genus Caretta, but could not resolve the position of the flatback, Natator depressus. A similar analysis based only on the control region sequence data suggested that N. depressus is affiliated with the Chelonini, but failed to resolve the position of E. imbricata and the loggerhead, Caretta caretta. In contrast to these results, the combination of both data sets with published cytochrome b data produced a phylogeny based on 1924 bp of sequence data which resolves the position of E. imbricata relative to Caretta and Lepidochelys and joins N. depressus as sister to the Carettini. Based on the molecular data, the Chelonini contains the Chelonia species, while the Carettini contains the remaining species of Cheloniidae. The control region sequence divergence between Pacific and Atlantic populations of the leatherback, Dermochelys coriacea, was relatively low (0.0081) when compared with the green turtle, Chelonia mydas (0.071-0.074). Atlantic and Pacific populations of Ch. mydas were found to be paraphyletic with respect to the black turtle, Ch. agassizi, suggesting that the current taxonomic designations within the Pacific Chelonia are questionable. This analysis shows the utility of combining sequence data for different regions of mtDNA that by themselves are insufficient to obtain robust phylogenies.

Characterization of Two Novel Gammapapillomaviruses, HPV179 and HPV184, Isolated from Common Warts of a Renal-Transplant Recipient

PubMed Central

Hošnjak, Lea; Kocjan, Boštjan J.; Pirš, Branko; Seme, Katja; Poljak, Mario

2015-01-01

Gammapapillomavirus (Gamma-PV) is a diverse and rapidly expanding PV-genus, currently consisting of 76 fully characterized human papillomavirus (HPV) types. In this study, DNA genomes of two novel HPV types, HPV179 and HPV184, obtained from two distinct facial verrucae vulgares specimens of a 64 year-old renal-transplant recipient, were fully cloned, sequenced and characterized. HPV179 and HPV184 genomes comprise 7,228-bp and 7,324-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2); the non-coding region is typically positioned between L1 and E6 genes. Phylogenetic analysis of the L1 nucleotide sequence placed both novel types within the Gamma-PV genus: HPV179 was classified as a novel member of species Gamma-15, additionally containing HPV135 and HPV146, while HPV184 was classified as a single member of a novel species Gamma-25. HPV179 and HPV184 type-specific quantitative real-time PCRs were further developed and used in combination with human beta-globin gene quantitative real-time PCR to determine the prevalence and viral load of the novel types in the patient’s facial warts and several follow-up skin specimens, and in a representative collection, a total of 569 samples, of HPV-associated benign and malignant neoplasms, hair follicles and anal and oral mucosa specimens obtained from immunocompetent individuals. HPV179 and HPV184 viral loads in patients’ facial warts were estimated to be 2,463 and 3,200 genome copies per single cell, respectively, suggesting their active role in the development of common warts in organ-transplant recipients. In addition, in this particular patient, both novel types had established a persistent infection of the skin for more than four years. Among immunocompetent individuals, HPV179 was further detected in low-copy numbers in a few skin specimens, indicating its cutaneous tissue tropism, while HPV184 was further detected in low-copy numbers in one mucosal and a few skin specimens, suggesting its dual tissue tropism. PMID:25748516

Molecular phylogeny and genome size evolution of the genus Betula (Betulaceae)

PubMed Central

Wang, Nian; McAllister, Hugh A.; Bartlett, Paul R.; Buggs, Richard J. A.

2016-01-01

Background and Aims Betula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus. Methods Internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry. Key Results As expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera. Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa. Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the ITS phylogeny. Species with large genomes tend to have narrow ranges. Conclusions Betula grossa may have formed via allopolyploidization between parents in subgenus Betula and subgenus Aspera. Betula bomiensis may also be a wide allopolyploid. Betula corylifolia may be a parental species of allopolyploids in the subsection Chinenses. Placements of B. maximowicziana, B. michauxii and B. nigra need further investigation. This analysis, in line with previous studies, suggests that section Apterocaryon is not monophyletic and thus dwarfism has evolved repeatedly in different lineages of Betula. Polyploidization has occurred many times independently in the evolution of Betula. PMID:27072644

Mcphersonarcys, a new genus for Pentatomaaequalis Say (Heteroptera: Pentatomidae)

USDA-ARS?s Scientific Manuscript database

A new monotypic genus, Mcphersonarcys, is erected to hold Pentatoma aequalis Say, a species formerly placed in the genus Hymenarcys. Based on the distribution of 19 character-states Hymenarcys forms a clade with its sister genus Coenus. Both genera are related to the large genus Euschistus. Mcphe...

Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.

PubMed

Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

1995-10-01

The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected].

Historical epistemology of the body-mind interaction in psychiatry

PubMed Central

Berrios, German E.

2018-01-01

This paper deals with the history of the relationship between the mind-body dualism and the epistemology of madness. Earlier versions of such dualism posed little problem in regard to the manner of their communication. The Cartesian view that mind and body did, in fact, name different substances introduced a problem of incommunicability that is yet to be resolved. Earlier views that madness may be related to changes in the brain began gaining empirical support during the 17th century. Writers on madness chose to resolve the mind-body problem differently Some stated that such communication was not needed; others, that mind was a redundant concept, as madness could be fully explained by structural changes in the brain; and yet others described psychological spaces for madness to inhabit as a symbolic conflict. The epistemology of the neurosciences bypasses the conundrum, as it processes all together the variables representing the brain, subjectivity, and behavior and bridges the “philosophical” gap by means of correlational structures. PMID:29946206

Alkali-metal induced band structure deformation investigated by angle-resolved photoemission spectroscopy and first-principles calculations

NASA Astrophysics Data System (ADS)

Ito, S.; Feng, B.; Arita, M.; Someya, T.; Chen, W.-C.; Takayama, A.; Iimori, T.; Namatame, H.; Taniguchi, M.; Cheng, C.-M.; Tang, S.-J.; Komori, F.; Matsuda, I.

2018-04-01

Alkali-metal adsorption on the surface of materials is widely used for in situ surface electron doping, particularly for observing unoccupied band structures by angle-resolved photoemission spectroscopy (ARPES). However, the effects of alkali-metal atoms on the resulting band structures have yet to be fully investigated, owing to difficulties in both experiments and calculations. Here, we combine ARPES measurements on cesium-adsorbed ultrathin bismuth films with first-principles calculations of the electronic charge densities and demonstrate a simple method to evaluate alkali-metal induced band deformation. We reveal that deformation of bismuth surface bands is directly correlated with vertical charge-density profiles at each electronic state of bismuth. In contrast, a change in the quantized bulk bands is well described by a conventional rigid-band-shift picture. We discuss these two aspects of the band deformation holistically, considering spatial distributions of the electronic states and cesium-bismuth hybridization, and provide a prescription for applying alkali-metal adsorption to a wide range of materials.

Time-frequency model for echo-delay resolution in wideband biosonar.

PubMed

Neretti, Nicola; Sanderson, Mark I; Intrator, Nathan; Simmons, James A

2003-04-01

A time/frequency model of the bat's auditory system was developed to examine the basis for the fine (approximately 2 micros) echo-delay resolution of big brown bats (Eptesicus fuscus), and its performance at resolving closely spaced FM sonar echoes in the bat's 20-100-kHz band at different signal-to-noise ratios was computed. The model uses parallel bandpass filters spaced over this band to generate envelopes that individually can have much lower bandwidth than the bat's ultrasonic sonar sounds and still achieve fine delay resolution. Because fine delay separations are inside the integration time of the model's filters (approximately 250-300 micros), resolving them means using interference patterns along the frequency dimension (spectral peaks and notches). The low bandwidth content of the filter outputs is suitable for relay of information to higher auditory areas that have intrinsically poor temporal response properties. If implemented in fully parallel analog-digital hardware, the model is computationally extremely efficient and would improve resolution in military and industrial sonar receivers.

The 3D model control of image processing

NASA Technical Reports Server (NTRS)

Nguyen, An H.; Stark, Lawrence

1989-01-01

Telerobotics studies remote control of distant robots by a human operator using supervisory or direct control. Even if the robot manipulators has vision or other senses, problems arise involving control, communications, and delay. The communication delays that may be expected with telerobots working in space stations while being controlled from an Earth lab have led to a number of experiments attempting to circumvent the problem. This delay in communication is a main motivating factor in moving from well understood instantaneous hands-on manual control to less well understood supervisory control; the ultimate step would be the realization of a fully autonomous robot. The 3-D model control plays a crucial role in resolving many conflicting image processing problems that are inherent in resolving in the bottom-up approach of most current machine vision processes. The 3-D model control approach is also capable of providing the necessary visual feedback information for both the control algorithms and for the human operator.

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, C.; Marx, A.; Epp, S. W.

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

DOE PAGES

Mueller, C.; Marx, A.; Epp, S. W.; ...

2015-08-18

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Birth of a resonant attosecond wavepacket

NASA Astrophysics Data System (ADS)

Argenti, L.; Gruson, V.; Barreau, L.; Jimenez-Galan, A.; Risoud, F.; Caillat, J.; Maquet, A.; Carre, B.; Lepetit, F.; Hergott, J.-F.; Ruchon, T.; Taieb, R.; Martin, F.; Salieres, P.

2016-05-01

Both amplitude and phase are needed to characterize the dynamics of a wavepacket. However, such characterization is difficult when both attosecond and femtosecond timescales are involved, as it is the case for broadband photoionization to a continuum encompassing autoionizing states. Here we demonstrate that Rainbow RABBIT, a new attosecond interferometry, allows the measurement of amplitude and phase of a photoelectron wavepacket created through a Fano resonance with unprecedented precision. In the experiment, a tunable attosecond pulse train is combined with the fundamental laser pulse to induce two-photon transitions in helium via an intermediate autoionizing state. From the energy and time-delay resolved signal, we fully reconstruct the resonant electron wavepacket as it builds up in the continuum. Measurements accurately match the predictions of a new time-resolved multi-photon resonant model, known to reproduce ab initio calculations. This agreement confirms the potential of Rainbow RABBIT to investigate photoemission delays in ultrafast processes governed by electron correlation, as well as to control structured electron wavepackets. now at Univ. Central Florida, Orlando, FL (USA).

Black hole firewalls require huge energy of measurement

NASA Astrophysics Data System (ADS)

Hotta, Masahiro; Matsumoto, Jiro; Funo, Ken

2014-06-01

The unitary moving mirror model is one of the best quantum systems for checking the reasoning of the original firewall paradox of Almheiri et al. [J. High Energy Phys. 02 (2013) 062] in quantum black holes. Though the late-time part of radiations emitted from the mirror is fully entangled with the early part, no firewall exists with a deadly, huge average energy flux in this model. This is because the high-energy entanglement structure of the discretized systems in almost maximally entangled states is modified so as to yield the correct description of low-energy effective field theory. Furthermore, the strong subadditivity paradox of firewalls is resolved using nonlocality of general one-particle states and zero-point fluctuation entanglement. Due to the Reeh-Schlieder theorem in quantum field theory, another firewall paradox is inevitably raised with quantum remote measurements in the model. We resolve this paradox from the viewpoint of the energy cost of measurements. No firewall appears, as long as the energy for the measurement is much smaller than the ultraviolet cutoff scale.

Single-spin stochastic optical reconstruction microscopy

PubMed Central

Pfender, Matthias; Aslam, Nabeel; Waldherr, Gerald; Neumann, Philipp; Wrachtrup, Jörg

2014-01-01

We experimentally demonstrate precision addressing of single-quantum emitters by combined optical microscopy and spin resonance techniques. To this end, we use nitrogen vacancy (NV) color centers in diamond confined within a few ten nanometers as individually resolvable quantum systems. By developing a stochastic optical reconstruction microscopy (STORM) technique for NV centers, we are able to simultaneously perform sub–diffraction-limit imaging and optically detected spin resonance (ODMR) measurements on NV spins. This allows the assignment of spin resonance spectra to individual NV center locations with nanometer-scale resolution and thus further improves spatial discrimination. For example, we resolved formerly indistinguishable emitters by their spectra. Furthermore, ODMR spectra contain metrology information allowing for sub–diffraction-limit sensing of, for instance, magnetic or electric fields with inherently parallel data acquisition. As an example, we have detected nuclear spins with nanometer-scale precision. Finally, we give prospects of how this technique can evolve into a fully parallel quantum sensor for nanometer resolution imaging of delocalized quantum correlations. PMID:25267655

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

2016-02-05

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion ismore » used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.« less

Infomechanical specializations for prey capture in knifefish

NASA Astrophysics Data System (ADS)

Maciver, Malcolm; Patankar, Neelesh; Curet, Oscar; Shirgaonkar, Anup

2007-11-01

How does an animal's mechanics and its information acquisition system work together to solve crucial behavioral tasks? We examine this question for the black ghost weakly electric knifefish (Apteronotus albifrons), which is a leading model system for the study of sensory processing in vertebrates. These animals hunt at night by detecting perturbations of a self-generated electric field caused by prey. While the fish searches for prey, it pitches at 30 . Fully resolved Navier-Stokes simulations of their swimming, which occurs through undulations of a long ribbon-like fin along the bottom edge of the body, indicates that this configuration enables maximal thrust while minimizing pitch moment. However, pitching the body also increases drag. Our analysis of the sensory volume for detection of prey shows this volume to be similar to a cylinder around the body. Thus, pitching the body enables a greater swept volume of scanned fluid. Examining the mechanical and information acquisition demands on the animal in this task gives insight into how these sometimes conflicting demands are resolved.

Sympatric species of Hibbertia (Dilleniaceae) vary in dormancy break and germination requirements: implications for classifying morphophysiological dormancy in Mediterranean biomes

PubMed Central

Hidayati, Siti N.; Walck, Jeffrey L.; Merritt, David J.; Turner, Shane R.; Turner, David W.; Dixon, Kingsley W.

2012-01-01

Background and Aims Several ecologically important plant families in Mediterranean biomes have seeds with morphophysiological dormancy (MPD) but have been poorly studied. The aim of this study was to understand the seed ecology of these species by focusing on the prominent, yet intractably dormant Australian genus Hibbertia. It was hypothesized that the slow germination in species of this genus is caused by a requirement for embryo growth inside the seed before germination, and that initiation of embryo growth is reliant upon a complex sequence of environmental cues including seasonal fluctuations in temperature and moisture, and an interplay with light and smoke. Using the results, the classification of the MPD level in species of Hibbertia is considered. Methods Four species of Hibbertia in winter rainfall south-western Australia were selected. These species, whilst differing in geographic distributions, are variously sympatric, and all are important understorey components of plant communities. The following aspects related to dormancy break, embryo growth and germination were investigated: temperature and moisture requirements; effects of karrikinolide, gibberellic acid and aerosol smoke; and phenology. Key Results Following exposure to wet/dry cycles at low or high temperatures, embryo growth and germination occurred, albeit slowly in all species at low temperatures when moisture was unlimited, corresponding to winter in south-west Australia. Photo regime influenced germination only in H. racemosa. Aerosol smoke triggered substantial germination during the 1st germination season in H. huegelii and H. hypericoides. Conclusions Although the study species are con-generic, sympatric and produce seeds of identical morphology, they possessed different dormancy-break and germination requirements. The physiological component of MPD was non-deep in H. racemosa but varied in the other three species where more deeply dormant seeds required >1 summer to overcome dormancy and, thus, germination was spread over time. Embryos grew during winter, but future studies need to resolve the role of cold versus warm stratification by using constant temperature regimes. To include Mediterranean species with MPD, some modifications to the current seed-dormancy classification system may need consideration: (a) wet/dry conditions for warm stratification and (b) a relatively long period for warm stratification. These outcomes have important implications for improving experimental approaches to resolve the effective use of broadcast seed for ecological restoration. PMID:22362661

Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia.

PubMed

Dobritsa, Anatoly P; Samadpour, Mansour

2016-08-01

It has been proposed to split the genus Burkholderia into two genera according to phylogenetic clustering: (1) a genus retaining this name and consisting mainly of animal and plant pathogens and (2) the genus Paraburkholderia including so-called environmental bacteria. The latter genus name has been validly published recently. During the period between the effective and valid publications of the genus name Paraburkholderia, 16 novel species of the genus Burkholderiawere described, but only two of them can be classified as members of this genus based on the emended genus description. Analysis of traits and phylogenetic positions of the other 11 species shows that they belong to the genus Paraburkholderia, and we propose to transfer them to this genus. The reclassified species names are proposed as Paraburkholderia dipogonis comb. nov., Paraburkholderia ginsengiterrae comb. nov., Paraburkholderia humisilvae comb. nov., Paraburkholderia insulsa comb. nov., Paraburkholderia kirstenboschensis comb. nov., Paraburkholderia metalliresistens comb. nov., Paraburkholderia monticola comb. nov., Paraburkholderia panaciterrae comb. nov., Paraburkholderia rhizosphaerae comb. nov., Paraburkholderia solisilvae comb. nov. and Paraburkholderia susongensis comb. nov. The remaining three species are transferred to the new genus Caballeronia gen. nov. proposed to accommodate twelve species of the genera Burkholderia and Paraburkholderia forming a distinctive clade in phylogenetic trees. The new genus members are Caballeronia choica comb. nov., Caballeronia cordobensis comb. nov., Caballeronia glathei comb. nov., Caballeronia grimmiae comb. nov., Caballeronia humi comb. nov., Caballeronia megalochromosomata comb. nov., Caballeronia jiangsuensis comb. nov., Caballeronia sordidicola comb. nov., Caballeronia telluris comb. nov., Caballeronia terrestris comb. nov., Caballeronia udeis comb. nov., and Caballeronia zhejiangensis comb. nov.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Time-resolved single-turnover of caa(3) oxidase from Thermus thermophilus. Fifth electron of the fully reduced enzyme converts O(H) into E(H) state.

PubMed

Siletsky, Sergey A; Belevich, Ilya; Belevich, Nikolai P; Soulimane, Tewfik; Verkhovsky, Michael I

2011-09-01

The oxidative part of the catalytic cycle of the caa(3)-type cytochrome c oxidase from Thermus thermophilus was followed by time-resolved optical spectroscopy. Rate constants, chemical nature and the spectral properties of the catalytic cycle intermediates (Compounds A, P, F) reproduce generally the features typical for the aa(3)-type oxidases with some distinctive peculiarities caused by the presence of an additional 5-th redox-center-a heme center of the covalently bound cytochrome c. Compound A was formed with significantly smaller yield compared to aa(3) oxidases in general and to ba(3) oxidase from the same organism. Two electrons, equilibrated between three input redox-centers: heme a, Cu(A) and heme c are transferred in a single transition to the binuclear center during reduction of the compound F, converting the binuclear center through the highly reactive O(H) state into the final product of the reaction-E(H) (one-electron reduced) state of the catalytic site. In contrast to previous works on the caa(3)-type enzymes, we concluded that the finally produced E(H) state of caa(3) oxidase is characterized by the localization of the fifth electron in the binuclear center, similar to the O(H)→E(H) transition of the aa(3)-type oxidases. So, the fully-reduced caa(3) oxidase is competent in rapid electron transfer from the input redox-centers into the catalytic heme-copper site. 2011 Elsevier B.V. All rights reserved.

A fully resolved active musculo-mechanical model for esophageal transport

NASA Astrophysics Data System (ADS)

Kou, Wenjun; Bhalla, Amneet Pal Singh; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

2015-10-01

Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multi-layered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, and the esophagus is modeled as an actively contracting, fiber-reinforced tube. Before considering the full model of the esophagus, however, we first consider a standard benchmark problem of flow past a cylinder. Next a simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Finally, three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal layers, are extensively tested. To our knowledge, these simulations are the first of their kind to incorporate the bolus, the multi-layered esophagus tube, and muscle activation into an integrated model. Consistent with experimental observations, our simulations capture the pressure peak generated by the muscle activation pulse that travels along the bolus tail. These fully resolved simulations provide new insights into roles of the mucosal layers during bolus transport. In addition, the information on pressure and the kinematics of the esophageal wall resulting from the coordination of muscle activation is provided, which may help relate clinical data from manometry and ultrasound images to the underlying esophageal motor function.

A fully resolved active musculo-mechanical model for esophageal transport

PubMed Central

Kou, Wenjun; Bhalla, Amneet Pal Singh; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

2015-01-01

Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multilayered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, and the esophagus is modeled as an actively contracting, fiber-reinforced tube. Before considering the full model of the esophagus, however, we first consider a standard benchmark problem of flow past a cylinder. Next a simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Finally, three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal layers, are extensively tested. To our knowledge, these simulations are the first of their kind to incorporate the bolus, the multi-layered esophagus tube, and muscle activation into an integrated model. Consistent with experimental observations, our simulations capture the pressure peak generated by the muscle activation pulse that travels along the bolus tail. These fully resolved simulations provide new insights into roles of the mucosal layers during bolus transport. In addition, the information on pressure and the kinematics of the esophageal wall resulting from the coordination of muscle activation is provided, which may help relate clinical data from manometry and ultrasound images to the underlying esophageal motor function. PMID:26190859

Fully quantum-state resolved study of NO{sub 2} photodissociation. Correlated NO({sup 2}{Pi}{sub {Omega}}, {nu} = 0 J,A) + O({sup 3}P{sub j}) distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanov, A.; Bieler, C.R.; Reisler, H.

1995-09-14

Relative O({sup 3}P{sub j} = 2.1.0) spin-orbit populations correlated with specific NO[{sup 2}{Pi}{sub {Omega}} = {1/2}, 3/2; {nu} = 0; f; {Lambda} = {Pi}(A{prime}), {Pi}(A{double_prime})] product states were obtained following photolysis of NO{sub 2} at excess energies E{sup {+-}} = 390, 425, and 1054 cm{sup -1}. These fully quantum state-resolved measurements were carried out by recording spatial profiles of recoiling NO({sup 2}{Pi}{sub {Omega}}, J, {Lambda}) products using polarized radiation for photolysis and state-selective laser ionization detection. The relative O({sup 3}P{sub j}) populations correlated with each NO({sup 2}{Pi}{sub {Omega}}, J, {Lambda}) state show marked fluctuations at each excess energy as amore » function of rotational state and {Lambda}-doublet component. The relative populations also fluctuate as a function of excess energy. The O({sup 3}P{sub j}) spin-orbit population ratios, when averaged over all measurements, exhibit distributions that are colder than statistical, in agreement with previous results. In particular, we find that, on average, O({sup 3}P{sub 1}):O({sup 3}P{sub 2}) population ratios correlated with the ground NO({sup 2}{Pi}{sub {1/2}}) state are colder than the corresponding ratios correlated with the excited NO({sup 2}{Pi}{sub 3/2}) spin-orbit state. These results are in agreement with the state-specific calculations of Katigiri and Kato. 45 refs., 12 figs., 3 tabs.« less

Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

NASA Astrophysics Data System (ADS)

Mitric, Roland

The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

PHAT+MaNGA: Using resolved stellar populations to improve the recovery of star formation histories from galaxy spectra

NASA Astrophysics Data System (ADS)

Byler, Nell

2017-08-01

Stellar Population Synthesis (SPS) models are routinely used to interpret extragalactic observations at all redshifts. Currently, the dominant source of uncertainty in SPS modeling lies in the degeneracies associated with synthesizing and fitting complex stellar populations to observed galaxy spectra. To remedy this, we propose an empirical calibration of SPS models using resolved stellar population observations from Hubble Space Telescope (HST) to constrain the stellar masses, ages, and star formation histories (SFHs) in regions matched to 2D spectroscopic observations from MaNGA. We will take advantage of the state of the art observations from the Panchromatic Hubble Andromeda Treasury (PHAT), which maps the dust content, history of chemical enrichment, and history of star formation across the disk of M31 in exquisite detail. Recently, we have coupled these observations with an unprecedented, spatially-resolved suite of IFU observations from MaNGA. With these two comprehensive data sets we can use the true underlying stellar properties from PHAT to properly interpret the aperture-matched integrated spectra from MaNGA. Our MaNGA observations target 20 regions within the PHAT footprint that fully sample the available range in metallicity, SFR, dust content, and stellar density. This transformative dataset will establish a comprehensive link between resolved stellar populations and the inferred properties of unresolved stellar populations across astrophysically important environments. The net data product will be a library of galaxy spectra matched to the true underlying stellar properties, a comparison set that has lasting legacy value for the extragalactic community.

Drug-related problems and pharmacist interventions in a cohort of patients with asthma and chronic obstructive pulmonary disease.

PubMed

Apikoglu-Rabus, Sule; Yesilyaprak, Gozde; Izzettin, Fikret Vehbi

2016-11-01

Asthma and chronic obstructive pulmonary disease are preventable and treatable chronic airway diseases with high incidence and prevalence. Pharmacists and clinical pharmacy based pharmaceutical care services have positive impact on therapy outcomes. The aim of this study is to describe drug related problems in a cohort of patients with asthma and chronic obstructive pulmonary disease and to assess interventions provided by the pharmacist to address these problems in a community pharmacy. Study population consisted of patients with asthma and chronic obstructive pulmonary disease older than 18 years who visited the study pharmacy during the pre-determined six-month period. The patients whose disease control states were "not fully controlled" were included in our study for further steps. On the first interview, present and potential drug related problems were addressed, interventions were provided. Follow-up interviews were held one month and two months later than the first interview. For the 44 patients with asthma, 59 drug-related problems and 134 causes for these problems were identified. Eighty-four interventions were made to resolve the problems; and 54.2% of the problems were resolved. For the 37 patients with chronic obstructive pulmonary disease, 60 drug-related problems and 128 causes for these problems were identified. Ninety-five interventions were made to resolve the problems; and 63.3% of the problems were resolved. Pharmacists taking part in therapy and management of asthma and chronic obstructive pulmonary disease can help patients be more educated about their disease and medications; and improve disease control and therapy outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

PubMed Central

Qin, Qi-Long; Xie, Bin-Bin; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhou, Jizhong; Oren, Aharon

2014-01-01

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. PMID:24706738

Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but this needs to be experimentally characterized with ecologically relevant phenotype properties. This study justifies the need to sequence multiple isolates, especially from P. fluorescens group in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.« less