GreenPhylDB: phylogenomic resources for comparative and functional genomics in plants

Poster presented at 9th PlantGEM 2011. Istanbul (Turkey), 4-7 May 201

Larvicidal activity of Persea americana Mill. against Aedes aegypti.

AbstractObjectiveTo evaluate the toxicity of the ethanol and hexane extracts of the different parts of Persea americana Mill. (P. americana) toward third and fourth instars larvae of Aedes aegypti (Ae. aegypti) and to characterize the ethanol extract by qualitative phytochemical analysis.MethodsThe seeds, peels and pulp of P. americana were processed for crude extraction using 95% ethanol and n-hexane. Crude extracts were bio-assayed for larvicidal activity against Ae. aegypti following the World Health Organization standard bioassay method. The mortality was observed at 24 h and 48 h after treatment and data were subjected to probit analysis to determine lethal concentrations (LC50 and LC90). The ethanol extract was characterized by phytochemical analysis.ResultsBoth the hexane and ethanol extracts from the different parts of P. americana exhibited evidence of larvicidal toxicity. The hexane extract from the seeds exhibited the highest toxicity with LC50 and LC90 values of 9.82 mg/L and 22.19 mg/L, respectively, while the ethanol seed extract exhibited LC50 of 16.48 mg/L and LC90 45.77 mg/L, respectively. This was closely followed by the ethanol extract of the peels with an LC50 of 10.35 mg/L and LC90 of 26.29 mg/L. The pulp extracted with ethanol also yielded great larvicidal toxicity with LC50 of 21.32 mg/L and LC90 of 59.45 mg/L. Results of the phytochemical analysis of the ethanol seed extract indicated presence of alkaloids, tannins, saponins, unsaturated steroids and triterpenoids, flavonoids (leucoanthocyanins), fats and oils.ConclusionsBoth the hexane and ethanol extracts of P. americana showed promising potential as an alternative source of a more sustainable, non-toxic and environmentally friendly solution for the control of dengue vector, Ae. aegypti

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately

Non-Compositional Term Dependence for Information Retrieval

Modelling term dependence in IR aims to identify co-occurring terms that are too heavily dependent on each other to be treated as a bag of words, and to adapt the indexing and ranking accordingly. Dependent terms are predominantly identified using lexical frequency statistics, assuming that (a) if terms co-occur often enough in some corpus, they are semantically dependent; (b) the more often they co-occur, the more semantically dependent they are. This assumption is not always correct: the frequency of co-occurring terms can be separate from the strength of their semantic dependence. E.g. "red tape" might be overall less frequent than "tape measure" in some corpus, but this does not mean that "red"+"tape" are less dependent than "tape"+"measure". This is especially the case for non-compositional phrases, i.e. phrases whose meaning cannot be composed from the individual meanings of their terms (such as the phrase "red tape" meaning bureaucracy). Motivated by this lack of distinction between the frequency and strength of term dependence in IR, we present a principled approach for handling term dependence in queries, using both lexical frequency and semantic evidence. We focus on non-compositional phrases, extending a recent unsupervised model for their detection [21] to IR. Our approach, integrated into ranking using Markov Random Fields [31], yields effectiveness gains over competitive TREC baselines, showing that there is still room for improvement in the very well-studied area of term dependence in IR

Nanopatterned sapphire substrates in deep UV LEDs is there an optical benefit?

Light emitting diodes LEDs in the deep ultra violet DUV offer new perspectives for multiple applications ranging from 3D printing to sterilization. However, insufficient light extraction severely limits their efficiency. Nanostructured sapphire substrates in aluminum nitride based LED devices have recently shown to improve crystal growth properties, while their impact on light extraction has not been fully verified. We present a model for understanding the impact of nanostructures on the light extraction capability of DUV LEDs. The model assumes an isotropic light source in the semiconductor layer stack and combines rigorously computed scattering matrices with a multilayer solver. We find that the optical benefit of using a nanopatterned as opposed to a planar sapphire substrate to be negligible, if parasitic absorption in the p side of the LED is dominant. If losses in the p side are reduced to 20 , then for a wavelength of 265 ,nm an increase of light extraction efficiency from 7.8 to 25.0 is possible due to nanostructuring. We introduce a concept using a diffuse Lambertian reflector as p contact, further increasing the light extraction efficiency to 34.2 . The results underline that transparent p sides and reflective p contacts in DUV LEDs are indispensable for enhanced light extraction regardless of the interface texture between semiconductor and sapphire substrate. The optical design guidelines presented in this study will accelerate the development of high efficiency DUV LEDs. The model can be extended to other multilayer opto electronic nanostructured devices such as photovoltaics or photodetector

Electrostatically gated membrane permeability in inorganic protocells

Although several strategies are now available to produce functional microcompartments analogous to primitive cell-like structures, little progress has been made in generating protocell constructs with self-controlled membrane permeability. Here we describe the preparation of water-dispersible colloidosomes based on silica nanoparticles and delineated by a continuous semipermeable inorganic membrane capable of self-activated, electrostatically gated permeability. We use crosslinking and covalent grafting of a pH-responsive copolymer to generate an ultrathin elastic membrane that exhibits selective release and uptake of small molecules. This behaviour, which depends on the charge of the copolymer coronal layer, serves to trigger enzymatic dephosphorylation reactions specifically within the protocell aqueous interior. This system represents a step towards the design and construction of alternative types of artificial chemical cells and protocell models based on spontaneous processes of inorganic self-organization

Caracterización quimioestratigráfica y facies carbonatadas de una plataforma ediacárica, Formación de Tamengo, Grupo de Corumbá: resultados preliminares

This study presents updates and upgrades concerning the stable isotopic register of the Tamengo Formation, upper part of the Corumbá Group, which crops out in the meridional portion of the Paraguay Belt. This work includes detailed stratigraphic sections paired with high-resolution δ13C and δ18O geochemistry from two mining sites near Corumbá (Mato Grosso do Sul, Brazil).Este estudio presenta una actualización del registro isotópico de la Formación de Tamengo, parte superior del Grupo Corumbá, que se encuentra en la parte meridional del Cinturón Paraguayo. Este trabajo incluye cortes estratigráficos detallados enlazados con la geoquímica de alta resolución δ13C y δ18O de dos yacimientos mineros cercanos a Corumbá (Mato Grosso do Sul, Brasil)

AlN overgrowth of nano-pillar-patterned sapphire with different offcut angle by metalorganic vapor phase epitaxy

We present overgrowth of nano-patterned sapphire with different offcut angles by metalorganic vapor phase epitaxy. Hexagonal arrays of nano-pillars were prepared via Displacement Talbot Lithography and dry-etching. 6.6 µm crack-free and fully coalesced AlN was grown on such substrates. Extended defect analysis comparing X-ray diffraction, electron channeling contrast imaging and selective defect etching revealed a threading dislocation density of about 109 cm−2. However, for c-plane sapphire offcut of 0.2° towards m direction the AlN surface shows step bunches with a height of 10 nm. The detrimental impact of these step bunches on subsequently grown AlGaN multi-quantum-wells is investigated by cathodoluminescence and transmission electron microscopy. By reducing the sapphire offcut to 0.1° the formation of step bunches is successfully suppressed. On top of such a sample an AlGaN-based UVC LED heterostructure is realized emitting at 265 nm and showing an emission power of 0.81 mW at 20 mA (corresponds to an external quantum efficiency of 0.86%)

AlN overgrowth of nano-pillar-patterned sapphire with different offcut angle by metalorganic vapor phase epitaxy

We present overgrowth of nano-patterned sapphire with different offcut angles by metalorganic vapor phase epitaxy. Hexagonal arrays of nano-pillars were prepared via Displacement Talbot Lithography and dry-etching. 6.6 µm crack-free and fully coalesced AlN was grown on such substrates. Extended defect analysis comparing X-ray diffraction, electron channeling contrast imaging and selective defect etching revealed a threading dislocation density of about 109 cm-2. However, for c-plane sapphire offcut of 0.2° towards m direction the AlN surface shows step bunches with a height of 10 nm. The detrimental impact of these step bunches on subsequently grown AlGaN multi-quantum-wells is investigated by cathodoluminescence and transmission electron microscopy. By reducing the sapphire offcut to 0.1° the formation of step bunches is successfully suppressed. On top of such a sample an AlGaN-based UVC LED heterostructure is realized emitting at 265 nm and showing an emission power of 0.81 mW at 20 mA (corresponds to an external quantum efficiency of 0.86 %)

Análisis paleontológicos a través límite Ediacárico-Cámbrico, Grupo Alto Corumbá, Brasil

This work presents the results of a palaeontological analysis focused on twenty-six species sampled in five sections of the Tamengo and Guaicurus formations, Corumbá and Ladário regions: Corcal and Laginha quarries, Porto Sobramil, Porto Figueiras and Ecoparque Cacimba. Besides, palaeoecological and palaeoenvironmental inferences are presented based on the occurrence of this fossil assemblage. Cloudina carinata Cortijo et al., 2010, previously documented in Spain and Siberia, presents an unprecedented occurrence in the American continent, in siltstones of the Tamengo Formation at Porto Figueiras section, Municipality of Corumbá, Mato Grosso do Sul State, Brazil. The biota of the Tamengo Formation is updated and composed of three biomineralizing metazoans, including poriferan spicules, putative sponge gemmule, and a sessile epibiontic prokaryotic colony. The present work also deals with the taxonomy and stratigraphic distribution of four ichnospecies and three vendotaenid species that integrate the updated benthic fauna for the upper portion of Corumbá Group. The species diversity of the Tamengo Formation was complemented by the occurrence of sixteen microfossil species that possibly represent a marine planktic assemblage. A dramatic change was identified in the palaeoenvironmental conditions of the Tamengo to Guaicurus formations, followed by a mass extinction event, possibly linked to the global Ediacaran- Cambrian mass extinction. In addition, organic-walled microfossils were prepared and analyzed from sections of three countries: nine species from the Nomtsas Formation, Namibia; four species from the Tagatiya Guazu Formation, Paraguay; and six species from the Dengying Formation, China. An international biostratigraphic essay consisting of six biozones is proposed for the uppermost Ediacaran and one biozone for the earliest Cambrian.Se presenta en este trabajo el análisis paleontológico de 26 especies fósiles muestradas en cinco cortes de las Formaciones de Tamengo y Guaicurus en las regines de Corumbá y Ladário: canteras de Corcal y Laginha, Porto Sobramil, Porto Figueiras y Ecoparque Cacimba. Además, se añaden varias interpretaciones paleoecológicas y ambientales, basadas en el registro fósil. Cloudina carinata Cortijo et al., 2010, previamente citada en España y Siberia, aparece por primera vez en el continente Americano, concretamente en limolitas de la Formación Tamengo en el corte de Porto Figueiras, Corumbá, Estado de Mato Grosso do Sul, Brasil. La biota de la Formación Tamengo incluye tres metazoos mineralizados, que incluyen espículas de poríferos, posibles gémulas de esponjas y una colonia sésil de procaiotas epibentónicos. Este trabajo se centra en la taxonomía y distribución estratigráfica de cuatro icnoespecies y tres especies de vendoténidos que forman la fauna bentónica de la parte superior del Grupo de Corumbá. La biodiversidad de la Formación Tamengo ha sido completada con el registro de 16 especies microfósiles que representan posiblemente una asociación plantónica marina. Se ha identificado un cambio drástico en las condiciones ambientales de las Formaciones Tamengo y Guaicurus, que culminan en un evento de extincinón masiva posiblemente relacionado con la extincición en masa que marca el tránsito global Ediácarico- Cámbrico. Por otro lado, se han extraído microfósiles de pared orgánica de varios afloramientos: nueve especies de la Formación de Nomtsas (Namibia), cuatro de la Formación Tagatiya Guazu (Paraguay) y seis de la Formación Dengying (China). Se propone un marco bioestratigráfico para el Ediacárico terminal que incluye seis biozonas y una biozona para el Cámbrico basal