Maximum parsimony (MP) phylogenetic relationships of <i>Epichloë</i> species based on intron portions of <i>tefA</i>.

<p>MP trees were constructed in the PAUP 4.0b10 package. MP trees were estimated using a heuristic search with tree bisection-reconnection (TBR) branch swapping and 100 random addition replicates. Alignment gaps were treated as missing information. Nucleotide substitutions were unordered and unweighted. Bootstrap support values were calculated with 1000 replications. Numbers on branches are bootstrap values. Branches with bootstrap values >50% are shown. Maximum likelihood (ML) bootstrap values are listed first on each branch, followed by MP bootstrap values. Red, blue and orange colors indicate the <i>Epichloë</i> species from China, Europe and North America, respectively. The partial figure is showed, for the full image please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127096#pone.0127096.s002" target="_blank">S2 Fig</a>.</p

Maximum parsimony (MP) phylogenetic relationships of <i>Epichloë</i> species based on intron portions of <i>tubB</i>.

<p>MP trees were constructed in the PAUP 4.0b10 package. MP trees were estimated using a heuristic search with tree bisection-reconnection (TBR) branch swapping and 100 random addition replicates. Alignment gaps were treated as missing information. Nucleotide substitutions were unordered and unweighted. Bootstrap support values were calculated with 1000 replicates. Numbers on the branches are bootstrap values. Branches with bootstrap values >50% are shown. Maximum likelihood (ML) bootstrap values are listed first on each branch, followed by MP bootstrap values. Red, blue and orange colors indicate the <i>Epichloë</i> species from China, Europe and North America, respectively. The partial figure is showed, for the full image please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127096#pone.0127096.s001" target="_blank">S1 Fig</a>.</p

Origin, Divergence, and Phylogeny of Asexual <i>Epichloë</i> Endophyte in <i>Elymus</i> Species from Western China

<div><p>Asexual <i>Epichloë</i> species are likely derived directly from sexual <i>Epichloë</i> species that then lost their capacity for sexual reproduction or lost sexual reproduction because of interspecific hybridization between distinct lineages of sexual <i>Epichloë</i> and/or asexual <i>Epichloë</i> species. In this study we isolated asexual <i>Epichloë</i> endophytes from <i>Elymus</i> species in western China and sequenced intron-rich regions in the genes encoding β-tubulin (<i>tubB</i>) and translation elongation factor 1-α (<i>tefA</i>). Our results showed that there are no gene copies of <i>tubB</i> and <i>tefA</i> in any of the isolates. Phylogenetic analysis showed that sequences in this study formed a single clade with asexual <i>Epichloë bromicola</i> from <i>Hordeum brevisubulatum</i>, which implies asexual <i>Epichloë</i> endophytes that are symbionts in a western Chinese <i>Elymus</i> species likely share a common ancestor with asexual <i>E</i>. <i>bromicola</i> from European <i>H</i>. <i>brevisubulatum</i>. In addition, our results revealed that asexual <i>E</i>. <i>bromicola</i> isolates that are symbionts in a western Chinese <i>Elymus</i> species and sexual <i>Epichloë</i> species that are symbionts in a North American <i>Elymus</i> species have a different origin. Further analysis found that <i>Epichloë</i> species likely originated in Eurasia. In addition, the results support the hypothesis that migratory birds or humans might have aided the dispersal of these fungal endophytes to other continents.</p></div

Estimates of nucleotide diversity and selection statistics for <i>tubB</i> and <i>tefA</i> sequences in <i>Epichloë</i> endophytes from western Chinese and North American <i>Elymus</i> species.

<p>Note: N: the number of sequences analyzed; h: the number of haplotypes; n: the number of the sites (excluding sites with gaps and missing data); s: number of polymorphic sites; π (Tajima’s π): nucleotide diversity; θ (Watterson’s θ): the diversity based on the number of polymorphic sites.</p><p>Estimates of nucleotide diversity and selection statistics for <i>tubB</i> and <i>tefA</i> sequences in <i>Epichloë</i> endophytes from western Chinese and North American <i>Elymus</i> species.</p

Rapid GUI development on legacy systems: a runtime model-based solution

Graphical User Interface (GUI) is a common feature for modern software systems, while there are still many legacy systems that do not have GUIs, but only provide text and commands for user interaction. In this paper, we report our experiment on using runtime models to support the rapid, generation-based development of simple GUIs for such legacy systems. We construct runtime models for the target system as an intermediate representations of the underlying system state, and in this way wrap the low-level interaction mechanisms of the legacy systems. After that, we visualize the models with a graphical editor. Due to the causal con- nection between runtime models and the runtime system state, users can monitor and control the system state by reading and writing the models, and in this way, using the graphical model editor as the GUI of the system. Based on the existing framework for runtime model construction and model visualization, it is possible to achieve the rapid devel- opment process of such GUIs in the form of high-level speci- cation and automated generation. We experiment with this idea by using two existing frameworks, Sm@rt and GMF, to develop a series of GUIs for an electricity simulation system named GridLAB-D. We also enhance the existing Sm@rt framework with cache mechanisms in order to suit GUIs

Inferring the data access from the clients of generic APIs

Many programs access external data sources through generic APIs. The class hierarchy of such a generic API does not reflect the schema of any particular data source, and thus it is hard to clarify what data an API client accesses and how it obtains them. This makes it difficult to maintain the API clients. In this paper, we show that the data access of an API client can be recovered through static analysis on the client’s source code. We provide a formal and intuitive way to represent the data access, as a graph of so-called summoning snippets. Each snippet stands for a type of data accessed by the client, and carries the code slice from the client about how to obtain the data via the API. We provide an automated approach to inferring a complete and well-simplified set of summoning snippets from the client source code, based on points-to analysis and code slicing.We implement this approach as a development assistant tool, and evaluate it on eight open source data processing programs, with average precision and recall of 89% and 95%, respectively. Further inspection of these clients, as well as a user study about writing data accessing code on their data sources, show that the inference results are useful in the inspection of existing clients and the development of new data access logics

Localization of the cargo prApe1 in the MKO strain, and localization of the receptor Atg19 and the adaptor Atg11 in the MKO strain

The MKO () strain and the MKO () strain transformed with a plasmid expressing YFP-Atg19 (pYFPATG19(416)) or HA-tagged CFP-Atg11 (pCuHACFPATG11(414)) were grown in selective SMD medium to mid-log phase and observed by fluorescence microscopy. DIC, differential interference contrast. (B) Colocalization of prApe1, Atg19, and Atg11. The MKO () strain was transformed with a plasmid expressing YFP-Atg19, HA-tagged CFP-Atg11, or both, grown to mid-log phase and observed by fluorescence microscopy. When Atg19 was coexpressed with prApe1 in the MKO () strain, the cargo prApe1 colocalized with the receptor Atg19 (top). When Atg19 was absent, the adaptor Atg11 (arrows) did not colocalize with the cargo (middle). When prApe1, Atg19, and Atg11 were all present, the three proteins colocalized to the same structure (bottom). Bars, 2.5 μm.<p><b>Copyright information:</b></p><p>Taken from "In vivo reconstitution of autophagy in "</p><p></p><p>The Journal of Cell Biology 2008;182(4):703-713.</p><p>Published online 25 Aug 2008</p><p>PMCID:PMC2518709.</p><p></p

(A) The role of Atg4 and the Atg12–Atg5 conjugation system in Atg8–PE formation

MKO () cells transformed with different combinations of plasmids were grown in selective SMD medium, collected at mid-log phase or 2 h after starvation, and then subjected to Western blot analysis using anti-Atg8 antiserum. 0.2 OD units of cells were loaded in each lane. Pgk1 was used as a loading control. Plasmids expressing Atg8 (pATG8(414)); Atg8, Atg4, Atg7, and Atg10 (pATG8-ATG4-ATG7-ATG10(414)); Atg5, HA-Atg12, and Atg16 (pATG5-HA-ATG12-ATG16(416)); and Atg8ΔR, Atg7, and Atg10 (pATG8ΔR-ATG7-ATG10(414)) were used as indicated. Atg8–PE was hardly detected in both growing and starvation conditions even when all the known components from the Atg8–PE and Atg12–Atg5 conjugation systems were expressed (lane 4). However, when Atg8ΔR was expressed and Atg4 was absent, a significant amount of Atg8–PE was observed (lane 5), and the amount was further increased when all the components from the Atg12–Atg5 conjugation system were also expressed (lane 6). Note that Atg8–PE migrates aberrantly during SDS-PAGE and runs lower than Atg8. (B) The role of the Atg12–Atg5 conjugation system on Atg8–PE formation. The experimental procedures were the same as in A. Plasmids expressing Atg8ΔR (pATG8ΔR(414)); Atg8ΔR, Atg4, Atg7, and Atg10 (pATG8ΔR-ATG4-ATG7-ATG10(414)); Atg8ΔR, Atg7, and Atg10; Atg5 (pATG5(416)); HA-tagged Atg12 (pHA-ATG12(416)); Atg16 (pATG16(416)); Atg5 and HA-Atg12 (pATG5-HA-ATG12(416)); and Atg5, HA-Atg12, and Atg16 were used as indicated. The strain transformed with the plasmid expressing Atg8ΔR (pATG8ΔR(414)) and the strain were used as controls (lanes 10 and 11). When Atg4 was present, an Atg8–PE band was not detected (compare lanes 3 and 4). Expression of Atg5, Atg12, or Atg16 alone did not improve Atg8–PE formation (compare lanes 5–7 to lane 4). When the Atg12–Atg5 conjugate was formed through the expression of Atg7, Atg10, Atg12, and Atg5, the efficiency of Atg8–PE formation was greatly enhanced (lane 8). Atg16 further facilitated Atg8–PE conjugation and/or enhanced the stability of the conjugate (lane 9).<p><b>Copyright information:</b></p><p>Taken from "In vivo reconstitution of autophagy in "</p><p></p><p>The Journal of Cell Biology 2008;182(4):703-713.</p><p>Published online 25 Aug 2008</p><p>PMCID:PMC2518709.</p><p></p

Model driven engineering of cross-layer monitoring and adaptation

Monitoring and adaptation of multilayer systems are challenging, because the mismatches and adaptations are interrelated across the layers. This interrelation introduces two important but difficult questions. 1) When a system change causes mismatches in one layer, how to identify all the cascaded mismatches on the other layers? 2) When an adaptation is performed at one layer, how to find out all the complementary adaptations required in other layers. This paper presents a model-driven engineering approach towards cross-layer monitoring and adaption of multilayer systems. We provide standard meta-modeling languages for system experts to specify the concepts and constraints separately for each layer, as well as the relations among the concepts from different layers. An automated engine uses these meta-level specifications to 1) represent the system states on each layer as a runtime model, 2) evaluate the constraints to detect mismatches and assist adaptations within a layer, and 3) synchronize the models to identify cascaded mismatches and complementary adaptations across the layers. We illustrate the approach on a simulated crisis management system, and are using it on a number of ongoing projects

Effective Formation of Oxygen Vacancies in Black TiO₂ Nanostructures with Efficient Solar-Driven Water Splitting

Black TiO₂ nanomaterials have attracted considerable attention since they usually exhibit excellent photocatalytic activities. Herein, we report the facile preparation of black TiO₂ nanostructures with ultrathin hollow sphere morphology, high crystalline quality, small grain size (∼8 nm), and ultrahigh surface area (168.8 m² g^–1) through Al reduction. Electron paramagnetic resonance (EPR) spectra demonstrate the existence of oxygen vacancies in black TiO₂ nanostructures, which could increase the donor density and effectively promote the separation and transportation of photogenerated electron–hole pairs. The black TiO₂ nanostructures exhibit a high solar-driven hydrogen generation rate (56.7 mmol h^–1 g^–1) under the full spectrum of solar light, which is nearly 2.5 times than that of pristine TiO₂ nanostructures and superior to those kinds of black TiO₂ photocatalytic materials reported previously