Resistance to Grapevine leafroll associated virus-2 is conferred by post-transcriptional gene silencing in transgenic Nicotiana benthamiana

Grapevine leafroll-associated virus-2 (GLRaV-2) is an important component of the leafroll disease complex in grapevine. We have previously sequenced the GLRaV-2 genome and identified the coat protein (CP) gene. The objective of this study is to test the concept of pathogen-derived resistance against a closterovirus associated with grapevine leafroll disease. Because GLRaV-2 is capable of infecting Nicotiana benthamiana, we decided to test the concept on this herbaceous host. Thirty-seven T0 transgenic N.benthamiana plants expressing the GLRaV-2 CP gene were regenerated following Agrobacterium-mediated transformation. Disease resistance was evaluated in greenhouse-grown T1 and T2 plants by mechanical inoculation with GLRaV-2. Although all the inoculated non-transgenic plants showed symptoms 2-4weeks post inoculation, various numbers of transgenic plants (16-100%) in 14 of 20 T1 lines tested were not infected. In these resistant plants, GLRaV-2 was not detectable by enzyme linked immunosorbent assay. Although virus resistance was confirmed in T2 progenies, the percentage of resistant plants was generally lower (0-63%) than that of the corresponding T1 lines (0-100%). Northern blot and nuclear run-off results showed that virus resistance in the transgenic plants was consistently associated with the low level of transgene RNA transcript suggesting a post-transcriptional gene silencing. The success of pathogen-derived resistance to GLRaV-2 in transgenic N.benthamiana plants represents the first step towards eventual control of the leafroll disease in grapevines using this strateg

Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production

Background In recent years, a number of serious disease outbreaks caused by viruses and viroids on greenhouse tomatoes in North America have resulted in significant economic losses to growers. The objectives of this study were to evaluate the effectiveness of commercial disinfectants against mechanical transmission of these pathogens, and to select disinfectants with broad spectrum reactivity to control general virus and viroid diseases in greenhouse tomato production. Methods A total of 16 disinfectants were evaluated against Pepino mosaic virus (PepMV), Potato spindle tuber viroid (PSTVd), Tomato mosaic virus (ToMV), and Tobacco mosaic virus (TMV). The efficacy of each disinfectant to deactivate the pathogen’s infectivity was evaluated in replicate experiments from at least three independent experiments. Any infectivity that remained in the treated solutions was assessed through bioassays on susceptible tomato plants through mechanical inoculation using inocula that had been exposed with the individual disinfectant for three short time periods (0–10 sec, 30 sec and 60 sec). A positive infection on the inoculated plant was determined through symptom observation and confirmed with enzyme-linked immunosorbent assay (PepMV, ToMV, and TMV) and real-time reverse transcription-PCR (PSTVd). Experimental data were analyzed using Logistic regression and the Bayesian methodology. Results Statistical analyses using logistic regression and the Bayesian methodology indicated that two disinfectants (2% Virkon S and 10% Clorox regular bleach) were the most effective to prevent transmission of PepMV, PSTVd, ToMV, and TMV from mechanical inoculation. Lysol all-purpose cleaner (50%) and nonfat dry milk (20%) were also effective against ToMV and TMV, but with only partial effects for PepMV and PSTVd. Conclusion With the broad spectrum efficacy against three common viruses and a viroid, several disinfectants, including 2% Virkon S, 10% Clorox regular bleach and 20% nonfat dry milk, are recommend to greenhouse facilities for consideration to prevent general virus and viroid infection on tomato plants

Vec2Gloss: definition modeling leveraging contextualized vectors with Wordnet gloss

Contextualized embeddings are proven to be powerful tools in multiple NLP tasks. Nonetheless, challenges regarding their interpretability and capability to represent lexical semantics still remain. In this paper, we propose that the task of definition modeling, which aims to generate the human-readable definition of the word, provides a route to evaluate or understand the high dimensional semantic vectors. We propose a `Vec2Gloss' model, which produces the gloss from the target word's contextualized embeddings. The generated glosses of this study are made possible by the systematic gloss patterns provided by Chinese Wordnet. We devise two dependency indices to measure the semantic and contextual dependency, which are used to analyze the generated texts in gloss and token levels. Our results indicate that the proposed `Vec2Gloss' model opens a new perspective to the lexical-semantic applications of contextualized embeddings

Non-uniform Black Strings with Schwarzschild-(Anti-)de Sitter Foliation

We present some exact non-uniform black string solutions of 5-dimensional pure Einstein gravity as well as Einstein-Maxwell-dilaton theory at arbitrary dilaton coupling. The solutions share the common property that their 4-dimensional slices are Schwarzchild-(anti-)de Sitter spacetimes. The pure gravity solution is also generalized to spacetimes of dimensions higher than 5 to get non-uniform black branes.Comment: LaTeX 14 pages, 3 eps figures. V2: version appeared in CQ

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

BACKGROUND: Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogaster based on insight into domain interactions. RESULTS: Three high-throughput yeast two-hybrid experiments and the collection in FlyBase were used as our starting datasets. The co-occurrences of domains in these interactive events are converted into a probability score of domain-domain interaction. These scores are used to infer putative interaction among all available open reading frames (ORFs) of fruit fly. Additionally, the likelihood function is used to estimate all potential protein-protein interactions. All parameters are successfully iterated and MLE is obtained for each pair of domains. Additionally, the maximized likelihood reaches its converged criteria and maintains the probability stable. The hybrid model achieves a high specificity with a loss of sensitivity, suggesting that the model may possess major features of protein-protein interactions. Several putative interactions predicted by the proposed hybrid model are supported by literatures, while experimental data with a low probability score indicate an uncertain reliability and require further proof of interaction. Fly-DPI is the online database used to present this work. It is an integrated proteomics tool with comprehensive protein annotation information from major databases as well as an effective means of predicting protein-protein interactions. As a novel search strategy, the ping-pong search is a naïve path map between two chosen proteins based on pre-computed shortest paths. Adopting effective filtering strategies will facilitate researchers in depicting the bird's eye view of the network of interest. Fly-DPI can be accessed at . CONCLUSION: This work provides two reference systems, statistical and biological, to evaluate the reliability of protein interaction. First, the hybrid model statistically estimates both experimental and predicted protein interaction relationships. Second, the biological information for filtering and annotation itself is a strong indicator for the reliability of protein-protein interaction. The space-temporal or stage-specific expression patterns of genes are also critical for identifying proteins involved in a particular situation

Identification of ankle sprain motion from common sporting activities by dorsal foot kinematics data

This study presented a method to identify ankle sprain motion from common sporting activities by dorsal foot kinematics data. Six male subjects performed 300 simulated supination sprain trials and 300 non-sprain trials in a laboratory. Eight motion sensors were attached to the right dorsal foot to collect three-dimensional linear acceleration and angular velocity kinematics data, which were used to train up a support vector machine (SVM) model for the identification purpose. Results suggested that the best identification method required only one motion sensor located at the medial calcaneus, and the method was verified on another group of six subjects performing 300 simulated supination sprain trials and 300 non-sprain trials. The accuracy of this method was 91.3%, and the method could help developing a mobile motion sensor system for ankle sprain detection

Experiment and analysis of state preparation for atom interferometry

The state preparation is a crucial procedure in atom interferometry; however, there is a shortage of detailed experimental studies on determining the optimal method for achieving this. This paper investigates and compares two methods for state preparation: the combined use of microwave and Raman light (M-R) and the combined use of optical pumping, microwave, and Raman light (O-M-W). The experimental results demonstrate that the M-R method improves the efficiency of Raman transitions for atom interference, which is helpful in enhancing the contrast of the interference fringes. The O-M-R method increases the quantity of prepared atoms, thereby enhancing the signal-to-noise ratio of the detected signals. This work helps provide a useful experimental basis and reference for researchers to design a suitable state preparation scheme