68 research outputs found
Adding Logical Operators to Tree Pattern Queries on Graph-Structured Data
As data are increasingly modeled as graphs for expressing complex
relationships, the tree pattern query on graph-structured data becomes an
important type of queries in real-world applications. Most practical query
languages, such as XQuery and SPARQL, support logical expressions using
logical-AND/OR/NOT operators to define structural constraints of tree patterns.
In this paper, (1) we propose generalized tree pattern queries (GTPQs) over
graph-structured data, which fully support propositional logic of structural
constraints. (2) We make a thorough study of fundamental problems including
satisfiability, containment and minimization, and analyze the computational
complexity and the decision procedures of these problems. (3) We propose a
compact graph representation of intermediate results and a pruning approach to
reduce the size of intermediate results and the number of join operations --
two factors that often impair the efficiency of traditional algorithms for
evaluating tree pattern queries. (4) We present an efficient algorithm for
evaluating GTPQs using 3-hop as the underlying reachability index. (5)
Experiments on both real-life and synthetic data sets demonstrate the
effectiveness and efficiency of our algorithm, from several times to orders of
magnitude faster than state-of-the-art algorithms in terms of evaluation time,
even for traditional tree pattern queries with only conjunctive operations.Comment: 16 page
Factors affecting storage stability of vitamin A, riboflavin and niacin in a broiler diet premix
Call number: LD2668 .T4 1985 Z58Master of Scienc
In-situ STEM imaging of growth and phase change of individual CuAlX precipitates in Al alloy
Age-hardening in Al alloys has been used for over a century to improve its mechanical properties. However, the lack of direct observation limits our understanding of the dynamic nature of the evolution of nanoprecipitates during age-hardening. Using in-situ (scanning) transmission electron microscopy (S/TEM) while heating an Al-Cu alloy, we were able to follow the growth of individual nanoprecipitates at atomic scale. The heat treatments carried out at 140, 160, 180 and 200 °C reveal a temperature dependence on the kinetics of precipitation and three kinds of interactions of nano-precipitates. These are precipitate-matrix, precipitate-dislocation, and precipitate-precipitate interactions. The diffusion of Cu and Al during these interactions, results in diffusion-controlled individual precipitate growth, an accelerated growth when interactions with dislocations occur and a size dependent precipitate-precipitate interaction: growth and shrinkage. Precipitates can grow and shrink at opposite ends at the same time resulting in an effective displacement. Furthermore, the evolution of the crystal structure within an individual nanoprecipiate, specifically the mechanism of formation of the strengthening phase, θ′, during heat-treatment is elucidated by following the same precipitate through its intermediate stages for the first time using in-situ S/TEM studies
Optimization of the cry1Ah1 Sequence Enhances the Hyper-Resistance of Transgenic Poplars to Hyphantria cunea
Increased expression of the insect control protein genes of Bacillus thuringiensis in Populus has been critical to the development of genetically improved plants with agronomically acceptable levels of insect resistance. Bacillus thuringiensis (Cry1Ah1) proteins with highly specific toxicity against Hyphantria cunea were screened using an indoor bioactivity assay to obtain hyper-resistant transgenic poplars. Then, the Cry1Ah1 sequence was optimized and transformed according to the optimal codon in poplar using software of our own design (http://120.79.60.226:8080/u/chen/w/codonpoplar). A vector was constructed to transform poplar NL895. The Cry1Ah1 gene was transformed to poplar NL895 and six transgenic lines were obtained. The expression and insecticidal effect of the Cry1Ah1 gene in transgenic poplar were evaluated by PCR and ELISA, and the specific indoor activity and field insecticidal activity against H. cunea were compared with a control. We concluded that the insecticidal activity of the transgenic NL895 was significantly better against lower instar larvae of H. cunea than against higher instar larvae. The mortality and pupation rates clearly differed among the various instar larvae and between transgenic and non-transgenic poplar. We obtained poplar seedlings with hyper-resistance to H. cunea by screening Bt genes and optimizing their genetic sequence
CRISPR-mediated genome editing in poplar issued by efficient transformation
BackgroundCRISPR has been increasingly used for plant genetic improvements because of its high efficiency and precision. Recently, the authors have reported the possibility of homology-directed repair (HDR) using CRISPR/Cas9 through woody plants such as poplar. HDR often replaces nucleotides with one donor DNA template (DDT), including homologous sequences.MethodsCRISPR–Cas9 was recruited, and three variables, Agrobacteria inoculator concentration, pDDT/pgRNA ratio, and homologous arm length, were designed to integrate nptII and 2XCamV 35S into the MKK2 promoter zone.ResultsHere, we showed that recovered poplars on kanamycin-supplemented media exhibited enhanced expression of MKK2 affected by the precise integration of 2XcamV 35S and nptII, improving biochemical and phenotypic properties. Our findings confirmed that Agrobacterium inoculator OD600 = 2.5, increased DDT numbers during cell division to 4:1 pDDT/pgRNA, and optimized homologous arms 700 bp caused efficient HDR and increased MKK2 expression.ConclusionEfficient transformations resulted from optimized variables, directly affecting the HDR efficiency through woody plants such as poplar
An Efficient Agrobacterium-Mediated Transformation System for Poplar
Poplar is a model system for the regeneration and genetic transformation of woody plants. To shorten the time required for studies of transgenic poplar, efforts have been made to optimize transformation methods that use Agrobacterium tumefaciens. In this study, an Agrobacterium infective suspension was treated at 4 °C for at least 10 h before infecting explants. By transforming the Populus hybrid clone “Nanlin895” (Populus deltoides × P. euramericana) with Agrobacterium harboring the PBI121:CarNAC6 binary vector, we showed that the transformation efficiency was improved significantly by multiple independent factors, including an Agrobacterium infective suspension with an OD600 of 0.7, an Agrobacterium infection for 120 min, an Agrobacterium infective suspension at a pH of 5.0, an acetosyringone concentration of 200 µM, a cocultivation at 28 °C, a cocultivation for 72 h and a sucrose concentration of 30 g/L in the cocultivation medium. We also showed that preculture of wounded leaf explants for two days increased the regeneration rate. The integration of the desired gene into transgenic poplars was detected using selective medium containing kanamycin, followed by southern blot analysis. The expression of the transgene in the transgenic lines was confirmed by northern blot analysis
Analysis of Synonymous Codon Usage Patterns in Seven Different Species
We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus , which is one of the most widely cultivated fruit trees
Transformation of a Thermostable G-Quadruplex Structure into DNA Duplex Driven by Reverse Gyrase
Reverse gyrase is a topoisomerase that can introduce positive supercoils to its substrate DNA. It is demonstrated in our studies that a highly thermal stable G-quadruplex structure in a mini-plasmid DNA was transformed into its duplex conformation after a treatment with reverse gyrase. The structural difference of the topoisomers were verified and analyzed by gel electrophoresis, atomic force microscopy examination, and endonuclease digestion assays. All evidence suggested that the overwinding structure of positive supercoil could provide a driven force to disintegrate G-quadruplex and reform duplex. The results of our studies could suggest that hyperthermophiles might use reverse gyrase to manipulate the disintegration of non-B DNA structures and safekeep their genomic information
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