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排序方式: 共有113条查询结果,搜索用时 62 毫秒
41.
42.
Richard J. Gualandi Jr. Robert M. Augé Dean A. Kopsell Bonnie H. Ownley Feng Chen Heather D. Toler Mary M. Dee Kimberly D. Gwinn 《Symbiosis (Philadelphia, Pa.)》2014,63(3):111-121
An emerging paradigm in sustainable biotechnique is the use of mutualists to enhance plant growth and secondary metabolism. Our objective was to determine impact of two groups of fungal mutualists on growth and phytochemistry of Echinacea purpurea. Growth, development, and phytochemical concentration were measured in greenhouse-grown 12-week-old plants colonized by arbuscular mycorrhizal fungi (AMF) (Rhizophagus intraradices and Gigaspora margarita) or the endophytic entomopathogen, Beauveria bassiana. In one experiment, all measured growth parameters were increased in mycorrhizal plants. Biomass of AMF-colonized plants was over 13-fold greater than non-mycorrhizal controls receiving the same levels of phosphorous, and over 4-fold greater than non-mycorrhizal controls given additional phosphorous. Endophytic colonization by B. bassiana had minor effects on growth. Colonization by AMF and B. bassiana alone or in combination altered concentrations of phytochemicals (pigments, polyphenolics, alkylamides, and terpenes). Mycorrhizal plants produced up to 4.6-fold higher concentration of polyphenolics. Specific alkylamides increased 1.7 fold in plants colonized only with B. bassiana and up to a 2.4-fold increase in plants colonized by both mutualists. Changes in other phytochemical classes were related to differences in plant size induced by AMF. Phytochemical content (concentration × biomass) was increased up to 30-fold in mycorrhizal plants. Phytochemical relationships to plant biomass were confirmed in a second experiment in which non-mycorrhizal plants were fertilized to produce biomass equivalent to that of mycorrhizal plants. Based on this study, mycorrhizal colonization of E. purpurea enhances phytochemical content; this has major implications for the natural product industries and growers of E. purpurea. 相似文献
43.
Viktorian Miok Saskia M Wilting Mark A van de Wiel Annelieke Jaspers Paula I van Noort Ruud H Brakenhoff Peter JF Snijders Renske DM Steenbergen Wessel N van Wieringen 《BMC bioinformatics》2014,15(1)
Background
To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.Results
Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.Conclusion
With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users. 相似文献44.
Ownley BH Griffin MR Klingeman WE Gwinn KD Moulton JK Pereira RM 《Journal of invertebrate pathology》2008,98(3):267-270
Seed application of Beauveria bassiana 11-98 resulted in endophytic colonization of tomato and cotton seedlings and protection against plant pathogenic Rhizoctonia solani and Pythium myriotylum. Both pathogens cause damping off of seedlings and root rot of older plants. The degree of disease control achieved depended upon the population density of B. bassiana conidia on seed. Using standard plating techniques onto selective medium, endophytic 11-98 was recovered from surface-sterilized roots, stems, and leaves of tomato, cotton, and snap bean seedlings grown from seed treated with B. bassiana 11-98. As the rate of conidia applied to seed increased, the proportion of plant tissues from which B. bassiana 11-98 was recovered increased. For rapid detection of B. bassiana 11-98 in cotton tissues, we developed new ITS primers that produce a PCR product for B. bassiana 11-98, but not for cotton. In cotton samples containing DNA from B. bassiana11-98, the fungus was detected at DNA ratios of 1:1000; B. bassiana 11-98 was detected also in seedlings grown from seed treated with B. bassiana 11-98. Using SEM, hyphae of B. bassiana11-98 were observed penetrating epithelial cells of cotton and ramifying through palisade parenchyma and mesophyll leaf tissues. B. bassiana11-98 induced systemic resistance in cotton against Xanthomonas axonopodis pv. malvacearum (bacterial blight). In parasitism assays, hyphae of B. bassiana 11-98 were observed coiling around hyphae of Pythium myriotylum. 相似文献
45.
Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis 总被引:6,自引:0,他引:6
Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected
vertebrates, we investigated the effects that constraints imposed by
secondary structure have on the phylogenetic analysis of rRNA sequence
data. Our analysis indicates that characters from both base-pairing regions
(stems) and non-base-pairing regions (loops) contain phylogenetic
information, as judged by the level of support of the phylogenetic results
compared with a well-established tree based on both morphological and
molecular data. The best results (the greatest level of support of
well-accepted nodes) were obtained when the complete data set was used.
However, some previously supported nodes were resolved using either the
stem or loop bases alone. Stem bases sustain a greater number of
compensatory mutations than would be expected at random, but the number is
< 40% of that expected under a hypothesis of perfect compensation to
maintain secondary structure. Therefore, we suggest that in phylogenetic
analyses, the weighting of stem characters be reduced by no more than 20%,
relative to that of loop characters. In contrast to previous suggestions,
we do not recommend weighting of stem positions by one-half, compared with
that of loop positions, because this overcompensates for the constraints
that selection imposes on the secondary structure of rRNA.
相似文献
46.
47.
A New Transformation-Deficient Mutant of Haemophilus influenzae Rd with Normal DNA Uptake 总被引:1,自引:0,他引:1
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Haemophilus influenzae Rd is a gram-negative natural transformer. A mutant strain, RJ248, that has normal DNA uptake and translocation but whose transformation frequency is 300 times lower than that of wild-type H. influenzae and whose phage recombination is 8 times lower was isolated. The affected gene, comM, is induced during competence development in wild-type H. influenzae but not in RJ248. 相似文献
48.
Paulsen IT Press CM Ravel J Kobayashi DY Myers GS Mavrodi DV DeBoy RT Seshadri R Ren Q Madupu R Dodson RJ Durkin AS Brinkac LM Daugherty SC Sullivan SA Rosovitz MJ Gwinn ML Zhou L Schneider DJ Cartinhour SW Nelson WC Weidman J Watkins K Tran K Khouri H Pierson EA Pierson LS Thomashow LS Loper JE 《Nature biotechnology》2005,23(7):873-878
Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5. 相似文献
49.
Clara Correia‐Melo Francisco DM Marques Rhys Anderson Graeme Hewitt Rachael Hewitt John Cole Bernadette M Carroll Satomi Miwa Jodie Birch Alina Merz Michael D Rushton Michelle Charles Diana Jurk Stephen WG Tait Rafal Czapiewski Laura Greaves Glyn Nelson Mohammad Bohlooly‐Y Sergio Rodriguez‐Cuenca Antonio Vidal‐Puig Derek Mann Gabriele Saretzki Giovanni Quarato Douglas R Green Peter D Adams Thomas von Zglinicki Viktor I Korolchuk João F Passos 《The EMBO journal》2016,35(7):724-742
50.