Rice blast fungus sequenced

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CastorDB: a comprehensive knowledge base for Ricinus communis

<p>Abstract</p> <p>Background</p> <p><it>Ricinus communis </it>is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, <it>R. communis </it>genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of <it>R. communis </it>is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant.</p> <p>Findings</p> <p>CastorDB is a specialized and comprehensive database for the oil seed plant <it>R. communis</it>, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein.</p> <p>Conclusion</p> <p>CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners.</p

Fifteenth Century Problems for the Twenty-First Century Gift: Human Tissue Transactions in Ethnically Diverse Societies

The language of the ‘gift’ continues to be drawn upon in attempts to encourage altruistic organ and tissue donation. My aim here is to consider the anxieties that come into focus when this rhetoric is deployed in the context of ethnic minorities and, moreover, their donation practices are situated within universalistic discourses of charity and the gift. The article considers ideas of the body, debt, obligation, relationality, and solidarity, and how these fit within the overarching projects of society, modernity, and democracy when the market figures as an ever more prominent feature of such projects. Drawing on a variety of examples, the piece reflects on the movement of tissue across ethnically and culturally marked corporeal boundaries and highlights the tensions that arise from refusal as well as acceptance of such transactions

A counter-selectable marker for genetic transformation of the yeast Schwanniomyces alluvius

We report here a counter-selectable marker system for genetic transformation of the yeast Schwanniomyces alluvius, based on the complementation of uracil auxotrophs defective in either orotidine-5'-phosphate decarboxylase (URA3) or orotidine-5'-pyrophosphatase (URA5). Uracil auxotrophs of S. alluvius were obtained by ethyl methanesulphonate mutagenesis and complemented using the ura3 gene from S. cerevisiae. A␣transformation frequency of approximately 104/μg DNA was obtained, which is tenfold higher than results described in earlier reports. Transformants were analysed by Southern blot hybridisation and were found to be mitotically stable. The extrachromosomal nature of the transforming DNA was confirmed by Southern hybridisation and plasmid rescue. The rescued plasmid DNA had a restriction pattern identical to that of the parent plasmid

Purification and characterization of laccase from the rice blast fungus, Magnaporthe grisea

A 70-kDa extracellular laccase was purified from the rice blast fungus Magnaporthe grisea using gel filtration and ion exchange chromatography The procedure provided 282-fold purification with a specific enzyme activity of 225.91 U mg−1 and a yield of 11.92%. The enzyme oxidized a wide range of substrates. The highest level of oxidation was detected with syringaldazine as the substrate. Using syringaldazine as the substrate, the enzyme exhibited a pH optimum of 6 and temperature optimum of 30°C, and its Kmwas 0.118 mM. The enzyme was strongly inhibited by Cu-chelating agents

Mg-SINE: a short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea.

A short interspersed nuclear element, Mg-SINE, was isolated and characterized from the genome of the rice blast fungus, Magnaporthe grisea. Mg-SINE was isolated as an insertion element within Pot2, an inverted-repeat transposon from M. grisea and shows typical features of a mammalian SINE. Mg-SINE is present as a 0.47-kb interspersed sequence at approximately 100 copies per haploid genome in both rice and non-rice isolates of M. grisea, indicating a common evolutionary origin. Secondary structure analysis of Mg-SINE revealed a tRNA-related region at the 5' end which folds into a cloverleaf structure. Genomic fusions resulting in chimeric Mg-SINEs (Ch-SINEs) composed of a sequence homologous to Mg-SINE at the 3' end and an unrelated sequence at its 5' end were also isolated, indicating that this and other DNA rearrangements mediated by these elements may have a major effect on the genomic architecture of this fungus

Functional analysis of a novel ABC transporter ABC4 from Magnaporthe grisea

The ATP-binding cassette (ABC) superfamily of membrane transporters has been implicated to play a role in pathogenesis in various phytopathogenic fungi. In an insertional mutagenesis screen for pathogenicity mutants of Magnaporthe grisea obtained via Agrobacterium tumefaciens-mediated transformation (ATMT), a novel gene belonging to the ABC transporter family was identified. The gene ABC4 was predicted to be 5045 bp in length coding for a protein of 1654 amino acids. The mutant did not form functional appressoria and was nonpathogenic. When compared with wild type, the mutant showed increased sensitivity to certain antifungal compounds and phytoalexins, implying the role of ABC4 in multidrug resistance (MDR) as well as establishment in the host. Reverse transcriptase PCR showed the expression of ABC4 in wild-type strain while it was absent in the mutant abc4. In real-time PCR, the expression of ABC4 was seen to be enhanced in the presence of various drugs tested. The data suggests that ABC4 is required for the pathogenicity of M. grisea, helping the fungus to cope with the cytotoxic environment during infection

Bacterial population structure of the jute-retting environment

Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria (~37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes (~11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; ~9, 7%), Verrucomicrobia (~6, 5%), Acidobacteria (~4, 5%), Chlorobiales (~5, 5%), and Actinobacteria (~4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the β-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria (~47%), Firmicutes (~22%), CFB group (~19%), and Actinobacteria (~13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality

Expression of a plant defensin in rice confers resistance to fungal phytopathogens

Transgenic rice (Oryza sativa L. cv. Pusa basmati 1), overexpressing the Rs-AFP2 defensin gene from the Raphanus sativus was generated by Agrobacterium tumefaciens-mediated transformation. Expression levels of Rs-AFP2 ranged from 0.45 to 0.53% of total soluble protein in transgenic plants. It was observed that constitutive expression of Rs-AFP2 suppresses the growth of Magnaporthe oryzae and Rhizoctonia solani by 77 and 45%, respectively. No effect on plant morphology was observed in the Rs-AFP2 expressing rice lines. The inhibitory activity of protein extracts prepared from leaves of Rs-AFP2 plants on the in vitro growth of M. oryzae indicated that the Rs-AFP2 protein produced by transgenic rice plants was biologically active. Transgene expression of Rs-AFP2 was not accompanied by an induction of pathogenesis-related (PR) gene expression, suggesting that the expression of Rs-AFP2 directly inhibits the pathogens. Here, we demonstrate that transgenic rice plants expressing the Rs-AFP2 gene show enhanced resistance to M. oryzae and R. solani, two of the most important pathogens of rice