Cool, wet conditions in the southern US during the maturing stages of rice in 1998 contributed to outbreaks of false smut caused by Ustilaginoidea virens. Water extracts of false smut galls in Asia have been reported ...Cool, wet conditions in the southern US during the maturing stages of rice in 1998 contributed to outbreaks of false smut caused by Ustilaginoidea virens. Water extracts of false smut galls in Asia have been reported to contain ustiloxin toxins, cyclic peptide antibiotics that interfered with microtubule function and caused “lupinosis”-like lesions in mice. Cell-free extracts from false smut galls on rice grown in Arkansas were fractionated by a published procedure for the purification of ustiloxins. The ustiloxin fraction was phytotoxic to Lemnapausicostata (duckweed) at ≥19 μg/ml, but the host plant, rice, was much less susceptible, exhibiting phytotoxic effects in germinating seeds at ≥1000 μg/ml. The aqueous extract of rice false smut galls showed no cytotoxicity to mammalian cell cultures at 200 μg/ml, but the ustiloxin fractionwas cytotoxic at 10 - 100 μg/ml. However, rice false smut galls were not toxic when fed to mice at 10% of chow, but caused feed refusal at higher concentrations. We conclude that for 1) the U. virens which causes false smut in southern USA differs from Asian isolates in that does not produce detectable ustiloxins;and 2) false smut affects the appearance, but not the food safety of rice in the United States.展开更多
High-density tiling arrays provide closer view of transcription than regular microarrays and can also be used for annotating functional elements in genomes. The identified transcripts usually have a complex overlappin...High-density tiling arrays provide closer view of transcription than regular microarrays and can also be used for annotating functional elements in genomes. The identified transcripts usually have a complex overlapping architecture when compared to the existing genome annotation. Therefore, there is a need for customized tiling array data analysis tools. Since most of the initial tiling arrays were conducted in eukaryotes, data analysis methods are well suited for eukaryofic genomes. For using whole-genome tiling arrays to identify previously unknown transcriptional elements like small RNA and antisense RNA in prokaryotes, existing data analysis tools need to be tailored for prokaryotic genome architecture. Furthermore, automation of such custom data analysis workflow is necessary for biologists to apply this powerful platform for knowledge discovery. Here we describe TAAPP, a web-based package that consists of two modules for prokaryotic tiling array data analysis. The transcript generation module works on normalized data to generate transcriptionally active regions （TARs）. The feature extraction and annotation module then maps TARs to existing genome annotation. This module further categorizes the transcription profile into potential novel non-coding RNA, antisense RNA, gene expression and operon structures. The implemented workflow is microarray platform independent and is presented as a web-based service. The web interface is freely available for acedemic use at http：//lims.lshi.mafes.msstate.edu/TAAPP-HTML/.展开更多
文摘Cool, wet conditions in the southern US during the maturing stages of rice in 1998 contributed to outbreaks of false smut caused by Ustilaginoidea virens. Water extracts of false smut galls in Asia have been reported to contain ustiloxin toxins, cyclic peptide antibiotics that interfered with microtubule function and caused “lupinosis”-like lesions in mice. Cell-free extracts from false smut galls on rice grown in Arkansas were fractionated by a published procedure for the purification of ustiloxins. The ustiloxin fraction was phytotoxic to Lemnapausicostata (duckweed) at ≥19 μg/ml, but the host plant, rice, was much less susceptible, exhibiting phytotoxic effects in germinating seeds at ≥1000 μg/ml. The aqueous extract of rice false smut galls showed no cytotoxicity to mammalian cell cultures at 200 μg/ml, but the ustiloxin fractionwas cytotoxic at 10 - 100 μg/ml. However, rice false smut galls were not toxic when fed to mice at 10% of chow, but caused feed refusal at higher concentrations. We conclude that for 1) the U. virens which causes false smut in southern USA differs from Asian isolates in that does not produce detectable ustiloxins;and 2) false smut affects the appearance, but not the food safety of rice in the United States.
基金supported by a grant from the National Science foundation of USA (Mississippi EPSCoR-0903787)
文摘High-density tiling arrays provide closer view of transcription than regular microarrays and can also be used for annotating functional elements in genomes. The identified transcripts usually have a complex overlapping architecture when compared to the existing genome annotation. Therefore, there is a need for customized tiling array data analysis tools. Since most of the initial tiling arrays were conducted in eukaryotes, data analysis methods are well suited for eukaryofic genomes. For using whole-genome tiling arrays to identify previously unknown transcriptional elements like small RNA and antisense RNA in prokaryotes, existing data analysis tools need to be tailored for prokaryotic genome architecture. Furthermore, automation of such custom data analysis workflow is necessary for biologists to apply this powerful platform for knowledge discovery. Here we describe TAAPP, a web-based package that consists of two modules for prokaryotic tiling array data analysis. The transcript generation module works on normalized data to generate transcriptionally active regions （TARs）. The feature extraction and annotation module then maps TARs to existing genome annotation. This module further categorizes the transcription profile into potential novel non-coding RNA, antisense RNA, gene expression and operon structures. The implemented workflow is microarray platform independent and is presented as a web-based service. The web interface is freely available for acedemic use at http：//lims.lshi.mafes.msstate.edu/TAAPP-HTML/.
