ABSTRACT
UNLABELLED: We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists. AVAILABILITY: PERL source code and essential files are available online at http://bat.ina.certh.gr/tools/masive/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.
Subject(s)
Computational Biology/methods , Genome, Plant , Retroelements/genetics , Software , Base Sequence , Databases, Genetic , Genome, Viral , Sequence Analysis, DNA/methods , Zea mays/geneticsABSTRACT
Prion propagation involves conversion of host PrP(C) to a disease-related isoform, PrP(Sc), which accumulates during disease and is the principal component of the transmissible agent. Proteolysis seems to play an important role in PrP metabolism. Plasminogen, a serine protease precursor, has been shown to interact with PrP(Sc). Plasminogen can be proteolytically activated by tissue plasminogen activator (tPA). Recent reports imply a crosstalk between tPA-mediated plasmin activation and PrP. In our study, both tPA activity and tPA gene expression were found elevated in TSE-infected brains as compared to their normal counterparts. Furthermore, it was proved that PrP(Sc), in contrast to PrP(C), could not be degraded by plasmin. In addition, it was observed that TSE symptoms and subsequent death of plasminogen-deficient and tPA-deficient scrapie challenged mice preceded that of wild-type controls. Our data imply that enhanced tPA activity observed in prion infected brains may reflect a neuro-protective response.
