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Many apparently divergent approaches to specifying formal semantics of programming languages are applications of initial algebra semantics. In this paper an overview of initial algebra semantics is provided. The major technical feature is an initial continuous algebra which permits unified algebraic treatment of iterative and recursive semantic features in(More)
This paper addresses changes in plant gene expression induced by inoculation with plant-growth-promoting rhizobacteria (PGPR). A gnotobiotic system was established with Arabidopsis thaliana as model plant, and isolates of Paenibacillus polymyxa as PGPR. Subsequent challenge by either the pathogen Erwinia carotovora (biotic stress) or induction of drought(More)
Antisense RNA control is now recognized as an efficient and specific means of regulating gene expression at the posttranscriptional level. Almost all naturally occurring cases have been found in prokaryotes, often in their accessory genetic elements. Several antisense RNA systems are now well-understood, and these display a spectrum of mechanisms of action,(More)
Efficient gene control by antisense RNA requires rapid bi-molecular interaction with a cognate target RNA. A comparative analysis revealed that a YUNR motif (Y=pyrimidine, R=purine) is ubiquitous in RNA recognition loops in antisense RNA-regulated gene systems. The (Y)UNR sequence motif specifies two intraloop hydrogen bonds forming U-turn structures in(More)
This paper extends our earlier work on abstract data types by providing an algebraic treatment of parametrized data types (e.g., sets-of-(), stacks-of-(), etc.), as well as answering a number of questions on the power and limitations of algebraic specification techniques. In brief: we investigate the “hidden function” problem (the need to(More)
The hok/sok, srnB and pnd systems of plasmids R1, F and R438 mediate plasmid maintenance by killing plasmid-free segregants. The systems encode exceptionally stable full-length mRNAs that code for potent cell toxins that kill the cells from within. The systems also produce truncated mRNAs whose appearance is correlated with killing activity. The truncated(More)
Antisense RNA-mediated transcriptional attenuation is the mode of replication control of several plasmids, among them pIP501. This mechanism implies that the repR mRNAs can fold into two mutually exclusive structures. The formation of one of these structures is induced by binding of the antisense RNA and results in premature termination. Since the fate of(More)