DNA regulatory motifs reflect the direct transcriptional interactions between regulators and their target genes and contain important information regarding transcriptional networks. In silico motif detection strategies search for DNA patterns that are present more frequently in a set of related sequences than in a set of unrelated sequences. Related sequences could be genes that are coexpressed...

An aspect-oriented modeling approach to the Car Crash Crisis Management System (CCCMS) using the High-Level Aspect Language (HiLA) is described. HiLA is a language for expressing aspects for UML static structures and UML state machines. In particular, HiLA supports both a static graph transformational and a dynamic approach of applying aspects. Furthermore, it facilitates methodologically turni...

UNLABELLED The transcription factors HilA and SsrB activate expression of two type III secretion systems (T3SSs) and cognate effectors that reprogram host cell functions to benefit infecting Salmonella in the host. These transcription factors, the secretion systems, and the effectors are all encoded by horizontally acquired genes. Using quantitative proteomics, we quantified the abundance of 2,...

Salmonella enterica invades the intestinal epithelium of the host using a type III secretion system encoded on Salmonella pathogenicity island 1 (SPI1). The bacteria integrate environmental signals from a variety of global regulatory systems to precisely induce transcription of SPI1. The regulatory circuit converges on expression of HilA, which directly regulates transcription of the SPI1 appar...

Modern web applications often contain features, such as landmarks, access control, or adaptation, that are difficult to model modularly with existing Model-Driven Web Engineering approaches. We show how HILA, an aspectoriented extensions for UML state machines, can represent these kinds of features as aspects. The resulting models achieve separation of concerns and satisfy the “Don’t Repeat You...

HilA activates the transcription of genes on Salmonella pathogenicity island 1 (SPI1), which encodes a type III secretion system (TTSS). Previous studies showed that transposon insertions in orgC, a gene located on SPI1, increase hilA expression. We characterize the orgC gene product and show that it is secreted via the SPI1 TTSS. We propose a model whereby OrgC functions as a secreted represso...

Mutual exclusion is a very common requirement in parallel systems. Yet its modeling is a tedious task in UML state machines, one of the most popular languages for behavior modeling. We present HiLA, an aspect-oriented extension of UML state machines, to address this problem. In HiLA, mutual exclusion can be modeled in a highly modular and declarative way. That is, the logic of mutual exclusion ...

It is proposed that the dematiaceous hyphomycete Cladosporium bantianum (Saccardo) Borelli be transferred to the genus Xylohypha (Fries) Mason as Xylohypha bantiana (Saccardo) McGinnis, Padhye, Borelli, et Ajello. This new combination is necessary because X. bantiana produces conidiophores that are indistinguishable from its vegetative hyphae and one-celled, smooth-walled conidia that are borne...

direct regenerations by using mature cotyledonary node as a explants has been shown to be time-saving and convenient strategy for micropropagation of soybean. so we have evaluated regeneration protocol through single shoot using cotyledonary node as a rapid and efficient protocol for two soybean cultivars and one mutant line. cotyledonary nodes explants obtained from 7-days-old in vitro seedlin...

The global regulator Mlc is a repressor of several genes and operons that are involved in sugar uptake and metabolism. A Salmonella enterica serovar Typhimurium mlc mutant showed reduced levels of invasion and cytotoxicity compared to the wild-type, and exhibited reduced expression levels of hilD, hilA and invF, which are regulatory genes in the Salmonella pathogenicity island 1 (SPI1). However...