The first coins with an owl as motif were minted in Athens from c. 575 BC on as incusum quadratum in electrum and silver [1. table 1], later (from c. 525 BC on) as a reverse motif with an obverse image of Athena in the Attic standard of coinage [1. table 2; 2. 44ff.]. Minting in bronze with this motif, beginning in the 3rd cent. BC, replaced the silver coins from 78/7 BC onward [3. 42] and ended in the middle of the 2nd cent. AD [1. table 88].
We present a discriminative learning method for pattern discovery of binding sites in nucleic acid sequences based on hidden Markov models. Sets of positive and negative example sequences are mined for sequence motifs whose occurrence frequency varies between the sets. The method offers several objective functions, but we concentrate on mutual information of condition and motif occurrence. We perform a systematic comparison of our method and numerous published motif-finding tools. Our method achieves the highest motif discovery performance, while being faster than most published methods. We present case studies of data from various technologies, including ChIP-Seq, RIP-Chip and PAR-CLIP, of embryonic stem cell transcription factors and of RNA-binding proteins, demonstrating practicality and utility of the method. For the alternative splicing factor RBM10, our analysis finds motifs known to be splicing-relevant. The motif discovery method is implemented in the free software package Discrover. It is applicable to genome- and transcriptome-scale data, makes use of available repeat experiments and aside from binary contrasts also more complex data configurations can be utilized.
The gastric pathogen H. pylori employs a type IV secretion system (T4SS) to inject the oncogenic effector protein CagA into the stomach epithelium of its human host. The T4SS protein CagL localizes to the T4SS pilus and is essential for injection of CagA into host cells. CagL harbors a RGD motif that probably mediates binding to host cell integrins.We solved the crystal structure of H. pylori CagL. (Barden et al. 2013). An elongated three-helix bundle forms the structural core of CagL, to which the N-terminal helix is associated only loosely. Structure comparisons suggest that CagL is a H. pylori specific protein. The RGD motif is exposed at the protein surface and thus accessible for interaction with a receptor molecule. In contrast to previously characterized RGD motifs, the RGD motif of CagL is not located in an extended or flexible loop structure but in the middle of a long helix.We now investigate the molecular basis of the interaction between CagL and host cell receptors.