28:T476,

Lack of large-scale efforts aimed at recognizing interactions between host and pathogens limits our understanding of many diseases. We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection. This dataset of putative in vitro interactions is combined with large-scale datasets of expression and sub-cellular localization. This integrated approach reduces drastically the number of false positives and hence can be used for generating testable hypotheses. We could recognize known interactions previously suggested in the literature. We also propose new predictions which involve interactions of some of the parasite proteins of yet unknown function. The method described is generally applicable to any host-pathogen pair and can thus be of general value to studies of host-pathogen protein-protein interactions.

29:T4f7,

Rapid diagnostics and risk assessment of the pathogens is possible by Real-Time Polymerase Chain Reaction (PCR) probes like TaqMan, Molecular Beacon (MB) and FRET. However, validation of such probes for real-life samples is an expensive and time consuming proposition. Hence, development and comparison of real-time probes in silico can be the first step in selection of most appropriate probe chemistry. The virulence genes specific for a model pathogen, Escherichia coli O157:H7, transmitted worldwide by contaminated water and food, were chosen to compare probe chemistries. MB was observed to be the best probe chemistry for virulence genes stx1, stx2 and eae, while FRET was preferred for hlyA gene, based on T $_{m}$ and free energy values for self-dimer, hairpin and cross-dimer. Secondary structure analysis indicated that MB design was flexible and less dependent on nucleotide arrangement and repetitive sequences in the genes compared to TaqMan and FRET probes. In addition, multiplexed MB probes could be a feasible option using a single non-fluorescent quencher for high throughput diagnostics.

2a:T459,

We have explored the roles played by C-H…π hydrogen bonds in interleukins. Main-chain to side-chain C-H…π interactions are the predominant type of interactions in interleukins. There was an average of 15 C-H…π interactions per protein and also there was an average of one significant C-H…π interaction for every 14 residues in the interleukins investigated. Significant contribution to C-H…π interactions was only from Asp, Gly, His, Lys, Phe, Pro, Ser, Thr, Trp and Tyr in interleukins. Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain 5 member aromatic ring and side-chain to side-chain C-H…π interactions. Short and medium-range C-H…π interactions are the predominant type of interactions in interleukins. More than 50% of C-H…π interacting residues had a conservation score of ⩾ 6. Significant percentage of C-H…π interacting residues had one or more stabilization centers; hence these residues may also contribute additional stability to structure of interleukins.

2b:T8b6,