Curation of viral genomes: challenges, applications and the way forward

BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies

Protein/Emulsifier Interactions

An important consequence of protein-lipid interaction is the effect on stability of the protein in solution as well as on its behavior at interfaces. Here we will discuss key aspects of protein aggregation and unfolding as well as the effects of protein structure (random coil proteins versus globular) that are relevant for our understanding protein-lipid interaction. The main types of emulsifiers are the (1) aqueous soluble, surfactant type and (2) lipids with low aqueous solubility. The monomer concentration as defined by cmc is an important parameter for the soluble lipids. For emulsifiers with low aqueous solubility the emulsifier self-assembly structure and its properties control the interaction with proteins. We will therefore summarize the main features of lipid self-assembly. It also allows us to define different plausible scenarios and principles and models for factors that control the interactions in real food (and Pharmaceutical) systems. For the food applications the fate of the lipid during digestion is important and therefore we will discuss some aspects of enzyme-catalyzed lipolysis in terms of the structural evolution. New products and concepts of using protein/emulsifier interactions will be exemplified by illustrating how food nanotechnology possibly can be used for the delivery of functionality