Computational Prediction of Immunodominant Epitopes on Outer Membrane Protein (Omp) H of Pasteurella multocida Toward De
Contemporary vaccine design necessitates discrimination between the immunogenic and non-immunogenic components within a pathogen. To successfully target a humoral immune response, the vaccine antigen should contain not only B-cell epitopes but abounding T
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Introduction The first step in contemporary vaccine development is the identification of those aspects of an infective organism that can evoke a safe, non-life-threatening immune response without causing a state of disease [1]. This step often follows a protracted course in the wet lab and can prove exceedingly labor and resource intensive. Computational immunology is evolving in its abilities to distinguish the immunogenic components of a pathogen, and the naïve tools of this science offer sufficient speed and cost effectiveness, making computational studies increasingly important in the overall vaccine development process [2]. However, the tools of computational immunology, naïve, as they have been already stated to be, cannot afford enough reliability. A compromising solution to this problem lies in the simultaneous use of several good-performing methods [3] and to abide with the consensus. Many approaches entailing weighted matrices and decision algorithms have been described that render the consensus quantitative; however, such approaches leave little space for an extremely important input in vaccinology—intuition. The prediction approach must not overlook the “underdog” immunogen, which just might fare better in the biological milieu. It can be safely stated at this point that sensitivity must find greater priority over specificity while making the computational predictions. Most vaccines target the humoral immune response that relies on the Class II pathway for processing of the exogenous antigen [1]. Figure 1 presents an oversimplistic view of the processes involved during this response. The current state of the art allows the outcomes of only three of these processes to be predicted com-
Sunil Thomas (ed.), Vaccine Design: Methods and Protocols, Volume 2: Vaccines for Veterinary Diseases, Methods in Molecular Biology, vol. 1404, DOI 10.1007/978-1-4939-3389-1_3, © Springer Science+Business Media New York 2016
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Bhaskar Ganguly
Fig. 1 Humoral immune response depends on Class II pathway for processing of the exogenous antigen . “Ps” have been used to identify the steps that can be predicted computationally (artwork courtesy Ms. Vandana Sharma)
putationally with varying confidence, namely, B-cell antigenicity, MHC-II binding, and Th-cell antigenicity. While many servers are available for the computational identification of these processes in humans, the corresponding number for animals is scant. P. multocida is a major scourge in livestock, especially in the tropics, where it causes recurring epidemics of hemorrhagic septicemia in cattle. It also primarily causes enzootic pneumonia in ruminants, fowl cholera in poultry, atrophic rhinitis in pigs, snuffles in rabbits, and meningitis and appendicitis in humans. As an opportunistic pathogen, it causes secondary diseases including bronchitis, pneumonia, wound infections, cellulitis, osteomyelitis, and appendicial abscesses [4]. Outer membrane protein (Omp) H, variably known as protein H or major outer membrane protein, is a conserved protein in the e
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