Host genotype and time dependent antigen presentation of viral peptides: predictions from theory

The rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degradation products at the cell surface to circulating T-cells. HLA alleles are associated with Gag-specific T-cell responses that are protective against progression of the disease. While Pol is the most conserved HIV sequence, its association with immune control is not as strong. To gain a more thorough quantitative understanding of the factors that contribute to immunodominance, we have constructed a model of the recognition of HIV infection by the MHC class I pathway. Our model predicts surface presentation of HIV peptides over time, demonstrates the importance of viral protein kinetics, and provides evidence of the importance of Gag peptides in the long-term control of HIV infection. Furthermore, short-term dynamics are also predicted, with simulation of virion-derived peptides suggesting that efficient processing of Gag can lead to a 50% probability of presentation within 3 hours post-infection, as observed experimentally. In conjunction with epitope prediction algorithms, this modelling approach could be used to refine experimental targets for potential T-cell vaccines, both for HIV and other viruses

Learning by Heart: Cultural Patterns in the Faunal Processing Sequence during the Middle Pleistocene

Social learning, as an information acquisition process, enables intergenerational transmission and the stabilisation of cultural forms, generating and sustaining behavioural traditions within human groups. Archaeologically, such social processes might become observable by identifying repetitions in the record that result from the execution of standardised actions. From a zooarchaeological perspective, the processing and consumption of carcasses may be used to identify these types of phenomena at the sites. To investigate this idea, several faunal assemblages from Bolomor Cave (Valencia, Spain, MIS 9-5e) and Gran Dolina TD10-1 (Burgos, Spain, MIS 9) were analysed. The data show that some butchery activities exhibit variability as a result of multiple conditioning factors and, therefore, the identification of cultural patterns through the resulting cutmarks presents additional difficulties. However, other activities, such as marrow removal by means of intentional breakage, seem to reflect standardised actions unrelated to the physical characteristics of the bones. The statistical tests we applied show no correlation between the less dense areas of the bones and the location of impacts. Comparison of our experimental series with the archaeological samples indicates a counter-intuitive selection of the preferred locus of impact, especially marked in the case of Bolomor IV. This fact supports the view that bone breakage was executed counterintuitively and repetitively on specific sections because it may have been part of an acquired behavioural repertoire. These reiterations differ between levels and sites, suggesting the possible existence of cultural identities or behavioural predispositions dependant on groups. On this basis, the study of patterns could significantly contribute to the identification of occupational strategies and organisation of the hominids in a territory. In this study, we use faunal data in identifying the mechanics of intergenerational information transmission within Middle Pleistocene human communities and provide new ideas for the investigation of occupational dynamics from a zooarchaeological approach