An alternative to current thinking about positive selection, negative selection and activation of T cells

Challenging the Tritope Model of T cell receptor structure-function relationships with classical data on 'super' and 'allo-MHC' antigens

The response of the immune system to allo-MHC-encoded antigens and Mls 'superantigens' has been experimentally analysed in detail, but the data have not been coupled to a theoretical framework. It should therefore be instructive to see how well the newly proposed Tritope Model of TCR structure-function relationships deals with the signalling interactions between the TCR and the above antigens. We will pay heed to William Bateson's admonition, 'treasure the exceptions', by showing how a meaningful theory interrogates the data with the same validity that the data interrogate the theory. The concordances, as well as the contradictions, with the Tritope Model are a test of its heuristic value.

On the logic of restrictive recognition of peptide by the T-cell antigen receptor

This essay provides an analysis of the inadequacy of the current view of restrictive recognition of peptide by the T-cell antigen receptor. A competing model is developed, and the experimental evidence for the prevailing model is reinterpreted in the new framework. The goal is to contrast the two models with respect to their consistency, coverage of the data, explanatory power, and predictability.

On the opposing views of the self-nonself discrimination by the immune system

Today's generally accepted view of the self-nonself discrimination was voiced by Miller(1) in 2004 in a thought-provoking essay. In spite of its popularity, this position has its limitations, which are analyzed here with a view toward establishing an interactive discussion that hopefully will culminate in agreed upon decisive experiments. The inadequacies of Miller's view of the self-nonself discrimination and their resolution under the associative recognition of antigen model are analyzed.

The Tritope Model for restrictive recognition of antigen by T-cells II. Implications for ontogeny, evolution and physiology

Based on the Tritope Model of the TCR [Cohn, M., 2005c. The Tritope Model for restrictive recognition of antigen by T-cells. I. What assumptions about structure are needed to explain function? Mol. Immunol. 42, 1419-1443], a set of functional and evolutionary problems surrounding restrictive recognition of antigen are discussed. These include the origin of allele-specific recognition, the selection pressures for polygeneism and polymorphism, the TCR signaling interactions, the centrality of effector T-helper (eTh)-dependence for activation, the role of haplotype exclusion, "nonclassical" MHC-elements, alloreactivity versus xenoreactivity, etc. Further, a set of observations believed to support the Standard Model are reinterpreted.

On a key postulate of T-cell receptor restrictive function: the V-gene loci act as a single pool encoding recognition of the polymorphic alleles of the species major histocompatibility complex

The proposition that single Valpha or Vbeta gene segments specify the recognition of the allele-specific determinants expressed on the major histocompatibility complex-encoded restricting elements of the species has as its consequence a totally different picture of the functioning of the T-cell receptor. This commentary justifies this assumption and outlines some of its most important consequences.

On ‘Credo 2004’ as Viewed Under the ‘Development-Context’ Model of Colin Anderson

In analysing the Zinkernagel and Hengartner's 'Credo 2004,' Anderson introduces his 'development-context model' for the immunity-tolerance discrimination. He compares this model with the 'geographical model of Credo 2004' and our 'time-based two-signal model'. The discussion here deals with the advantages and limitations of the Anderson model considered largely at the level of principle. A meaningful discussion requires that we agree on the principle which separates the pathway of the effector output into two decision steps, the sorting of the repertoire and the regulation of effector class. The mechanism for the sorting of the repertoire is what might be referred to as the Self-Nonself discrimination. The black box approach, antigen-in, effector response-out, is what is referred to as the immunity-tolerance discrimination which includes the sorting of the repertoire. If this point of principle is accepted then we are left with a 'time-based two signal default model'.

The multigenic structure of the MHC locus contributes to positive selection efficiency: a role for MHC class II gene-specific restriction

The study of T cell positive selection in the thymus has long been focused on the specificity of the MHC-TCR interactions, making use of genetically manipulated mice that display TCR specificities or selecting peptides of limited diversity. However, little is known on the role of the MHC molecules irrespective of the peptide specificity and the implications of MHC multigenic structure in thymic positive selection have not been addressed. Here, we investigated the effect of MHC class II genetic configuration on the positive selection efficiency of naturally generated pre-selection repertoires in the mouse thymus. Analysis of positively selected thymocyte populations in MHC-congenic and -transgenic mice revealed that expression of I-E molecule in the thymic cortex increases positive selection efficiency of CD4 cells by approximately 50%. We show that increments in positive selection attributable to either the I-A and I-E genes are not due to increased MHC class II expression in the thymic cortex and are not affected by the number of MHC alleles. Collectively, our findings imply that MHC class II gene-restricted TCR specificities significantly contribute to positive selection efficiency, introducing the notion that multigenic structure of the MHC locus serves to increase selection of non-overlapping TCR repertoires.

A commentary on the Zinkernagel-Hengartner 'Credo 2004'

In 'Credo 2004', Zinkernagel and Hengartner give us a food-for-thought analysis of immune responsiveness based on a 'pragmatic and empiric point of view.' The Credo 2004 postulates derived by inductive extrapolation from observation to generalization do not satisfactorily account for immune behaviour because they lack a conceptualization as illustrated here. Nevertheless, Credo 2004 is certainly valuable in a limited framework because it is based on the most likely of assumptions namely that the immune system was evolutionarily selected to protect against infectious agents, and therefore the study of pathogens will most accurately reveal how the immune system responds normally to protect. After reformulating them, the postulates of Credo 2004 are analysed with respect to their generality.

Flipping Coins in the Fly Retina

Color vision in Drosophila melanogaster relies on the presence of two different subtypes of ommatidia: the "green" and "blue." These two classes are distributed randomly throughout the retina. The decision of a given ommatidium to take on the "green" or "blue" fate seems to be based on a stochastic mechanism. Here we compare the stochastic choice of photoreceptors in the fly retina with other known examples of random choices in both sensory and other systems.