Antiviral CD8+ T cell effector activities in situ are regulated by target cell type

In the lungs of mice infected with influenza, the activity of cytotoxic T lymphocytes is modulated by the type of target cell encountered

Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data

Role of Co-stimulatory Molecules in T Helper Cell Differentiation

CD4+ T cells play a central role in orchestrating the immune response to a variety of pathogens but also regulate autoimmune responses, asthma, allergic responses, as well as tumor immunity. To cover this broad spectrum of responses, naïve CD4+ T cells differentiate into one of several lineages of T helper cells, including Th1, Th2, Th17, and TFH, as defined by their cytokine pattern and function. The fate decision of T helper cell differentiation integrates signals delivered through the T cell receptor, cytokine receptors, and the pattern of co-stimulatory signals received. In this review, we summarize the contribution of co-stimulatory and co-inhibitory receptors to the differentiation and maintenance of T helper cell responses