RESPONSE AND MOLECULAR CONTROL OF CD8 T CELLS DURING INFECTION AND CANCER

CD8 T cells are potent immune effector cells capable of vast clonal expansion and clearance of infected or cancerous cells. After control of the pathogenic insult, CD8 T cells develop into quiescent, long-lived memory populations that are poised to mediate rapid protection upon reencounter with cognate antigen. These properties make control of CD8 T cell responses a highly desirable outcome of vaccine strategies and immunotherapy. Therefore, understanding how the effector function and memory differentiation of CD8 T cells are controlled at a molecular level is of great importance. In the context of infection with gammaherpesviruses (γHV), which form a latent infection that persists for the life span of the host, CD8 T cells play a vital role in control of γHV associated lymphomagenesis. The following studies utilize murine gammaherpesvirus (MHV)-68 and a novel model of γHV-associated B cell lymphoma, EM61 to dissect the mechanisms of CD8 T cell mediated control of γHV associated lymphomagenesis. These studies indicate γHV-specific CD8 T cells control EM61 through mechanisms that partially overlap with those used to control viral replication, however, we note important differences as well. We additionally describe γHV-specific, tissue-resident, memory CD8 T cells (TRM) that form after infection with MHV-68. In the absence of CD4 T cell help, which causes reactivation of γHV during latency, the γHV-specific TRM compartment exhibits changes that are distinct from those observed in the context of acute viral infection. Additional work focused on the molecular control of CD8 T cells by the BTB-ZF family transcription factor (TF), Zbtb20, which restricts CD8 T cell memory differentiation. Using single cell techniques, we identify programs of transcriptional and epigenetic regulation associated with memory CD8 T cell differentiation that underly enhanced memory cell formation in the absence of Zbtb20. Furthermore, using a sensitive technique to interrogate Zbtb20-DNA binding, we describe DNA motifs and genomic annotations from the direct genomic targets of Zbtb20 in CD8 T cells. Together, this work provides new knowledge relevant to the response and control of CD8 T cells to infection and cancer

Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage

BACKGROUND A major hurdle to transcriptome profiling by deep-sequencing technologies is that abundant transcripts, such as rRNAs, can overwhelm the libraries, severely reducing transcriptome-wide coverage. Methods for depletion of such unwanted sequences typically require treatment of RNA samples prior to library preparation, are costly and not suited to unusual species and applications. Here we describe Probe-Directed Degradation (PDD), an approach that employs hybridisation to DNA oligonucleotides at the single-stranded cDNA library stage and digestion with Duplex-Specific Nuclease (DSN). RESULTS Targeting Saccharomyces cerevisiae rRNA sequences in Illumina HiSeq libraries generated by the split adapter method we show that PDD results in efficient removal of rRNA. The probes generate extended zones of depletion as a function of library insert size and the requirements for DSN cleavage. Using intact total RNA as starting material, probes can be spaced at the minimum anticipated library size minus 20 nucleotides to achieve continuous depletion. No off-target bias is detectable when comparing PDD-treated with untreated libraries. We further provide a bioinformatics tool to design suitable PDD probe sets. CONCLUSION We find that PDD is a rapid procedure that results in effective and specific depletion of unwanted sequences from deep-sequencing libraries. Because PDD acts at the cDNA stage, handling of fragile RNA samples can be minimised and it should further be feasible to remediate existing libraries. Importantly, PDD preserves the original RNA fragment boundaries as is required for nucleotide-resolution footprinting or base-cleavage studies. Finally, as PDD utilises unmodified DNA oligonucleotides it can provide a low-cost option for large-scale projects, or be flexibly customised to suit different depletion targets, sample types and organisms.This work was supported by an Australian Research Council Discovery Grant (DP130101928) and a NHMRC Senior Research Fellowship (514904) awarded to TP. NES was supported by a Go8 European Fellowship. We acknowledge technical support from the Australian Cancer Research Foundation Biomolecular Resource Facility

A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice

Epigenetic changes can be induced by adverse environmental exposures, such as nutritional imbalance, but little is known about the nature or extent of these changes. Here we have explored the epigenomic effects of a sustained nutritional change, excess dietary methyl donors, by assessing genomic CpG methylation patterns in isogenic mice exposed for one or six generations. We find stochastic variation in methylation levels at many loci; exposure to methyl donors increases the magnitude of this variation and the number of variable loci. Several gene ontology categories are significantly overrepresented in genes proximal to these methylation-variable loci, suggesting that certain pathways are susceptible to environmental influence on their epigenetic states. Long-term exposure to the diet (six generations) results in a larger number of loci exhibiting epigenetic variability, suggesting that some of the induced changes are heritable. This finding presents the possibility that epigenetic variation within populations can be induced by environmental change, providing a vehicle for disease predisposition and possibly a substrate for natural selection.This work was supported by the Australian Research Council (DP0771859) and the National Health and Medical Research Council (#459412, #635510)

Programmability and Performance of Parallel ECS-based Simulation of Multi-Agent Exploration Models

While the traditional objective of parallel/distributed simulation techniques has been mainly in improving performance and making very large models tractable, more recent research trends targeted complementary aspects, such as the “ease of programming”. Along this line, a recent proposal called Event and Cross State (ECS) synchronization, stands as a solution allowing to break the traditional programming rules proper of Parallel Discrete Event Simulation (PDES) systems, where the application code processing a specific event is only allowed to access the state (namely the memory image) of the target simulation object. In fact with ECS, the programmer is allowed to write ANSI-C event-handlers capable of accessing (in either read or write mode) the state of whichever simulation object included in the simulation model. Correct concurrent execution of events, e.g., on top of multi-core machines, is guaranteed by ECS with no intervention by the programmer, who is in practice exposed to a sequential-style programming model where events are processed one at a time, and have the ability to access the current memory image of the whole simulation model, namely the collection of the states of any involved object. This can strongly simplify the development of specific models, e.g., by avoiding the need for passing state information across concurrent objects in the form of events. In this article we investigate on both programmability and performance aspects related to developing/supporting a multi-agent exploration model on top of the ROOT-Sim PDES platform, which supports ECS

Vaccine strategies: Optimising outcomes

AbstractSuccessful immunisation programmes generally result from high vaccine effectiveness and adequate uptake of vaccines. In the development of new vaccination strategies, the structure and strength of the local healthcare system is a key consideration. In high income countries, existing infrastructures are usually used, while in less developed countries, the capacity for introducing new vaccines may need to be strengthened, particularly for vaccines administered beyond early childhood, such as the measles or human papillomavirus (HPV) vaccine. Reliable immunisation service funding is another important factor and low income countries often need external supplementary sources of finance. Many regions also obtain support in generating an evidence base for vaccination via initiatives created by organisations including World Health Organization (WHO), the Pan American Health Organization (PAHO), the Agence de Médecine Préventive and the Sabin Vaccine Institute. Strong monitoring and surveillance mechanisms are also required. An example is the efficient and low-cost approaches for measuring the impact of the hepatitis B control initiative and evaluating achievement of goals that have been established in the WHO Western Pacific region. A review of implementation strategies reveals differing degrees of success. For example, in the Americas, PAHO advanced a measles-mumps-rubella vaccine strategy, targeting different population groups in mass, catch-up and follow-up vaccination campaigns. This has had much success but coverage data from some parts of the region suggest that children are still not receiving all appropriate vaccines, highlighting problems with local service infrastructures. Stark differences in coverage levels are also observed among high income countries, as is the case with HPV vaccine implementation in the USA versus the UK and Australia, reflecting differences in delivery settings. Experience and research have shown which vaccine strategies work well and the factors that encourage success, which often include strong support from government and healthcare organisations, as well as tailored, culturally-appropriate local approaches to optimise outcomes