Prion diseases, also known as transmissible spongiform encephalopathies, are characterized by the accumulation of misfolded prion proteins (PrPSc), which resists clearance due to impaired removal mechanisms and immune tolerance. Although strategies aimed at enhancing intracellular clearance pathways, including autophagy, have shown promise, effective in vivo interventions remain limited. Innate immune stimulation with CpG oligodeoxynucleotides (CpG ODN), a Toll-like receptor 9 agonist that mimics bacterial DNA containing unmethylated CpG motifs, has been reported to extend survival in prion-infected mice; however, the underlying mechanisms involved remain incompletely defined. In this study, we examined the effects of CpG ODN in both in vitro and in vivo models of prion disease using the 22L scrapie strain. Mice treated with CpG ODN prior to infection exhibited prolonged mean survival compared with vehicle-treated controls and showed reduced PrPSc accumulation in spleen and brain tissues at 60 and 170 days post-infection, respectively. These changes were correlated with increased AMPK (Tyr172) phosphorylation and alterations in autophagy-associated signaling markers in the brain tissue. In 22L scrapie-infected neuronal cells, CpG ODN treatment significantly reduced PrPSc levels, and this effect was attenuated by pharmacological inhibition of autophagy-associated and lysosomal degradative processes. Collectively, these findings indicate that CpG ODN reduces PrPSc accumulation and prolongs survival in prion-infected mice, supporting the involvement of autophagy-associated degradative processes without establishing enhanced autophagic flux.

Open chromatin profiling identifies regulatory DNA regions that are accessible to transcription factors and other proteins, offering insights into gene regulation. Although ATAC-seq is commonly used for mapping open chromatin, standard techniques such as DNase-seq and ATAC-seq have limitations, including the need for large cell numbers or fresh (unfixed) samples. NicE-seq offers an alternative approach by using nicking endonucleases combined with polymerase–mediated biotin labeling. Here, we present a detailed analysis framework for NicE-seq data in plants using Arabidopsis thaliana as our reference species, adapted from the nf-core/atacseq pipeline with specific modifications. We emphasize the analytical differences between NicE-seq and ATAC-seq, describe data processing workflows, and illustrate methods for peak calling, annotation, and integration with transcriptomic data. This computational resource aims to guide researchers in applying NicE-seq, providing a basis for selecting between NicE-seq and ATAC-seq in plant epigenomic research, especially when working with challenging samples such as archived tissues or small cell populations.

The synaptic nanocluster refers to the nanoscale accumulation of synaptic proteins that ensures the fidelity of synaptic transmission. These nanoclusters align pre- and post-synaptic machineries across the synaptic cleft, enabling neurotransmitter release to occur precisely opposite postsynaptic receptors. In vertebrates, neuroligins are key postsynaptic cell adhesion molecules that help maintain synaptic function. Recent superresolution microscopy studies have shown that neuroligins themselves form nanoclusters and regulate the nanoscale distribution of synaptic proteins, suggesting a role in orchestrating synaptic strength through nanocluster organization. In this review, we summarize recent advances in understanding how neuroligin subtype specificity influences the organization of postsynaptic receptors and how neuroligin-ligand interactions modulate nanoscale architecture. We also discuss how disruption in those nanoclusters can disturb synaptic strength.

In this MiniResource, we outlined practical approaches for preparing murine T cells, from isolation to in vitro activation, with emphasis on reproducibility and viability. While specific experimental conditions should be tailored to individual assays, the principles summarized here provide a framework for establishing robust T cell preparation across diverse research settings. By integrating standard methodologies with troubleshooting insights, this resource aims to support both basic immunological studies and future applications in T cell engineering.