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Mitochondria are crucial for neuronal growth, neuronal plasticity, and synaptic activity. However, not all synapses contain mitochondria, and not all synaptic mitochondria harbor nucleoids—protein–DNA complexes that contain the mitochondrial genome. The functional consequences of the presence of nucleoids in synaptic mitochondria remain poorly understood. Using super-resolution optical microscopy, we will systematically characterize presynaptic mitochondria with and without nucleoids, analyze the localization of mitochondrial mRNAs, and investigate the mechanisms that contribute to the synaptic enrichment of nucleoid-containing mitochondria. In addition, we will quantify functional, structural, and compositional differences between these mitochondrial populations.