Electron microscopy gene reporters based on bioengineered encapsulin nanocompartments
The biological engineering project EMcapsulins will create the first suite of multiplexed genetic reporters for electron microscopy (EM) to augment today’s merely structural brain circuit diagrams (connectomes) with crucial information on neuronal type and activation history.

My team will generate this new toolbox based on genetically encoded nanocompartments of the prokaryotic ‘encapsulin’ family that we have recently shown to enable genetically controlled compartmentalization of multicomponent processes in mammalian cells. 

By encapsulating metal-organizing cargo proteins in the lumen of the semi-permeable encapsulin nanospheres, they serve as fully genetic EM gene reporters (EMcapsulins) that provide robust and spatially precise contrast by conventional EM in mammalian cells. 

To enable geometric multiplexing in EM in analogy to multi-color light microscopy, we will explore the large geometrical feature space of EMcapsulins to establish three core Functionalities: 
① different shell structures and diameters, 
② modular and tunable shell functionalizations, and 
③ multiplexed and triggered cargo loading.   

We will combine these Functionalities to produce geometrically multiplexed EMcapsulin markers of neuronal identity in serial EM (Application ❶). 

We will also engineer EMcapsulin reporters for activity-dependent gene expression, calcium signaling, and synaptic activity that can ‘write’ geometrically encoded records of neuronal activation history into EM connectomics data (Application ❷). 

These ‘multi-color’ and modular EMcapsulin markers and reporters deliver the missing bridging technology between time-resolved light microscopy measurements of neuronal activation dynamics and structural EM connectomics data. 

EMcapsulin technology will convert structural to functional EM connectomes to enable a systematic analysis of how brains write molecular signaling dynamics into structural patterns to store information for later retrieval.