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.

Aquaculture is an important source for food, nutrition, income and livelihoods for millions of people around the globe. Intensive fish farming is often associated with pathogen outbreaks and therefore high amounts of veterinary drugs are used worldwide. As in many other environments, mostly application of antimicrobials triggers the development of (multi)resistant microbiota. This process might be fostered by co-selection as a consequence of the additional use of antiparasitics. Usage of antimicrobials in aquaculture does not only affect the cultured fish species, but - to a so far unknown extent - also aquatic ecosystems connected to fish farms including microbiota from water and sediment as well as its eukaryotes. Effects include increases in the number of (multi)resistant microbes, as well as complete shifts in microbial community structure and function. This dysbiosis might have pronounced consequences for the functioning of aquatic ecosystems. Thus in the frame of this project we want to study consequences of antimicrobial/-parastic application in aquaculture for the cultured fish species as well as for the aquatic environments. To consider the variability of aquaculture practices worldwide four showcases representing typical systems from the tropics, the Mediterranean and the temperate zone will be studied including freshwater and marine environments. For one showcase a targeted mitigation approach to reduce the impact on aquatic ecosystems will be tested.