Genetically encoded nano-barcode


April 18, 2023

(Nanowerk News) How do the nerve cells in our brain communicate with each other? What process occurs when T cells render cancer cells harmless? The details of the mechanism at the cellular level remain hidden from view. Now, a special reporter protein developed by a research team led by the Technical University of Munich (TUM) can help unravel this mechanism.

Peeking through the electron microscope gives scientists the deepest views into cellular structure – the resolution lies in the sub-nanometer range. Even cell components such as mitochondria or the connections between nerve cells can be seen. Despite this, many important structures and processes remain hidden. “It’s like looking at a city map,” explains Gil Gregor Westmeyer, Professor of Neurobiological Engineering at TUM and Director of the Synthetic Biomedical Institute at Helmholtz Munich. “It’s enough to get a visual sense of the surroundings and see where the road is. But it doesn’t tell us how often traffic lights are turned off, how much traffic was there at any given point, and when or where something is currently under construction.” ”

But the ability to intervene in faulty processes, or to recreate them in artificial tissues and organs, absolutely requires an understanding of processes within and between cells. Westmeyer and his colleagues have developed what’s called a genetic reporter system that does the inside-cell surveillance work for them. The gene reporter is a protein capsule that is large enough to be seen with an electron microscope.

Identification by barcode

The capsule is produced by the cell itself. Their genetic blueprint is attached to specific target genes. Reporter proteins are produced when a target gene becomes active. The basic principle behind this method has become standard procedure in light microscopy. There, the researchers worked with fluorescent proteins. However, this method is not suitable for electron microscopy, because rather than color, different shapes are distinguished by their electron density, for example.

Researchers exploit this by inserting metal-binding proteins into different sized capsules. These “EMcapsulins” appear as concentric circles of various sizes under the electron microscope and can be quickly identified and assigned like a barcode using artificial intelligence.

Make invisible structures visible

So, how exactly can researchers take advantage of this reporter protein? On the one hand, they can use it to pinpoint the activity of certain genes, but also to discover structures that would not be visible under an electron microscope – for example electrical synapses between nerve cells or receptors that influence interactions between cancer cells and T cells.

“If we also impart the fluorescent properties of EMcapsulins, this will enable us to examine the structure in living tissue initially using light microscopy,” said Felix Sigmund, first author of the study (Natural Biotechnology, “Genetically encoded barcodes for correlative volume electron microscopy”). In the process, striking dynamics and structures can be observed, which in later steps can then be remarkably resolved under the electron microscope.

“In the future it may also be envisioned to deploy reporter proteins as sensors that change their structure, for example, when a cell becomes active. In this way, the relationship between cell function and cell structure can be better explained, which is also relevant. to understand disease processes, as well as to generate therapeutic cells and tissues,” added Westmeyer.

To this end, the researchers will also use the new Electron Microscopy Facility at TUM and collaborate with TUM’s new Organoid Systems Center (COS).


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