Molecular Mechanisms of Axonal Injury

Axonal biology: mechanisms and new chemical biology-based tools for studying molecular and cellular dynamics

Keeping axonal function and structure intact is crucial for normal functioning of the nervous system. Axons transmit electrical impulses and transport cargos between neuronal cell bodies and synapses. Due to their unique roles and architecture, they can cover remarkable distances and are highly prone to injury. In neuroinflammatory diseases, such as multiple sclerosis (MS), axons are damaged by infiltrating immune cells.

Previous work (Nikić et al., Nature Medicine 2011) identified a novel form of neuroinflammatory axon loss - focal axonal degeneration (FAD). Focal axonal degeneration is a sequential process, induced by neuroinflammatory oxidative stress and characterized by an intermediate stage with focal axonal swellings that can persist for several days, progress to degeneration but also spontaneously recover. However, many questions about focal axonal degeneration remain open, e.g. what determines if an axon will recover or not, what happens at the earliest sights of injury, what mediates changes in the axonal shape.

Methods: fluorescence microscopy and minimal tags for protein labelling

We study mechanisms of axonal injury in mouse and in vitro models. In addition to more standard microscopy techniques (live cell and intravital widefield imaging, confocal microscopy), we use modern super-resolution microscopy techniques, such as stochastic optical reconstruction microscopy (STORM), to obtain molecular-scale information. We are also using and developing new cutting-edge protein engineering tools based on selective incorporation of unnatural amino acids (Nikić et al., Angewandte 2014; Nikić, Kang, Girona et al., Nature Protocols 2015; Nikić & Lemke, Current Opinion in Chemical Biology 2016; Nikić et al., Angewandte 2016). Unnatural amino acids give us a unique opportunity to introduce new properties/functional groups, such as dyes, affinity tags for proteomics, post-translation modifications, cross-linkers, optogenetic tools, etc. into proteins at a single cell and even whole organism level.  

Selected and most recent publications

Nikić I, Merkler D, Sorbara C, Brinkoetter M, Kreutzfeldt M, Bareyre FM, Brück W, Bishop D , Misgeld T and Kerschensteiner M. 2011. A reversible form of axon damage in experimental autoimmune encephalomyelitis and multiple sclerosis. Nature Medicine 17(4):495-9.

Bishop D, Nikić I, Brinkoetter M, Knecht S, Potz S, Kerschensteiner M and Misgeld T. 2011. NIRB - near infrared branding efficiently correlates light and electron microscopy. Nature Methods 8(7):568-70.

Nikić I, Plass T, Schraidt O, Szymański J, Briggs JAG, Schultz C, Lemke EA. 2014. Minimal Tags for Rapid Dual-Color Live-Cell Labeling and Super-Resolution Microscopy. Angewandte Chemie International Edition 53(8):2245-9.

Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. 2016. Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angewandte Chemie International Edition 55(52):16172-16176

Nikić-Spiegel I. 2018. Genetic code expansion-and click chemistry-based site--specific protein labelling for intracellular DNA-PAINT imaging. Methods in Molecular Biology. 1728:279-295.

Das D, Govindan R, Nikić-Spiegel I, Krammer F, Lemke EA, Munro J. 2018. Direct visualization of the conformational dynamics of single influenza hemagglutinin trimers, Cell. 174(4):926-937

Lu M, Ma X, Castillo-Menendez L, Gorman J, Ermel U, Terry D, ChambersM , PengD , Reichard N, Wang K, Grove J, Carman B, Nikić-Spiegel I, Sugawara A, Arthos J, Finzi A, Lemke EA, Smith A, Abrams C, Munro J, McDermott A, Kwong P, Blanchard S, Sodroski J, Mothes W. 2019. Associating HIV-1 Env trimer structures with conformational states defined by single-molecule FRET. Nature. 568(7752):415-419

Arsić A, Stajković N, Spiegel R, Nikić-Spiegel I. 2020. Effect of Vectashield-induced fluorescence quenching on conventional and super-resolution microscopy. Scientific Reports. 10(1):6441. doi: 10.1038/s41598-020-63418-5

Nikić-Spiegel I. Expanding the genetic code for neuronal studies. Expanding the genetic code for neuronal studies.  ChemBioChem. Accepted Author Manuscript. doi:10.1002/cbic.202000300

For a complete list of publications, please check my ORCID profile:


Work in our laboratory is supported by the Emmy Noether Programme of the German Research Foundation.

Open positions

March 2020: We are currently looking for creative and motivated postdoc(s) to join our team.

If interested, please send your application including a CV, a letter of motivation stating why you are interested in our research and names of 2-3 referees to

Group Leader and Further Information

Ivana Nikić-Spiegel
Molecular Mechanisms of Axonal Injury
Werner Reichardt Centre for Integrative Neuroscience
Otfried-Mueller-Str. 25
72076 Tübingen

Phone: +49 (0)7071 29 89181
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