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Samora Okujeni

Akademischer Rat and Lecturer
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  Dr. Samora Okujeni
  Biomicrotechnology
  Dept. for Microsystems Engineering IMTEK
  University of Freiburg
  Georges-Koehler-Allee 102
  D-79110 Freiburg i. Br.
 
  Tel.: +49 (0)761 203-7523
  

 

Research Projects

Homeostatic activity-dependent self-organization of neuronal networks

  • Dependencies between structural plasticity (cellular motility, neurite outgrowth) and network architecture [4, 6].
  • Morphogenic impact of inhibition during network development [1, 3].


Structure-function dependencies in neuronal networks

  • Neuronal clustering, structural modularity and self-organized criticality [2, 9].
  • Network structure and the regulation of spontaneous activity in neuronal networks [5].
  • Dependencies between structural and functional E/I balance in vitro [1].


Control of neuronal network response dynamics

  • Neuronal network response-clamp via closed-loop electrical stimulation [7, 8].

Research Topics

My research focuses on activity-dependent self-organization and structure-function-dependencies in neuronal networks.

Albeit coarsely instructed by genetic programs during early development, neuronal connectivity in the brain is considerably shaped by activity-dependent interactions between neurons impacting on their structural and functional differentiation. Synaptic and spiking activity, for instance, regulate neuronal migration, neurite field elaboration, synaptogenesis and the maturation of inhibition. A homeostatic regulation of activity is furthermore essential for neuronal survival and neurons failing to embed themselves sufficiently into a network are prone to apoptosis. Excess connectivity and activity, in turn, entails pruning of connections and may likewise trigger apoptosis. Hence, consistent with evolutionary optimization, functionally useless or disturbing neurons seem to be programmed to disintegrate if they fail to (re)align into the circuit. Accordingly, individual neurons seek to dynamically establish and maintain a morphological embedding that satisfies certain activity requirements.

The concrete rules mapping activity to morphogenic processes crucially impact on the self-organization of network architecture at microscopic to mesoscopic scales. In the developmental context, I am fascinated by the idea that stereotypical and functionally relevant architectural patterns may emerge, almost miraculously, from local neuronal interactions. With experimental in vitro networks and computational models, we investigate how changes in activity-dependent morphogenesis or in developmental conditions influence the evolution of network connectivity.

Examples are research projects focusing on the morphogenic impact of neuronal migration, external stimulation or maturing inhibition on activity-dependent network self-organization in vitro using pharmacological, electrophysiological and optogenetic tools. We study the topological and functional consequences of altered network architecture by means of immunohistochemistry and morphological reconstruction, and by recording network and single neuron activity using micro-electrode arrays, patch-clamp and calcium imaging. We combine our experimental findings with reduced models of neuronal network growth or connectivity-dependent activity propagation to gain insight into the process of network-self-organization and into structure-function dependencies. Aware of the complex biochemical and genetic meshwork underneath, we aim to derive an abstracted mechanistic understanding of neuronal network self-organization, emerging activity dynamics and the functional consequences.

Techniques

  • Neuronal cell culture
  • Microelectrode array recordings
  • Calcium Imaging
  • Optogenetics Patch-Clamp
  • Immunohistochemistry
  • Morphometric and electrophysiological data analysis (Matlab)
  • Network simulations (Matlab)
  • Acute slice recordings from brain and retina (teaching)
  • Oxygen and PH measurements in brain slices (former project) 

Academic Background

  • 2007 - 2013:  Doctoral studies, Doctor Rerum Naturalium (PhD equivalent), University Freiburg, Germany. Thesis: “Coevolution of structure and activity dynamics in self-organizing networks of cortical neurons”
  • 2000 - 2007: Studies in biology, Albert-Ludwigs-University Freiburg, Germany 

Research Positions

  • 2019 – present Akademischer Rat (Lecturer)
  • 2013 –2019 Postdoctoral Researcher, Laboratory for Biomicrotechnology, Institute of Microsystems Engineering – IMTEK, Technical Faculty, University Freiburg, Germany
  • 2007 – 2013 Doctoral Candidate, Bernstein Center Freiburg, University Freiburg, Germany Project “Interaction of biological and computational neuronal networks in a hybrid circuit”
  • 2004 – 2006 Student assistant, Faculty of Biology, University Freiburg, Germany Project “Oxygen and pH measurements in in vitro brain slices mounted on perforated electrode MEAs” 

Honors and Awards

  • 2009 Stipend for the Annual meeting of the Sloan-Swartz foundation Center for Brain Science, Harvard University, Cambridge, USA. 

Current Grants

 

Journal Publications

[2] Okujeni S and Egert U (2023): Structural modularity tunes mesoscale criticality in biological neuronal networks. Journal of Neuroscience 43(14), 2515-2526.
DOI: https://doi.org/10.1523/JNEUROSCI.1420-22.2023

[3] Al-Absi A-R, Qvist P, Okujeni S, Khan AR, Glerup S, Sanchez C, Nyengaard JR (2020). Layers II/III of prefrontal cortex in Df(h22q11)/+ mouse model of the 22q11.2 deletion display loss of parvalbumin interneurons and modulation of neuronal morphology and excitability. Mol Neurobiol 57, 4978–4988.

[4] Okujeni S, Egert U (2019). Self-organization of modular network architecture by activity-dependent neuronal migration and outgrowth. eLife 8:e47966.

[5] Okujeni S, Egert U (2019). Inhomogeneities in network structure and excitability govern initiation and propagation of spontaneous burst activity. Front Neurosci 13:543.

[6] Okujeni S, Kandler S, Egert U (2017). Mesoscale Architecture Shapes Initiation and Richness of Spontaneous Network Activity. J Neurosci 37:3972–3987.

[7] Kumar SS, Wülfing J, Okujeni S, Boedecker J, Riedmiller M, Egert U (2016). Autonomous Optimization of Targeted Stimulation of Neuronal Networks. PLOS Comput Biol 12:e1005054.

[8] Weihberger O, Okujeni S, Mikkonen JE, Egert U (2013). Quantitative examination of stimulus-response relations in cortical networks in vitro. J Neurophysiol 109:1764–1774.

[9] Tetzlaff C, Okujeni S, Egert U, Wörgötter F, Butz M (2010). Self-organized criticality in developing neuronal networks. PLoS Comput Biol 6:e1001013. 

Conference Contributions

  • Okujeni S (2022). Structural modularity promotes mesoscale criticality in neuronal networks in vitro. Talk at the Bernstein Conference 2022, Sept 13 – 14. Satellite workshop: “Advance in network dynamics of in vitro neural systems” Chairs: Oleg Vinogradov, Paul Spitzner.
  • Okujeni S (2021). Self-organized network inhomogeneity governs spontaneous activity dynamics / L'inhomogénéité des réseaux auto-organisés régit la dynamique des activités spontanées.Talk at the NeuroFrance 2021, International virtual meeting, May 19 – 20. Symposium 40: “Structural plasticity and adaptive processes in neuronal networks. / Plasticité structurelle et processus adaptatifs dans des circuits neuronaux”, Chairs: Ulrich Egert and Stefan Rotter.
  • Okujeni S (2019). Self-organized network inhomogeneity governs spontaneous activity dynamics. Talk at the 13th Goettingen Meeting of the German Neuroscience Society 2019, Mar 20 –23, Goettingen, Germany. Symposium 14, “Adaptive processes and inhomogeneous neuronal networks – two sides of the same coin?”, Chairs: Ulrich Egert and Stefan Rotter.
  • Okujeni S (2018). Self-organized mesoscale inhomogeneity promotes rich activity dynamics. Talk at the Bernstein Conference 2018, Sept 25 –26, Berlin, Germany. Satellite workshop “Adaptivity and Inhomogeneity in Neuronal Networks”, Chairs: Ulrich Egert and Stefan Rotter, Freiburg.
  • Okujeni S and Egert U (2018). Mesoscale network architecture regulates spontaneous activity. Conference Abstract: MEA Meeting 2018 | 11th International Meeting on Substrate Integrated Microelectrode Arrays. doi: 10.3389/conf.fncel.2018.38.000422018
  • Kumar SS, Wülfing J, Okujeni S, Boedecker J, Riedmiller M and Egert U (2016). A Machine Learning Based Approach to Control Network Activity. Front. Neurosci. Conference Abstract: MEA Meeting 2016 | 10th International Meeting on Substrate-Integrated Electrode Arrays. doi: 10.3389/conf.fnins.2016.93.00117
  • Heizmann S, Kilias A, Okujeni S, Boehler C, Ruther P, Egert U, Asplund M (2015). Accurate neuronal tracing of microelectrodes based on PEDOT-dye coatings. 7th International IEEE/EMBS Conference on Neural Engineering (NER), 2015, Montpellier, France
  • Kumar SS, Wülfing J, Okujeni S, Boedecker J, Wimmer R, Riedmiller M, Becker B, Egert U (2014). Autonomous Control of Network Activity. Proceedings MEA Meeting 2014. pp. 76-77.
  • Okujeni,S., Moenig,N., Kandler,S., Weihberger,O., and Egert,U. (2012). Clustered network structure promotes spontaneous burst initiation in vitro. In: A. Stett (ed.) Proceedings MEA Meeting 2012, Stuttgart: BIOPRO Baden-Württemberg GmbH 2012, pp. 47-48.
  • Jarvis S, Okujeni S, Kandler S, Rotter S, Egert U (2012). Axonal anisotropy and connectivity inhomogeneities in 2D networks. BMC Neuroscience 2012, 13 (Suppl 1):P145
  • Jarvis S, Kandler S, Okujeni S, Rotter S, and Egert U (2012). A simple but plausible culture model recreates fast burst propagation and predicts their persistence. In: A. Stett (ed.) Proceedings MEA Meeting 2012, Stuttgart: BIOPRO Baden-Württemberg GmbH 2012, pp. 108.
  • Okujeni S, Mönig N, Kandler S, Weihberger O and Egert U (2012). Clustered connectivity promotes synchronous burst initiation in vitro. Front. Comput. Neurosci. Conference Abstract: Bernstein Conference 2012. doi: 10.3389/conf.fncom.2012.55.00112
  • Okujeni S (2011). Network inhomogeneity support burst initiation in vitro. Talk at the Annual Computational Neuroscience Meeting 2011, Jul 27-28, Stockholm, Sweden. Workshop ”Structural plasticity”, Chairs: Markus Butz and Arjen van Ooyen.
  • Weihberger, O., Lavi, A., Okujeni, S., Ashery, U., Egert, U. (2011). State-dependent modulation of stimulus-response relations in cortical networks in vitro. BMC Neuroscience 2011, 12(Suppl 1):O6
  • Weihberger O, Lavi A, Okujeni S, Ashery U and Egert U (2011). Quantitative models for stimulus-response relations in neuronal networks in vitro. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00059
  • Kandler S, Okujeni S, Reinartz S and Egert U (2011). Developmental changes of activity in simple biological neuronal networks. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00042
  • Podrygajlo G, Okujeni S, Dini P, Goddard M and Egert U (2011). Identification of electrophysiological endpoints in stem cell-based systems for developmental neurotoxicity testing.. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00057
  • Okujeni S, Moenig N, Kandler S, Weihberger O and Egert U (2011). Network inhomogeneity promotes spontaneous bursting in vitro. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00051
  • Teppola H, , Okujeni S, Linne ML, Egert U (2011). AMPA, NMDA and GABAA RECEPTOR mediated network burst dynamics in cortical cultures in vitro. Proceedings of the 8th International Workshop on Computational Systems Biology, Zurich, Switzerland.
  • Teppola H, Okujeni S, Linne M and Egert U (2011). The role of fast inhibition in AMPA and NMDA receptor mediated network burst dynamics in cortical cultures. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00043
  • Okujeni S, Moenig N, Kandler S, Weihberger O and Egert U (2011). Network inhomogeneity supports burst initiation in vitro. BMC Neuroscience 2011, 12(Suppl 1):P84
  • Gürel T, Okujeni S, Weihberger O, Rotter S, Egert U (2011). Modeling persistent temporal patterns in dissociated cortical cultures using reservoir computing. BMC Neuroscience 2010, 11(Suppl 1):P42
  • Okujeni S, Moenig N, Kandler S, Weihberger O and Egert U (2010). Network Structure and the Origin of Synchronized Bursts In vitro. In: A. Stett (ed.) Proceedings 7th MEA Meeting 2010, Stuttgart: BIOPRO Baden-Württemberg GmbH 2010, pp. 28-29. 28-29.
  • Weihberger O, Okujeni S and Egert U (2010). How to reduce stimulus/response variability in cortical neuronal networks. In: A. Stett (ed.) Proceedings 7th MEA Meeting 2010, Stuttgart: BIOPRO Baden-Württemberg GmbH 2010, pp. 51-52.
  • Kandler S, Okujeni S, Reinartz S and Egert U (2010). Networks in dissociated culture follow native cortical development. In: A. Stett (ed.) Proceedings MEA Meeting 2010, Stuttgart: BIOPRO Baden-Württemberg GmbH 2010, pp. 44-45.
  • Okujeni S, Kandler S, Weihberger O and Egert U (2009). Impaired structural plasticity increases connectivity in developing cortical networks. BMC Neuroscience 2009, 10(Suppl 1):P208
  • Okujeni S (2009). Linking connectivity and dynamics in generic networks of cortical neurons. Talk at the Annual Computational Neuroscience Meeting 2009, Jul 23, Berlin. Workshop “Activity-Dependent Structural Plasticity – from cell cultures to cortical networks”, Chair: Markus Butz and Arjen van Ooyen.
  • Tetzlaff C, Okujeni S, Egert U, Wörgötter F and Butz M (2009). Self-organized criticality of developing artificial neuronal networks and dissociated cell cultures. BMC Neuroscience 2009, 10(Suppl 1):P215
  • Okujeni S, Kandler S and Egert U (2008). Homeostatic regulation of connectivity in cortical networks. In: A. Stett (ed.) Proceedings 6th MEA Meeting 2008, Stuttgart: BIOPRO Baden-Württemberg GmbH 2008, pp. 74-75. 74-75.
  • Okujeni S, Kandler S and Egert U (2008). Connectivity statistics and their implications on activity dynamics in cortical cell cultures. Front. Comput. Neurosci. Conference Abstract: Bernstein Symposium 2008. doi: 10.3389/conf.neuro.10.2008.01.097
  • Tetzlaff C, Okujeni S, Egert U, Wörgötter F and Butz M (2008). Self-organized criticality of developing artificial neuronal networks and dissociated cell cultures. Front. Comput. Neurosci. Conference Abstract: Bernstein Symposium 2008. doi: 10.3389/conf.neuro.10.2008.01.119
  • Kandler S, Okujeni S, Reinartz S and Egert U (2008). Local connectivity and embedding of individual neurons in cultured neuronal networks. Front. Comput. Neurosci. Conference Abstract: Bernstein_Symposium_2008. doi: 10.3389/conf.neuro.10.2008.01.070
  • Kandler S, Woerz A, Okujeni S, Mikkonen JE, Ruehe J and Egert U (2008). Structure-function relations in generic neuronal networks. In: A. Stett (ed.) Proceedings 6th MEA Meeting 2008, Stuttgart: BIOPRO Baden-Württemberg GmbH 2008, pp. 55-56.
  • Weihberger O, Mikkonen JE, Okujeni S, Kandler S and Egert U (2008). Network-state Dependent Stimulation Efficacy and Interaction with Bursting Activity in Neuronal Networks in vitro. In: A. Stett (ed.) Proceedings 6th MEA Meeting 2008, Stuttgart:BIOPRO Baden-Württemberg GmbH 2008, pp. 149-152.
  • Gürel T, Okujeni S, Weihberger O, Rotter S and Egert U (2008). Burst Clustering and Prediction in Neuronal Cultures. Front. Comput. Neurosci. Conference Abstract: Bernstein Symposium 2008. doi: 10.3389/conf.neuro.10.2008.01.053
  • Egert U, Okujeni S, Nisch W, Boven K, Rudorf R, Gottschlich N and Stett A (2006) Optimized Oxygen Availability and Signal-to-Noise Ratio in Brain Slice Recordings with Perforated Microelectrode Arrays. Stett A. (ed): Proceedings MEA Meeting 2006. BIOPRO edition. BIOPRO Baden-Württemberg GmbH, Stuttgart, 3 : 174-177
  • Egert U, Okujeni S, Nisch W, Boven KH, Rudorf R, Gottschlich N and Stett A (2005) Perforated microelectrode arrays optimize oxygen availability and signal-to-noise ratio in brain slice recordings. MST Kongress 2005, 431-434