Head: Jakub Włodarczyk



2014 DSc Habil, Nencki Institute of Experimental Biology, PAS
2006 PhD in Physical Science, Institute of Experimental Physics, Warsaw University
2001 MSc in Physics, Institute of Experimental Physics, Warsaw University


Research trainings:

2008 Short term fellowship, Centre Medical Universitaire, Geneva, Switzerland
2006–2008 Postdoctoral training: Max Planck Institute, Göttingen, Germany


Professional employments:
2014-present Associate Professor, Nencki Institute of Experimental Biology, PAS
2012-present Head of the Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, PAS
2008-2012 Assistant professor, Laboratory of Neurobiology, Nencki Institute of Experimental Biology, PAS
2006-2008 Postdoc, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
2001-2006 PhD student, Faculty of Physics, Warsaw University


Honors and fellowships:
2015 Konorski Distinguished Work: Stawarski et al., Biomaterials 2014
2015 Award of Polish Academy of Science, Division II
2013-present Member of the Network of European Neuroscience Institute (ENI NET)
2006-2008  Max  Planck  Institute  for  Biophysical Chemistry Scholarship from Prof. E. Neher
2008 EMBO Short Term Fellowship

Staff: Svitlana Antoniuk (PhD student), Anna Bartkowiak-Kaczmarek (PhD student), Ewa Bączyńska (PhD student), Monika Bijata, Izabela Figiel-Ożóg, Joanna Kielan, Adam Krzystyniak, Marta Magnowska (PhD student), Matylda Roszkowska (PhD student), Monika Zaręba-Kozioł

Research profile:


Processes like learning and memory require functional modification of neuronal networks through reorganization of existing synapses, modification of their efficacy, or modulation of neuronal endogenous excitability. Synapses are particularly prone to dynamic alterations and thus are believed to play a major role in plasticity. We study structural and functional synaptic modifications regulated by posttranslational modifi- cations including: i) protein-specific proteolysis by extracellular matrix proteolytic modifiers, ii) S-nitrosylation and S-palmitoylation i.e. addition of palmitate or nitric oxide that reversibly modifies numerous classes of neuronal proteins. We focus on the role of rapid posttranslational modifications of synaptic proteins in protein organization in the synapse under physiological stimuli as well as pathological conditions (such as chronic stress). We employ novel imaging based techniques and mass spectrometry methods to assess the reorganization of activity patterns accompanied by local volumetric and molecular changes at the synapses.

Current research activities:

  • cooperative involvement of serotonin signaling pathways and extracellular matrix in synaptic plasticity underlying the pathogenesis of stress-related disorders
  • structural brain plasticity driven by extracellular matrix modifiers
  • quantitative analysis of dendritic spine turnover, morphological changes and receptor composition within the spine
  • interplay between the posttranslational modifications in the chronic stress disorders
  • novel methodical approaches to analyze posttranslational modifications.

Selected recent publications:


Magnowska M., Górkiewicz T., Suska A., Wawrzyniak M., Rutkowska-Włodarczyk I., Kaczmarek L., Włodarczyk J. (2016) Transient ECM protease activity promotes synaptic plasticity. Sci Rep, 6: 27757.


Basu S., Plewczyński S., Saha S., Roszkowska M., Magnowska M., Bączyńska E., Włodarczyk J. (2016) 2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. Bioinformatics, 32(16): 2490-2498.


Tang Z., Junhong Luo O., Li X., Zheng M., Jufen Zhu J., Szalaj, Trzaskoma P., Magalska A., Włodarczyk J., Ruszczycki B., Michalski P., Piecuch E., Wang P., Wang D., Zhongyuan Tian S., Penrad-Mobayed M., M Sachs L., Ruan X., Wei C., T Liu E., Wilczyński G., Plewczyński D., Li G., Ruan Y. (2015) CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell, 163 (7): 1611-1627.


Bijata M., Włodarczyk J., Figiel I. (2015) Dystroglycan controls dendritic morphogenesis of hippocampal neurons in vitro. Front Cell Neurosci, 9: 199.


Stawarski M., Rutkowska-Wlodarczyk I., Zeug A., Bijata M., Madej H., Kaczmarek L., Wlodarczyk J. (2014) Genetically encoded FRET-based biosensor for imaging MMP-9 activity. Biomaterials, 35: 1402-1410.