Department of Cell Biophysics

Head

Prof Jerzy Dobrucki, PhD, DSc
room: C041 (2.01.32), phone: +48 12 664 63 82

Staff

Mirosław Zarębski, PhD
room: B004 (3.01.32), phone: +48 12 664 63 81, e-mail: miroslaw.zarebski@uj.edu.pl

Agnieszka Waligórska, PhD
room: B004 (3.01.32), phone: +48 12 664 62 81, e-mail: agnieszka.waligorska@uj.edu.pl

Magdalena Kordon, PhD
room: C002 (2.01.33), phone: +48 12 664 62 19, e-mail: magdalena.kordon@uj.edu.pl 

Paulina Rybak, PhD
room: C043 (2.01.30), phone: +48 12 664 61 30, e-mail: paulina.rybak@uj.edu.pl

Kamil Solarczyk, PhD
room: C002 (2.01.33), phone: +48 12 664 62 19, e-mail: kj.solarczyk@uj.edu.pl

Krzysztof Berniak, MSc
pokój: C043 (2.01.30), phone: +48 12 664 62 19, e-mail: krzysztof.berniak@uj.edu.pl

Marta Hoffmann, MSc
room: C002 (2.01.33), phone: +48 12 664 62 19, mail: marta1990.hoffmann@uj.edu.pl

PhD students

Agnieszka Hoang-Bujnowicz, room: C043 (2.01.30), phone: +48 12 664 61 30
Oskar Szelest, room: C002 (2.01.33), phone: +48 12 664 62 19
Julita Wesołowska, room: C043 (2.01.30), phone: +48 12 664 61 30
Michał Mroziński, room:  C002 (2.01.33), phone: +4812 664 62 19

Research topics

Research conducted in Department of Cell Biophysics is focused on understanding of mechanisms leading to damage inflicted on human genome, on the processes of damage detection and DNA repair. We are interested in factors leading to damage repair, cell death or neoplastic transformation.

Methods and specialistic equipment

The principal research methods used in Department of Cell Biophysics embrace various modern optical imaging approaches, including fluorescence confocal microscopy, microscopy methods of investigating dynamics and protein-protein interactions in situ, in live cells – FRAP, FRET, FCS, BiFc, PLA, etc. as well as the newest super-resolution microscopy methods (dSTORM, SMLM, STED). Major equipment in Department of Biophysics includes Leica SP5 SMD (FLIM, FCS), Leica SP5 (STED), and Bio-Rad MRC2014 confocal microscopes, and a super-resolution microscope for detection of single molecules (SMLM, single molecule localisation microscopy). 

Current projects

  1. Krzysztof Berniak: Heterochromatin protein 1 (HP1) as a structure-stabilising factor in repair of DNA double-strand breaks. (2016-2019). PRELUDIUM 10, National Science Centre (NCN).
  2. Jerzy Dobrucki: Super-resolution optical imaging of higher order chromatin structures in nuclei of human cells, during DNA replication and repair. (2014-2018). OPUS 6, National Scince Centre (NCN).

Selected publications

  1. Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res2017 May 5;45(8):e56. doi: 10.1093/nar/gkw1301. PubMed PMID: 28082388; PubMed Central PMCID: PMC5416826.
  2. Rybak P, Hoang A, Bujnowicz L, Bernas T, Berniak K, Zarębski M, Darzynkiewicz Z, Dobrucki J. Low level phosphorylation of histone H2AX on serine 139 (γH2AX) is not associated with DNA double-strand breaks. Oncotarget. 2016 Aug 2;7(31):49574-49587. doi: 10.18632/oncotarget.10411. PubMed PMID: 27391338; PubMed Central PMCID: PMC5226530.
  3. Pierzyńska-Mach A, Szczurek A, Cella Zanacchi F, Pennacchietti F, Drukała J, Diaspro A, Cremer C, Darzynkiewicz Z, Dobrucki JW. Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy. Cell Cycle2016;15(8):1156-67. doi: 10.1080/15384101.2016.1158377. PubMed PMID: 27097376; PubMed Central PMCID: PMC4889244.
  4. Solarczyk KJ, Kordon M, Berniak K, Dobrucki JW. Two stages of XRCC1 recruitment and two classes of XRCC1 foci formed in response to low level DNA damage induced by visible light, or stress triggered by heat shock. DNA Repair (Amst)2016 Jan;37:12-21. doi: 10.1016/j.dnarep.2015.10.006. Epub 2015 Nov 2. PubMed PMID: 26630398.
  5. Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk UJ, Dobrucki JW, Cremer C. Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res2016 May 1;343(2):97-106. doi: 10.1016/j.yexcr.2015.08.020. Epub 2015 Sep 1. PubMed PMID: 26341267.
  6. Berniak K, Rybak P, Bernas T, Zarębski M, Biela E, Zhao H, Darzynkiewicz Z, Dobrucki JW. Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis. Cytometry A2013 Oct;83(10):913-24. doi: 10.1002/cyto.a.22327. Epub 2013 Jul 11. PubMed PMID: 23846844; PubMed Central PMCID: PMC3888650.
  7. Zurek-Biesiada D, Kędracka-Krok S, Dobrucki JW. UV-activated conversion of Hoechst 33258, DAPI, and Vybrant DyeCycle fluorescent dyes into blue-excited, green-emitting protonated forms. Cytometry A2013 May;83(5):441-51. doi: 10.1002/cyto.a.22260. Epub 2013 Feb 15. PubMed PMID: 23418106.
  8. Trembecka-Lucas DO, Szczurek AT, Dobrucki JW. Dynamics of the HP1β-PCNA-containing complexes in DNA replication and repair. Nucleus2013 Jan-Feb;4(1):74-82. doi: 10.4161/nucl.23683. Epub 2013 Jan 1. PubMed PMID: 23337132; PubMed Central PMCID: PMC3585030.
  9. Solarczyk KJ, Zarębski M, Dobrucki JW. Inducing local DNA damage by visible light to study chromatin repair. DNA Repair (Amst). 2012 Dec 1;11(12):996-1002. doi: 10.1016/j.dnarep.2012.09.008. Epub 2012 Oct 22. PubMed PMID: 23089313. 
  10. Luijsterburg MS, Dinant C, Lans H, Stap J, Wiernasz E, Lagerwerf S, Warmerdam DO, Lindh M, Brink MC, Dobrucki JW, Aten JA, Fousteri MI, Jansen G, Dantuma NP, Vermeulen W, Mullenders LH, Houtsmuller AB, Verschure PJ, van Driel R. Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol2009 May 18;185(4):577-86. doi: 10.1083/jcb.200810035. PubMed PMID: 19451271; PubMed Central PMCID: PMC2711568.

Batchelor/master thesis topics

  • The role of heterochromatin protein 1 (HP1) in DNA damage repair
  • The role of X-ray repair cross-complementing protein 1 (XRCC1) in repair of single strand DNA breaks
  • The structure of repair foci formed at single strand DNA breaks
  • Mechanism of induction of local DNA damage by visible light and applications of this phenomenon in studies of DNA repair
     

Requirements for candidates

We welcome students who are interested in genomics, biophysics, cell biology, biochemistry, physics, modelling of biological processes and structures and wish to supplement these interests with experimental work.